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About this archive
Starting: Thu Jan 03 2013 - 06:24:44 CST
Ending: Tue Dec 30 2014 - 07:38:36 CST
- angles between residues luca belmonte (Tue Dec 30 2014 - 07:38:14 CST)
- Lone Pair on H2S JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:39 CST)
- Lone Pair on H2S JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:40 CST)
- Lone Pair on H2S JAVAD NOROOZI (Sat Dec 27 2014 - 09:42:25 CST)
- warnings while using amber files amin_at_imtech.res.in (Thu Dec 25 2014 - 05:14:20 CST)
- NAMD 2.10b1: occasional corrupted frame in binary dcd output Tristan Croll (Tue Dec 23 2014 - 16:39:46 CST)
- Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 11:15:31 CST)
- Error on write to binary file Mihaela Drenscko (Mon Dec 22 2014 - 18:02:54 CST)
- .inpcrd to .pdb Shalton Evans (Sun Dec 21 2014 - 13:56:30 CST)
- Free Energy Workshop, Mnster, March 9-11Q_2015?= Vlad Cojocaru (Fri Dec 19 2014 - 12:02:00 CST)
- Re: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 08:33:31 CST)
- problem in installation of charm-6.4.0 in bluegeneL] Santosh Kumar Chaudhary (Fri Dec 19 2014 - 05:49:45 CST)
- FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Thu Dec 18 2014 - 14:39:51 CST)
- Re: Asking help on results of our GPU benchmark 周文昌 (Thu Dec 18 2014 - 13:24:59 CST)
- AW: Asking help on results of our GPU benchmark Norman Geist (Fri Dec 19 2014 - 00:30:22 CST)
- Re: Asking help on results of our GPU benchmark 周文昌 (Fri Dec 19 2014 - 16:06:33 CST)
- Re: Asking help on results of our GPU benchmark 周文昌 (Mon Dec 22 2014 - 12:11:18 CST)
- Re: Asking help on results of our GPU benchmark 周文昌 (Tue Dec 23 2014 - 14:05:30 CST)
- Re: Constant Pressure, Variable Volume, Minimization Miss. State (Thu Dec 18 2014 - 13:01:05 CST)
- Asking help on results of our GPU benchmark 周文昌 (Wed Dec 17 2014 - 15:13:24 CST)
- Loading Velocity DCD file JAVAD NOROOZI (Wed Dec 17 2014 - 13:23:20 CST)
- Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Dec 17 2014 - 10:24:50 CST)
- setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Wed Dec 17 2014 - 06:21:17 CST)
- RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Wed Dec 17 2014 - 07:07:23 CST)
- Re: setting up namd simulation in IBM Blue Gene/L Jim Phillips (Fri Dec 19 2014 - 12:55:33 CST)
- Implementing the Virtual Bond Algorithm Using Colvars David Huggins (Wed Dec 17 2014 - 06:25:33 CST)
- Extracting Kinetic Energy of Certain Atoms JAVAD NOROOZI (Wed Dec 17 2014 - 03:19:09 CST)
- Is it so different when setting reinitvels or not? Zhao Lina (Wed Dec 17 2014 - 00:03:25 CST)
- Transferring bond list to new molecule Mert Gür (Tue Dec 16 2014 - 23:17:02 CST)
- Running Charmrun/NAMD with more than 10 processes fails K Miura (Tue Dec 16 2014 - 02:53:36 CST)
- Inspiration for most efficient implementation of coarse grained forcefield. Ajasja Ljubetič (Mon Dec 15 2014 - 12:08:03 CST)
- Error compiling NAMD2.9 after patching with PLUMED2.1 Rubén Granero (Mon Dec 15 2014 - 06:47:27 CST)
- NAMD 2.10 released Jim Phillips (Fri Dec 12 2014 - 16:35:38 CST)
- Info: Pairlistdist is too small for 3 computes during timestep 115001 Santosh Kumar Chaudhary (Fri Dec 12 2014 - 10:34:41 CST)
- question about FEP for amphiphile in lipid bilayer Leonardo Darre (Wed Dec 10 2014 - 08:08:27 CST)
- the difference of PCA and EDA СӨ (Wed Dec 10 2014 - 02:31:30 CST)
- Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD (Tue Dec 09 2014 - 02:43:22 CST)
- Choosing of windows and width for Umbrella Sampling Kevin C Chan (Mon Dec 08 2014 - 06:48:19 CST)
- query about the cross term in psf Kshatresh Dutta Dubey (Sat Dec 06 2014 - 13:31:42 CST)
- colvars angle centerReference Jeff Comer (Fri Dec 05 2014 - 15:00:44 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Tue Dec 09 2014 - 18:35:22 CST)
- Re: colvars angle centerReference Jeff Comer (Tue Dec 09 2014 - 21:41:26 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Tue Dec 09 2014 - 21:54:55 CST)
- Re: colvars angle centerReference Jim Phillips (Wed Dec 10 2014 - 07:31:11 CST)
- Re: colvars angle centerReference Jeff Comer (Wed Dec 10 2014 - 08:41:06 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Wed Dec 10 2014 - 08:44:22 CST)
- Re: colvars angle centerReference Jeff Comer (Wed Dec 10 2014 - 09:22:10 CST)
- Re: colvars angle centerReference Jeff Comer (Tue Dec 09 2014 - 21:41:26 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Tue Dec 09 2014 - 18:35:22 CST)
- information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 16:50:11 CST)
- Re: information about simulation speed Axel Kohlmeyer (Tue Dec 02 2014 - 16:53:44 CST)
- Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:04:31 CST)
- Re: information about simulation speed Axel Kohlmeyer (Tue Dec 02 2014 - 17:07:15 CST)
- Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:22:28 CST)
- Re: information about simulation speed Josh Vermaas (Tue Dec 02 2014 - 17:08:55 CST)
- Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:35:14 CST)
- Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:45:32 CST)
- Re: information about simulation speed Jeff Comer (Tue Dec 02 2014 - 18:09:54 CST)
- AW: information about simulation speed Norman Geist (Wed Dec 03 2014 - 02:31:26 CST)
- Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:04:31 CST)
- Re: information about simulation speed Axel Kohlmeyer (Tue Dec 02 2014 - 16:53:44 CST)
- Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Michel van der List (Mon Dec 01 2014 - 08:40:46 CST)
- question about CUDA-enabled maryam atabay (Sat Nov 29 2014 - 10:19:49 CST)
- running NAMD in parallel Kshatresh Dutta Dubey (Fri Nov 28 2014 - 19:29:43 CST)
- Re: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 04:04:49 CST)
- Fw: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 03:47:41 CST)
- anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 02:48:51 CST)
- colvar DistanceZ Kevin C Chan (Tue Nov 25 2014 - 21:03:55 CST)
- (no subject) flavio seixas (Tue Nov 25 2014 - 19:13:24 CST)
- question about CUDA-enabled maryam atabay (Tue Nov 25 2014 - 01:05:32 CST)
- Colvars error Kevin C Chan (Tue Nov 25 2014 - 00:10:05 CST)
- "BAK" format files Ramin Ekhteiari (Mon Nov 24 2014 - 06:52:20 CST)
- Fwd: question about CUDA-enabled maryam atabay (Mon Nov 24 2014 - 05:08:04 CST)
- CGenFF atom type N- Francesco Pietra (Mon Nov 24 2014 - 02:55:04 CST)
- Misleading failure of VMD with charge/CGenFF from waterbox Francesco Pietra (Sun Nov 23 2014 - 03:21:38 CST)
- Fwd: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Sat Nov 22 2014 - 02:45:10 CST)
- 11/22/2014 6:32:52 PM jeremy adler (Sat Nov 22 2014 - 00:32:52 CST)
- A problem in ABF simulations Azadeh Alavi (Sat Nov 22 2014 - 05:50:03 CST)
- tilt colvar JC Gumbart (Fri Nov 21 2014 - 11:09:55 CST)
- Re: tilt colvar Giacomo Fiorin (Fri Nov 21 2014 - 11:35:25 CST)
- Re: tilt colvar JC Gumbart (Fri Nov 21 2014 - 18:12:31 CST)
- Re: tilt colvar Jérôme Hénin (Sat Nov 22 2014 - 06:00:10 CST)
- Re: tilt colvar JC Gumbart (Sat Nov 22 2014 - 08:10:23 CST)
- Re: tilt colvar Jérôme Hénin (Mon Nov 24 2014 - 08:46:48 CST)
- Re: tilt colvar Ajasja Ljubetič (Mon Nov 24 2014 - 09:27:37 CST)
- Re: tilt colvar Giacomo Fiorin (Mon Nov 24 2014 - 09:34:32 CST)
- Re: tilt colvar JC Gumbart (Mon Nov 24 2014 - 14:42:43 CST)
- Re: tilt colvar Jérôme Hénin (Mon Nov 24 2014 - 15:09:14 CST)
- Re: tilt colvar Giacomo Fiorin (Mon Nov 24 2014 - 16:53:25 CST)
- Re: tilt colvar JC Gumbart (Mon Nov 24 2014 - 17:57:44 CST)
- Re: tilt colvar JC Gumbart (Tue Dec 02 2014 - 18:30:22 CST)
- Re: tilt colvar JC Gumbart (Fri Nov 21 2014 - 18:12:31 CST)
- Re: tilt colvar Giacomo Fiorin (Fri Nov 21 2014 - 11:35:25 CST)
- problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:09:52 CST)
- Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
- Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
- Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 09:56:11 CST)
- Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 10:06:28 CST)
- Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 10:42:05 CST)
- Re: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 10:54:20 CST)
- Re: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 12:50:22 CST)
- Re: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Josh Vermaas (Fri Nov 21 2014 - 10:54:56 CST)
- Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
- Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
- create psf file without hydrogens Revthi Sanker (Thu Nov 20 2014 - 12:26:48 CST)
- carboxyl NBFIX on proteins Jeff Comer (Thu Nov 20 2014 - 09:18:45 CST)
- about the vdw Interpolation calculation in NAMD source code ¬ (Thu Nov 20 2014 - 02:44:40 CST)
- Re: about the vdw Interpolation calculation in NAMD source code Jeff Comer (Thu Nov 20 2014 - 08:20:54 CST)
- Re: about the vdw Interpolation calculation in NAMD source code Jim Phillips (Thu Nov 20 2014 - 08:29:27 CST)
- Topology and parameter files for some engineered residues KK R (Wed Nov 19 2014 - 09:31:33 CST)
- Re: About NAMD Douglas Houston (Tue Nov 18 2014 - 09:32:59 CST)
- NAMD 2.10b2 released Jim Phillips (Mon Nov 17 2014 - 14:22:52 CST)
- Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 07:41:31 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Giacomo Fiorin (Mon Nov 17 2014 - 08:49:18 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 09:57:37 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Jérôme Hénin (Mon Nov 17 2014 - 10:07:38 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 10:14:58 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Ajasja Ljubetič (Mon Nov 17 2014 - 10:28:20 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 10:49:57 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Ajasja Ljubetič (Mon Nov 17 2014 - 11:30:45 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 12:12:42 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Jérôme Hénin (Mon Nov 17 2014 - 13:13:07 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Tue Nov 18 2014 - 03:40:53 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 09:57:37 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Giacomo Fiorin (Mon Nov 17 2014 - 08:49:18 CST)
- how to fix the problem Liqun Zhang (Fri Nov 14 2014 - 17:19:37 CST)
- water-protein interation sunyeping (Fri Nov 14 2014 - 02:32:11 CST)
- Atomselect for coor, vel, xsc Kevin C Chan (Thu Nov 13 2014 - 22:49:02 CST)
- Umbrella Sampling in NAMD Kevin C Chan (Thu Nov 13 2014 - 10:25:13 CST)
- Simulation of a membrane protein with large extracellular domains Fotis Baltoumas (Thu Nov 13 2014 - 07:30:54 CST)
- APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) Bin He (Thu Nov 13 2014 - 01:53:42 CST)
- namd simulation for solids withoy solvation Subbusinger N (Thu Nov 13 2014 - 00:02:42 CST)
- unsubscribe Gurpreet Kaur Dhindsa (Wed Nov 12 2014 - 19:04:28 CST)
- Can NAMD does Langevin Dynamics Simulation Fidan Sumbul (Wed Nov 12 2014 - 14:48:25 CST)
- SOD topology with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:02:22 CST)
- Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 10:11:00 CST)
- Re: Dioxygen atom type with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 11:07:25 CST)
- Re: Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:19:17 CST)
- Re: Dioxygen atom type with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 12:46:48 CST)
- Re: Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 13:34:13 CST)
- Re: Dioxygen atom type with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 14:19:40 CST)
- Re: Dioxygen atom type with CHARMM36 Francesco Pietra (Wed Nov 12 2014 - 01:17:44 CST)
- Re: Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:19:17 CST)
- Re: Dioxygen atom type with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 11:07:25 CST)
- Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Mon Nov 10 2014 - 13:51:15 CST)
- AW: FATAL ERROR: error parsing config file while executing <feff> Norman Geist (Mon Nov 10 2014 - 08:20:48 CST)
- Reg: QM/MM calculations in NAMD Akshay Bhatnagar (Mon Nov 10 2014 - 07:05:40 CST)
- FATAL ERROR: error parsing config file while executing <feff> Mihaela Drenscko (Sun Nov 09 2014 - 11:39:11 CST)
- Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Sat Nov 08 2014 - 01:24:32 CST)
- multiple harmonic constrains Azadeh Alavi (Sat Nov 08 2014 - 01:36:16 CST)
- ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 09:14:15 CST)
- CUDA Fatal Error While Trying to Run Under Windows 8.1 Justin Sanders (Thu Nov 06 2014 - 12:01:58 CST)
- NAMD on SLURM Abhishek TYAGI (Wed Nov 05 2014 - 23:30:20 CST)
- Multiple input and output files Debashis Kundu (Wed Nov 05 2014 - 20:20:37 CST)
- 1-5 Intramolecular repulsions Rebecca Lindsey (Wed Nov 05 2014 - 11:54:40 CST)
- Re: 1-5 Intramolecular repulsions Kenno Vanommeslaeghe (Wed Nov 05 2014 - 12:33:12 CST)
- Re: 1-5 Intramolecular repulsions Jeffrey Potoff (Wed Nov 05 2014 - 12:51:02 CST)
- Re: 1-5 Intramolecular repulsions Rebecca Lindsey (Wed Nov 05 2014 - 13:07:49 CST)
- Re: 1-5 Intramolecular repulsions rocwhite168 (Wed Nov 05 2014 - 14:55:05 CST)
- Re: 1-5 Intramolecular repulsions Axel Kohlmeyer (Wed Nov 05 2014 - 15:12:43 CST)
- 崔幼恬 自动回复: Re: 1-5 Intramolecular repulsions cuiyoutian_at_163.com (Wed Nov 05 2014 - 15:12:43 CST)
- Re: 1-5 Intramolecular repulsions rocwhite168 (Wed Nov 05 2014 - 13:02:55 CST)
- Re: 1-5 Intramolecular repulsions Jeffrey Potoff (Wed Nov 05 2014 - 12:51:02 CST)
- Re: 1-5 Intramolecular repulsions Kenno Vanommeslaeghe (Wed Nov 05 2014 - 12:33:12 CST)
- colvars fatal error Leili Zhang (Tue Nov 04 2014 - 22:44:05 CST)
- vdW-only fep between two ions Christopher Rowley (Tue Nov 04 2014 - 14:43:08 CST)
- harmonic restraints between multiple atom pairs Neelanjana Sengupta (Mon Nov 03 2014 - 22:42:33 CST)
- explicit membrane in implicit solvent Gisella Alfonsino (Mon Nov 03 2014 - 05:00:36 CST)
- Why RDF increases as r increase instead of constant Nifeng Guo hui (Sat Nov 01 2014 - 17:07:32 CDT)
- Reg: dielectric constant calculations in NAMD Akshay Bhatnagar (Fri Oct 31 2014 - 00:51:24 CDT)
- Mechanical Properties of protein chin chun (Thu Oct 30 2014 - 19:18:11 CDT)
- SMD constant velocity not constant Charles Whidborne (Wed Oct 29 2014 - 19:25:08 CDT)
- Dioxygen params charmm36 Francesco Pietra (Wed Oct 29 2014 - 16:27:17 CDT)
- namd ibverbs compile target Bennion, Brian (Tue Oct 28 2014 - 18:04:52 CDT)
- Carma v.1.4 released. Nicholas M Glykos (Mon Oct 27 2014 - 06:09:24 CDT)
- jeremy adler jeremy adler (Thu Oct 23 2014 - 06:21:43 CDT)
- Reg: error in log file Akshay Bhatnagar (Tue Oct 21 2014 - 20:36:48 CDT)
- Improving MDFF results Kevin C Chan (Mon Oct 20 2014 - 22:15:59 CDT)
- running a calculation during simulation btreece_at_andrew.cmu.edu (Mon Oct 20 2014 - 16:08:12 CDT)
- Graphene simualtion Abhishek TYAGI (Mon Oct 20 2014 - 03:28:51 CDT)
- AW: wrapping in two dimensions Norman Geist (Mon Oct 20 2014 - 01:14:02 CDT)
- Replica Exchange Simulation in NAMD Precompiled binary in single node. Nizar Masbukhin (Thu Oct 16 2014 - 17:09:05 CDT)
- wrapping in two dimensions Maria Bykhovskaia (Thu Oct 16 2014 - 15:33:34 CDT)
- AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 08:26:37 CDT)
- AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 08:11:59 CDT)
- velocity manipulation mostafa raeesi (Thu Oct 16 2014 - 06:37:02 CDT)
- ffTK problem: initial parameter file is void of of atoms! Zeinab Emami (Thu Oct 16 2014 - 04:15:55 CDT)
- ffTK problem: initial parameter fiel is viod of atoms! Zeinab Emami (Wed Oct 15 2014 - 07:42:57 CDT)
- VRPN cannot connect to Falcon George Patargias (Wed Oct 15 2014 - 04:58:11 CDT)
- NAMD and usable FFs Francesco Pietra (Wed Oct 15 2014 - 04:34:31 CDT)
- Re: NAMD and usable FFs Josh Vermaas (Wed Oct 15 2014 - 09:20:08 CDT)
- Re: NAMD and usable FFs Francesco Pietra (Thu Oct 16 2014 - 12:59:10 CDT)
- Re: NAMD and usable FFs Josh Vermaas (Thu Oct 16 2014 - 13:05:27 CDT)
- Re: NAMD and usable FFs Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:45:05 CDT)
- Re: NAMD and usable FFs Francesco Pietra (Thu Oct 16 2014 - 16:41:59 CDT)
- Re: NAMD and usable FFs Kenno Vanommeslaeghe (Thu Oct 16 2014 - 17:53:13 CDT)
- Re: NAMD and usable FFs Francesco Pietra (Fri Oct 17 2014 - 03:12:48 CDT)
- Re: NAMD and usable FFs Kenno Vanommeslaeghe (Fri Oct 17 2014 - 11:15:18 CDT)
- Re: NAMD and usable FFs Francesco Pietra (Thu Oct 16 2014 - 12:59:10 CDT)
- Re: NAMD and usable FFs Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:37:11 CDT)
- Re: NAMD and usable FFs Josh Vermaas (Wed Oct 15 2014 - 09:20:08 CDT)
- colvars replica exchange oddity JC Gumbart (Tue Oct 14 2014 - 22:27:07 CDT)
- VRPN compilation error George Patargias (Tue Oct 14 2014 - 08:43:59 CDT)
- Performance difference of prcompiled binary VS source code Nizar Masbukhin (Mon Oct 13 2014 - 19:23:43 CDT)
- MPICH 3 with Namd2/Charm Daniel Strahs (Mon Oct 13 2014 - 18:04:45 CDT)
- long running sim dies Thomas C. Bishop (Mon Oct 13 2014 - 08:29:43 CDT)
- Re: vmd-l: making psf files Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
- Re:tutorial-l: Protein structure distorted after Energy minimization with NAMD sunyeping (Wed Oct 08 2014 - 21:58:02 CDT)
- Umbrella sampling tilt with respect to Z-axis Mitchell Gleed (Wed Oct 08 2014 - 15:38:29 CDT)
- question about '+devices' ukulililixl (Wed Oct 08 2014 - 01:06:50 CDT)
- Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Oct 07 2014 - 11:30:07 CDT)
- String method in NAMD 2.10b1? Jenny lou (Mon Oct 06 2014 - 12:58:17 CDT)
- Parameter colvars Z (Mon Oct 06 2014 - 05:26:21 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 05:45:41 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 05:56:07 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 06:27:23 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 07:02:28 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 07:03:38 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 09:47:28 CDT)
- Re: Parameter colvars Jérôme Hénin (Mon Oct 06 2014 - 10:01:52 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 11:20:41 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 15:25:06 CDT)
- Re: Parameter colvars Grace Brannigan (Mon Oct 06 2014 - 15:56:18 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 22:05:28 CDT)
- Re: Parameter colvars Giacomo Fiorin (Tue Oct 07 2014 - 13:04:53 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 05:56:07 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 06:55:44 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 05:45:41 CDT)
- Does NAMD have some way to test the result? ukulililixl (Fri Oct 03 2014 - 21:50:52 CDT)
- Newbie GPU user, please help with my submission line Jose Borreguero (Thu Oct 02 2014 - 14:03:24 CDT)
- Re: Self-Assemble Monolayer--Periodic Boundary Conditions Natnael Doilicho (Wed Oct 01 2014 - 16:14:52 CDT)
- How to Amend a PBD file for NAMD Zeinab Emami (Wed Oct 01 2014 - 09:27:15 CDT)
- AW: vmd-l: Stray PME grid Norman Geist (Wed Oct 01 2014 - 02:27:31 CDT)
- FATAL ERROR: Setting parameter colvars from script failed! Mihaela Drenscko (Tue Sep 30 2014 - 09:27:18 CDT)
- Folic acid parameters Haleh a (Tue Sep 30 2014 - 08:44:38 CDT)
- Self-Assemble Monolayer--Periodic Boundary Conditions Natnael Doilicho (Mon Sep 29 2014 - 18:03:18 CDT)
- PCL dcd files Mihaela Drenscko (Mon Sep 29 2014 - 11:09:40 CDT)
- Molecular Dynamics of Rigid Linear Molecules in NAMD. Javad Noroozi (Sun Sep 28 2014 - 00:44:28 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 03:03:10 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 06:50:36 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Aron Broom (Sun Sep 28 2014 - 10:25:13 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Kenno Vanommeslaeghe (Sun Sep 28 2014 - 13:06:06 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Axel Kohlmeyer (Sun Sep 28 2014 - 13:31:59 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Kenno Vanommeslaeghe (Sun Sep 28 2014 - 14:00:43 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 06:50:36 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 03:03:10 CDT)
- SMD pulling speed Charles Whidborne (Sat Sep 27 2014 - 20:45:48 CDT)
- namd coulomb conversion factor Mohan maruthi sena (Sat Sep 27 2014 - 01:09:43 CDT)
- Reg: minimization Akshay Bhatnagar (Wed Sep 24 2014 - 23:35:16 CDT)
- getting different dihedral energy with two identical backbones Joyce Yang (Wed Sep 24 2014 - 16:45:52 CDT)
- expected speed up after fixing atoms? Jose Borreguero (Wed Sep 24 2014 - 12:44:48 CDT)
- Problem with running namdenergy plugin from text interface zeynab mohamad hoseyni (Mon Sep 22 2014 - 14:53:04 CDT)
- which namd versions compatible with CUDA 5.5 and other CUDA woes Robert Wohlhueter (Mon Sep 22 2014 - 13:39:19 CDT)
- Re: Is there any point in running NAMD over an ethernet-linked cluster? Nicholas M Glykos (Sun Sep 21 2014 - 13:21:53 CDT)
- Simulation Do not Run in the Cluster Roy Fernando (Sun Sep 21 2014 - 12:16:44 CDT)
- Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 12:04:44 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Siva Dasetty (Wed Sep 17 2014 - 13:23:53 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 13:41:34 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Jason Swails (Wed Sep 17 2014 - 13:47:53 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Aron Broom (Wed Sep 17 2014 - 13:54:57 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 14:27:10 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Kenno Vanommeslaeghe (Thu Sep 18 2014 - 15:39:49 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 13:41:34 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Siva Dasetty (Wed Sep 17 2014 - 13:23:53 CDT)
- simulation options available with GPU Ana Celia Vila Verde (Tue Sep 16 2014 - 02:52:51 CDT)
- Constraining two sets of atoms Natnael Doilicho (Tue Sep 16 2014 - 12:06:38 CDT)
- simulation options available with GPU Ana Celia Vila Verde (Tue Sep 16 2014 - 02:58:28 CDT)
- Setting constraints for SMD simulation Charles Whidborne (Mon Sep 15 2014 - 20:20:39 CDT)
- Annealing process of silica with excluded block Marzieh Alishahi (Fri Sep 12 2014 - 10:22:51 CDT)
- Qh Lurong Pan (Thu Sep 11 2014 - 08:22:22 CDT)
- Unsubscribe Katherine Parra (Wed Sep 10 2014 - 09:12:24 CDT)
- I would like to unsubscribe Maria Kopp (Wed Sep 10 2014 - 09:04:54 CDT)
- Colvars simulation running slow? Tristan Croll (Tue Sep 09 2014 - 20:31:06 CDT)
- GBIS using CUDA enabled NAMD Siva Dasetty (Tue Sep 09 2014 - 18:59:01 CDT)
- [ANN] MDTraj 1.0: Trajectory Analysis in Python Robert McGibbon (Mon Sep 08 2014 - 17:19:00 CDT)
- Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:04:32 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Branko (Mon Sep 08 2014 - 09:13:35 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Andreas Frster (Mon Sep 08 2014 - 09:29:51 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:43:47 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Ajasja Ljubetič (Mon Sep 08 2014 - 09:51:03 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 10:38:45 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Kenno Vanommeslaeghe (Mon Sep 08 2014 - 11:56:01 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Ajasja Ljubetič (Mon Sep 08 2014 - 12:26:27 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Kenno Vanommeslaeghe (Mon Sep 08 2014 - 13:08:11 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:43:47 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Gergely Gyimesi (Mon Sep 08 2014 - 09:51:33 CDT)
- GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 10:03:12 CDT)
- SASA calculation Siva Dasetty (Thu Sep 04 2014 - 09:03:56 CDT)
- FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Wed Sep 03 2014 - 02:34:06 CDT)
- Question to NAMD source Norman Geist (Thu Sep 04 2014 - 08:02:31 CDT)
- Re: Question to NAMD source Jim Phillips (Thu Sep 04 2014 - 11:25:48 CDT)
- AW: Question to NAMD source Norman Geist (Fri Sep 05 2014 - 01:32:29 CDT)
- Re: AW: Question to NAMD source Jim Phillips (Fri Sep 05 2014 - 14:34:55 CDT)
- AW: AW: Question to NAMD source Norman Geist (Mon Sep 08 2014 - 01:19:49 CDT)
- AW: AW: Question to NAMD source Norman Geist (Mon Sep 08 2014 - 04:40:10 CDT)
- Re: AW: AW: Question to NAMD source Jim Phillips (Mon Sep 08 2014 - 08:43:00 CDT)
- AW: Question to NAMD source Norman Geist (Fri Sep 05 2014 - 01:32:29 CDT)
- Re: Question to NAMD source Jim Phillips (Thu Sep 04 2014 - 11:25:48 CDT)
- Alignment Zeinab Emami (Thu Sep 04 2014 - 07:12:14 CDT)
- efficient way to apply time-dependent electric field Azadeh Alavi (Thu Sep 04 2014 - 05:38:12 CDT)
- computing forces on atoms by postprocessing a dcd file generated with FEP enabled Harris, Robert C. (Wed Sep 03 2014 - 14:05:40 CDT)
- INCONSISTENCY messages and minimization in toturial 1-2-sphere Yan Zhou (Wed Sep 03 2014 - 03:14:30 CDT)
- FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Tue Sep 02 2014 - 15:12:17 CDT)
- FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Sat Aug 30 2014 - 09:06:14 CDT)
- RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Tristan Croll (Tue Sep 02 2014 - 17:27:20 CDT)
- problems running ABF simulation Charles Whidborne (Tue Sep 02 2014 - 00:37:40 CDT)
- Re: Fixing atoms while equilibration Siva Dasetty (Mon Sep 01 2014 - 07:33:57 CDT)
- problem in calculating binding energy using MMGBSA with namd-2.9 Shailesh Pandey (Mon Sep 01 2014 - 07:31:34 CDT)
- Reg: solvation in DMSO Akshay Bhatnagar (Mon Sep 01 2014 - 00:01:44 CDT)
- restraining bonds Neelanjana Sengupta (Sun Aug 31 2014 - 23:50:24 CDT)
- NAMD energy minimization Siva Dasetty (Sun Aug 31 2014 - 14:30:56 CDT)
- RDF calculation of crystal system Fatemeh Omidbeygi (Sat Aug 30 2014 - 00:41:02 CDT)
- Fixing atoms while equilibration Siva Dasetty (Fri Aug 29 2014 - 20:12:21 CDT)
- Re: ibverb&&smp build NAMD ukulililixl (Fri Aug 29 2014 - 06:41:21 CDT)
- Assessing convergence in FEP calculations Gianluca Interlandi (Thu Aug 28 2014 - 14:00:08 CDT)
- Combining interleaved and top posting is considered harmful. Nicholas M Glykos (Thu Aug 28 2014 - 11:11:40 CDT)
- Set exact molarity in cell Stephan Grein (Thu Aug 28 2014 - 09:08:42 CDT)
- ibverb&&smp build NAMD ukulililixl (Thu Aug 28 2014 - 04:30:47 CDT)
- (no subject) BIPLAB NANDI (Wed Aug 27 2014 - 22:13:06 CDT)
- Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Aug 27 2014 - 13:05:05 CDT)
- Window for FEP calculations Gianluca Interlandi (Tue Aug 26 2014 - 19:35:33 CDT)
- NAMD 2.10b1 CUDA PME offload Norman Geist (Tue Aug 26 2014 - 09:25:48 CDT)
- Metadynamics test along eigenvector Floquet Nicolas (Tue Aug 26 2014 - 02:58:00 CDT)
- (no subject) ukulililixl (Tue Aug 26 2014 - 01:22:20 CDT)
- Siginificant speedup by updating nvidia driver Norman Geist (Mon Aug 25 2014 - 11:06:38 CDT)
- Nucleic acid stains parameters Sebastián Gutiérrez (Mon Aug 25 2014 - 10:37:04 CDT)
- Metadynamics with eigenvector Nicolas Floquet (Mon Aug 25 2014 - 09:40:06 CDT)
- NAMD 2.10b1 released Jim Phillips (Mon Aug 25 2014 - 07:49:51 CDT)
- question in NAMD with icc & cuda ukulililixl (Mon Aug 25 2014 - 06:40:48 CDT)
- ABF hBond Charles Whidborne (Mon Aug 25 2014 - 02:52:45 CDT)
- AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:21:25 CDT)
- Re: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 08:22:43 CDT)
- AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:56:32 CDT)
- Re: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 08:59:26 CDT)
- AW: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Mon Aug 25 2014 - 01:07:21 CDT)
- Re: AW: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Mon Aug 25 2014 - 07:34:34 CDT)
- AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:56:32 CDT)
- Re: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 08:22:43 CDT)
- FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 06:40:06 CDT)
- Re: NAMD 2.10 Manual Ajasja Ljubetič (Fri Aug 22 2014 - 03:30:05 CDT)
- NAMD 2.10 Manual Norman Geist (Fri Aug 22 2014 - 03:14:47 CDT)
- Installation Protocol of NAMD on Linux Cluster Viswanath Pasumarthi (Thu Aug 21 2014 - 14:46:27 CDT)
- SMP vs Multicore Maxime Boissonneault (Thu Aug 21 2014 - 09:26:43 CDT)
- Fwd: [External] Boost value in aMD simulation Thomas Evangelidis (Thu Aug 21 2014 - 06:05:05 CDT)
- wrapping a protein Maria Bykhovskaia (Wed Aug 20 2014 - 17:40:30 CDT)
- Accelerated molecular dynamics: Energy value in output file Kapil jain (Tue Aug 19 2014 - 23:53:20 CDT)
- using CHARMM-format Amber parameters in NAMD Basheer Subei (Tue Aug 19 2014 - 19:16:43 CDT)
- "Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 10:48:30 CDT)
- Re: "Beefier" benchmark Phil Greer (Tue Aug 19 2014 - 11:10:28 CDT)
- Re: "Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 11:14:31 CDT)
- Re: "Beefier" benchmark Phil Greer (Tue Aug 19 2014 - 11:30:38 CDT)
- AW: "Beefier" benchmark Norman Geist (Wed Aug 20 2014 - 01:38:51 CDT)
- Re: AW: "Beefier" benchmark Maxime Boissonneault (Wed Aug 20 2014 - 09:20:15 CDT)
- AW: AW: "Beefier" benchmark Norman Geist (Thu Aug 21 2014 - 03:04:01 CDT)
- Re: AW: AW: "Beefier" benchmark Maxime Boissonneault (Thu Aug 21 2014 - 07:32:10 CDT)
- AW: AW: AW: "Beefier" benchmark Norman Geist (Thu Aug 21 2014 - 08:43:05 CDT)
- Re: AW: AW: AW: "Beefier" benchmark Maxime Boissonneault (Thu Aug 21 2014 - 09:04:42 CDT)
- Re: "Beefier" benchmark Aron Broom (Tue Aug 19 2014 - 11:15:29 CDT)
- Re: "Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 11:14:31 CDT)
- Re: "Beefier" benchmark Phil Greer (Tue Aug 19 2014 - 11:10:28 CDT)
- Fwd: [External] Boost value in aMD simulation Thomas Evangelidis (Tue Aug 19 2014 - 05:24:17 CDT)
- NVT, NPT, order & combination Zeinab Emami (Tue Aug 19 2014 - 03:23:26 CDT)
- Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 12:25:49 CDT)
- Re: Atom selection in Tcl Force script with Amber partop file Maxim Belkin (Fri Aug 15 2014 - 16:48:12 CDT)
- Martini forcefield RBCG and ENM Raul Araya (Fri Aug 15 2014 - 10:05:01 CDT)
- Hwo to switch from NPT to NVT Zeinab Emami (Fri Aug 15 2014 - 07:14:05 CDT)
- Hwo to switch from NPT to NVT Zeinab Emami (Fri Aug 15 2014 - 07:12:39 CDT)
- H-Bond measurements Stephan Grein (Thu Aug 14 2014 - 01:57:40 CDT)
- Hybrid MPI + Multicore + Cuda build Maxime Boissonneault (Wed Aug 13 2014 - 11:46:59 CDT)
- Root mean square deviation.......... Gurpreet Kaur Dhindsa (Tue Aug 12 2014 - 12:58:38 CDT)
- Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Aug 12 2014 - 09:31:17 CDT)
- NAMD CVS_CUDA ERROR: "all CUDA-capable devices are busy or unavailable" Samuel Bowerman (Mon Aug 11 2014 - 11:50:45 CDT)
- Running NAMD via GROMACS topology Mike Makowski (Sun Aug 10 2014 - 17:44:35 CDT)
- Unsubscribe Katherine Parra (Sun Aug 10 2014 - 11:30:22 CDT)
- (no subject) Shalton Evans (Sat Aug 09 2014 - 23:00:48 CDT)
- Energy term in output file of Accelerated dynamics Kapil jain (Fri Aug 08 2014 - 02:14:56 CDT)
- ABF simulation, free energy to remove a DNA strand Charles Whidborne (Tue Aug 05 2014 - 01:54:14 CDT)
- (no subject) sudipta.mml (Sat Aug 02 2014 - 20:01:46 CDT)
- Intermolecular potential energy function in NAMD Viswanath Pasumarthi (Fri Aug 01 2014 - 06:31:21 CDT)
- Silent crash NAMD-multicore-CUDA MEHRAN MB (Wed Jul 30 2014 - 17:23:10 CDT)
- Loss of Translational entropy calculation in FEP Daniel Torrente (Wed Jul 30 2014 - 16:57:08 CDT)
- +p option on Windows 7 Kukol, Andreas (Wed Jul 30 2014 - 09:56:28 CDT)
- Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Tue Jul 29 2014 - 16:38:28 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Jul 29 2014 - 17:59:19 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Jul 29 2014 - 23:21:58 CDT)
- Re: Kb, Ktheta values for TIP3P water model JC Gumbart (Wed Jul 30 2014 - 10:27:16 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Thu Jul 31 2014 - 14:03:00 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Thu Jul 31 2014 - 14:14:43 CDT)
- automatic extraction of RMSD values of the heavy atoms of residues from NAMD output? Andras Borosy (Mon Aug 04 2014 - 05:32:53 CDT)
- Re: automatic extraction of RMSD values of the heavy atoms of residues from NAMD output? Maxim Belkin (Mon Aug 04 2014 - 11:25:15 CDT)
- Re: Kb, Ktheta values for TIP3P water model JC Gumbart (Thu Jul 31 2014 - 16:24:06 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Thu Jul 31 2014 - 17:28:09 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Aug 05 2014 - 02:14:00 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Aug 05 2014 - 09:54:35 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi Dinpajooh (Tue Aug 05 2014 - 11:52:44 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Aug 05 2014 - 13:41:12 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Aug 05 2014 - 14:10:14 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Tue Aug 05 2014 - 14:28:04 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Aug 05 2014 - 14:29:22 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Aug 05 2014 - 14:49:48 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Tue Aug 05 2014 - 14:59:14 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Wed Aug 06 2014 - 13:57:26 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Wed Aug 06 2014 - 14:11:01 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Wed Aug 06 2014 - 14:41:58 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Wed Aug 06 2014 - 15:28:23 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Wed Aug 06 2014 - 15:40:22 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Wed Aug 06 2014 - 15:48:57 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Wed Aug 06 2014 - 16:07:27 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Wed Aug 06 2014 - 17:28:12 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Wed Aug 06 2014 - 17:39:50 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Thu Aug 07 2014 - 10:50:24 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Thu Aug 07 2014 - 12:36:33 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Thu Aug 07 2014 - 15:08:39 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Thu Aug 07 2014 - 17:15:09 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Sun Aug 10 2014 - 17:49:01 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Sun Aug 10 2014 - 20:59:58 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Sun Aug 10 2014 - 22:10:43 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Sun Aug 10 2014 - 22:29:55 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Sun Aug 10 2014 - 23:16:19 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Mon Aug 11 2014 - 06:40:43 CDT)
- Re: Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Mon Aug 11 2014 - 12:56:00 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Mon Aug 11 2014 - 14:08:41 CDT)
- Re: Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Tue Aug 12 2014 - 12:19:00 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Tue Aug 12 2014 - 12:27:25 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Aug 12 2014 - 13:31:04 CDT)
- Re: Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Tue Aug 12 2014 - 14:11:40 CDT)
- Re: Kb, Ktheta values for TIP3P water model Axel Kohlmeyer (Tue Aug 12 2014 - 14:26:05 CDT)
- Re: Kb, Ktheta values for TIP3P water model Maxim Belkin (Tue Aug 12 2014 - 23:11:43 CDT)
- Re: Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Wed Aug 13 2014 - 02:27:24 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Aug 05 2014 - 15:00:49 CDT)
- Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Jul 29 2014 - 23:21:58 CDT)
- Re: Kb, Ktheta values for TIP3P water model Maxim Belkin (Mon Aug 11 2014 - 18:05:41 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Jul 29 2014 - 17:59:19 CDT)
- Analysis problem (Data vector empty) Stephan Grein (Tue Jul 29 2014 - 04:06:27 CDT)
- temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 10:19:10 CDT)
- Re: temperature for lipid-protein assembly Kenno Vanommeslaeghe (Mon Jul 28 2014 - 10:57:41 CDT)
- Re: temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 12:06:34 CDT)
- Re: temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 12:08:15 CDT)
- Re: temperature for lipid-protein assembly Kenno Vanommeslaeghe (Mon Jul 28 2014 - 12:40:18 CDT)
- Re: temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 12:46:39 CDT)
- Re: temperature for lipid-protein assembly Kenno Vanommeslaeghe (Mon Jul 28 2014 - 13:33:00 CDT)
- Re: temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 12:06:34 CDT)
- Re: temperature for lipid-protein assembly Kenno Vanommeslaeghe (Mon Jul 28 2014 - 10:57:41 CDT)
- Rule of thumb for equilibration Stephan Grein (Mon Jul 28 2014 - 09:45:43 CDT)
- segmentation fault in accelMD Anna Modzelewska (Mon Jul 28 2014 - 05:56:05 CDT)
- RE: The water box shrinks at the start of the MD simulation sunyeping (Sun Jul 27 2014 - 19:19:15 CDT)
- The water box shrinks at the start of the MD simulation Zheng Fulu (Sun Jul 27 2014 - 13:53:55 CDT)
- The water box shrinks at the start of the MD simulation #ZHENG FULU# (Sun Jul 27 2014 - 06:13:52 CDT)
- Fwd: membrane lipid involvement of cholesterol Thomas Evangelidis (Sat Jul 26 2014 - 06:39:30 CDT)
- Accelerated MD (aMD) Ramin Ekhteiari (Sat Jul 26 2014 - 06:06:25 CDT)
- membrane lipid involvement of cholesterol Ramin Ekhteiari (Sat Jul 26 2014 - 03:14:38 CDT)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) Cenk Denktas (Fri Jul 25 2014 - 15:30:40 CDT)
- Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
- Reg: LangevinPistonDecay and LangevinPistonPeriod Akshay Bhatnagar (Thu Jul 24 2014 - 02:04:25 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 14:24:45 CDT)
- Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 06:30:12 CDT)
- NAMD_energy_plot sananda chatterjee (Tue Jul 22 2014 - 17:08:56 CDT)
- (no subject) Carlos Navarrro Retamal (Tue Jul 22 2014 - 11:43:10 CDT)
- (no subject) Mitul Saha (Tue Jul 22 2014 - 11:27:04 CDT)
- ABF/colvar error in NAMD2.9 Harish Vashisth (Tue Jul 22 2014 - 11:23:13 CDT)
- Subject: RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 06:28:57 CDT)
- Cost of a colvar calculation George Patargias (Tue Jul 22 2014 - 06:27:52 CDT)
- Re: Cost of a colvar calculation Jérôme Hénin (Tue Jul 22 2014 - 06:56:42 CDT)
- Re: Cost of a colvar calculation Ivan Gregoretti (Tue Jul 22 2014 - 07:33:14 CDT)
- Re: Cost of a colvar calculation Branko (Tue Jul 22 2014 - 07:44:04 CDT)
- Re: Cost of a colvar calculation Ivan Gregoretti (Tue Jul 22 2014 - 08:41:41 CDT)
- Re: Cost of a colvar calculation Aron Broom (Tue Jul 22 2014 - 10:56:45 CDT)
- Re: Cost of a colvar calculation Axel Kohlmeyer (Tue Jul 22 2014 - 11:02:47 CDT)
- Re: Cost of a colvar calculation Jérôme Hénin (Tue Jul 22 2014 - 11:20:56 CDT)
- Re: Cost of a colvar calculation George Patargias (Wed Jul 23 2014 - 01:33:23 CDT)
- Re: Cost of a colvar calculation Branko (Wed Jul 23 2014 - 07:45:31 CDT)
- Re: Cost of a colvar calculation Jérôme Hénin (Tue Jul 22 2014 - 07:43:30 CDT)
- Re: Cost of a colvar calculation Ivan Gregoretti (Tue Jul 22 2014 - 07:33:14 CDT)
- Re: Cost of a colvar calculation Jo, Sunhwan (Tue Jul 22 2014 - 13:06:12 CDT)
- Re: Cost of a colvar calculation Jérôme Hénin (Tue Jul 22 2014 - 06:56:42 CDT)
- Subject: Re: Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 05:04:09 CDT)
- Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 15:03:30 CDT)
- Reg: deciding cell basis vector Akshay Bhatnagar (Mon Jul 21 2014 - 08:57:57 CDT)
- exchange force constants Lu Hong (Mon Jul 21 2014 - 08:50:24 CDT)
- Calculating the force needed to constrain a protein Shane.OMahony (Fri Jul 18 2014 - 11:18:05 CDT)
- School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014 Axel Kohlmeyer (Thu Jul 17 2014 - 14:48:33 CDT)
- running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? Andras Borosy (Thu Jul 17 2014 - 09:27:46 CDT)
- NAMD/MIC & CUDA on Stampede Jeffery Klauda (Wed Jul 16 2014 - 13:28:27 CDT)
- Re:Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Wed Jul 16 2014 - 01:27:52 CDT)
- RE: Force field design Gianluca Interlandi (Wed Jul 16 2014 - 00:32:49 CDT)
- autopsf (patch) Cenk Denktas (Tue Jul 15 2014 - 12:41:48 CDT)
- Force field design Abhishek TYAGI (Tue Jul 15 2014 - 11:55:35 CDT)
- Re: Force field design Aron Broom (Tue Jul 15 2014 - 21:58:07 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:06:23 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Tue Jul 22 2014 - 10:40:37 CDT)
- Re: Force field design Axel Kohlmeyer (Tue Jul 22 2014 - 11:14:16 CDT)
- RE: Force field design Abhishek TYAGI (Tue Jul 22 2014 - 23:04:23 CDT)
- Re: Force field design Axel Kohlmeyer (Tue Jul 22 2014 - 23:36:30 CDT)
- RE: Force field design Abhishek TYAGI (Wed Jul 23 2014 - 00:23:36 CDT)
- RE: Force field design Axel Kohlmeyer (Wed Jul 23 2014 - 05:13:16 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Wed Jul 23 2014 - 18:20:53 CDT)
- Re: Force field design Axel Kohlmeyer (Wed Jul 23 2014 - 22:06:21 CDT)
- Re: Force field design R.J. Swett (Wed Jul 23 2014 - 23:03:48 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Thu Jul 24 2014 - 11:12:18 CDT)
- Re: Force field design Gianluca Interlandi (Thu Jul 24 2014 - 14:22:41 CDT)
- Re: Force field design Thomas Evangelidis (Thu Jul 24 2014 - 14:31:31 CDT)
- Re: Force field design Axel Kohlmeyer (Thu Jul 24 2014 - 14:35:11 CDT)
- Re: Force field design Gianluca Interlandi (Wed Jul 23 2014 - 23:30:58 CDT)
- RE: Force field design Abhishek TYAGI (Wed Jul 23 2014 - 19:57:40 CDT)
- Re: Force field design Gianluca Interlandi (Tue Jul 15 2014 - 22:32:35 CDT)
- Re: Force field design Mayne, Christopher G (Wed Jul 16 2014 - 10:46:48 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:24:29 CDT)
- RE: Force field design Abhishek TYAGI (Tue Jul 22 2014 - 05:40:00 CDT)
- Re: Force field design Aron Broom (Tue Jul 15 2014 - 21:58:07 CDT)
- NADH topology file Kevin C Chan (Tue Jul 15 2014 - 05:41:51 CDT)
- Fwd: Re: Branko (Mon Jul 14 2014 - 13:24:43 CDT)
- (no subject) Eifler, Jay Q. (UMKC-Student) (Mon Jul 14 2014 - 13:05:36 CDT)
- Re: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Fri Jul 11 2014 - 06:14:59 CDT)
- AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Norman Geist (Fri Jul 11 2014 - 02:51:44 CDT)
- Regarding free energy cost incurred by using pseudo bonds Sharmon (Thu Jul 10 2014 - 13:29:29 CDT)
- variable force constant Lu Hong (Thu Jul 10 2014 - 12:34:58 CDT)
- Fwd: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Thu Jul 10 2014 - 09:31:03 CDT)
- Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Thu Jul 10 2014 - 04:30:20 CDT)
- parameter and topology files for martini polarizable water Klas Karis (Wed Jul 09 2014 - 18:30:23 CDT)
- accelerated MD as the engine for loop refirement James Starlight (Wed Jul 09 2014 - 14:39:08 CDT)
- Re: accelerated MD as the engine for loop refirement Gianluca Interlandi (Wed Jul 09 2014 - 15:08:17 CDT)
- Re: accelerated MD as the engine for loop refirement Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:32:38 CDT)
- Re: accelerated MD as the engine for loop refirement Gianluca Interlandi (Thu Jul 10 2014 - 17:59:24 CDT)
- Re: accelerated MD as the engine for loop refirement James Starlight (Sat Jul 12 2014 - 09:28:21 CDT)
- Re: accelerated MD as the engine for loop refirement James Starlight (Sun Jul 13 2014 - 14:05:10 CDT)
- RE: accelerated MD as the engine for loop refirement Tristan Croll (Mon Jul 14 2014 - 00:40:11 CDT)
- Re: accelerated MD as the engine for loop refirement James Starlight (Mon Jul 14 2014 - 05:16:46 CDT)
- Re: accelerated MD as the engine for loop refirement Chris Ing (Mon Jul 14 2014 - 16:53:07 CDT)
- RE: accelerated MD as the engine for loop refirement Tristan Croll (Mon Jul 14 2014 - 18:18:05 CDT)
- Re: accelerated MD as the engine for loop refirement Ramin Ekhteiari (Tue Jul 15 2014 - 01:30:12 CDT)
- Re: accelerated MD as the engine for loop refirement Gianluca Interlandi (Tue Jul 15 2014 - 02:05:30 CDT)
- Re: accelerated MD as the engine for loop refirement Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:32:38 CDT)
- Re: accelerated MD as the engine for loop refirement Ajasja Ljubetič (Wed Jul 09 2014 - 15:22:15 CDT)
- Re: accelerated MD as the engine for loop refirement Gianluca Interlandi (Wed Jul 09 2014 - 15:08:17 CDT)
- how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 18:20:48 CDT)
- Re: how to quantify and visualize the flow of water into a protein Maxim Belkin (Tue Jul 08 2014 - 18:40:15 CDT)
- Re: how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 19:04:01 CDT)
- Re: how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 19:12:40 CDT)
- Re: how to quantify and visualize the flow of water into a protein Maxim Belkin (Tue Jul 08 2014 - 19:20:12 CDT)
- Re: how to quantify and visualize the flow of water into a protein Mo Chen (Tue Jul 08 2014 - 19:43:35 CDT)
- Re: how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 19:04:01 CDT)
- Re: how to quantify and visualize the flow of water into a protein Joshua Adelman (Tue Jul 08 2014 - 19:36:02 CDT)
- Re: how to quantify and visualize the flow of water into a protein Maxim Belkin (Tue Jul 08 2014 - 18:40:15 CDT)
- Bad global crossterm count! Mitul Saha (Tue Jul 08 2014 - 16:46:17 CDT)
- About asterisk in IC statements in topology files Kevin C Chan (Tue Jul 08 2014 - 02:30:25 CDT)
- Hexagonal cell instability during lipid bilayer sim in NAMD 2.9 Michael Bokoch (Mon Jul 07 2014 - 21:42:54 CDT)
- NAMD energy plugin - dielectric constant Ramin Ekhteiari (Mon Jul 07 2014 - 14:59:42 CDT)
- (no subject) sudipta.mml (Mon Jul 07 2014 - 01:08:12 CDT)
- Regarding NAMD and MD simulations Joel Moniz (Mon Jul 07 2014 - 01:42:04 CDT)
- two O atoms in CTER are unusually close Fulu Zheng (Sat Jul 05 2014 - 02:05:28 CDT)
- Nanotube tutorial Adam Kells (Fri Jul 04 2014 - 13:19:33 CDT)
- (no subject) zmhoseyni (Thu Jul 03 2014 - 22:36:44 CDT)
- PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Thu Jul 03 2014 - 15:58:23 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 04:53:32 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 05:38:48 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 05:42:02 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 09:42:41 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Tue Jul 08 2014 - 12:14:10 CDT)
- REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 01:15:21 CDT)
- namd-slurm file Ramin Ekhteiari (Wed Jul 02 2014 - 10:08:31 CDT)
- (no subject) zmhoseyni (Wed Jul 02 2014 - 00:25:31 CDT)
- Invalid command error Adam Kells (Mon Jun 30 2014 - 06:49:07 CDT)
- calculating free energy Alireza Mansouri (Sat Jun 28 2014 - 12:22:40 CDT)
- Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326) Prija Ponnan (Fri Jun 27 2014 - 06:40:43 CDT)
- Namd grid forces -distance between molecule and surface Mohan maruthi sena (Fri Jun 27 2014 - 05:20:29 CDT)
- Restraints between ion and small molecule Daniel Torrente (Thu Jun 26 2014 - 11:53:49 CDT)
- Re: Restraints between ion and small molecule Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:16:31 CDT)
- Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Shailesh Pandey (Thu Jun 26 2014 - 04:41:49 CDT)
- NAMD energy calculation Ramin Ekhteiari (Wed Jun 25 2014 - 11:45:33 CDT)
- PMF and work distribution Mustafa Tekpinar (Wed Jun 25 2014 - 05:50:30 CDT)
- Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Tue Jun 24 2014 - 20:02:49 CDT)
- Re: Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Tue Jun 24 2014 - 23:07:02 CDT)
- AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Wed Jun 25 2014 - 00:31:47 CDT)
- How to apply a magnetic field with NAMD Faezeh Mottaghitalab (Tue Jun 24 2014 - 16:00:48 CDT)
- paricle type in residue based coarse graining of NAMD Yongcheng Zhou (Mon Jun 23 2014 - 09:14:12 CDT)
- paricle type in residue based coarse graining of NAMD Yongcheng Zhou (Mon Jun 23 2014 - 14:37:16 CDT)
- Fatal error.. Gurpreet Kaur Dhindsa (Sun Jun 22 2014 - 17:32:16 CDT)
- memory problem Adam Moser (Fri Jun 20 2014 - 15:01:30 CDT)
- NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 14:07:31 CDT)
- Unsubscribe jafar azamat (Fri Jun 20 2014 - 03:27:10 CDT)
- ffTK and phase angles Benjamin Hill (Thu Jun 19 2014 - 17:43:28 CDT)
- Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Thu Jun 19 2014 - 03:21:33 CDT)
- Unsubscribe Dhanashree Khanale (Thu Jun 19 2014 - 03:19:51 CDT)
- Should PME be used for electrostatic interaction energy calculations? Fotis Baltoumas (Wed Jun 18 2014 - 12:59:16 CDT)
- AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:25:49 CDT)
- Re: Should PME be used for electrostatic interaction energy calculations? Thomas Evangelidis (Thu Jun 19 2014 - 02:38:50 CDT)
- AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
- Constraint failure in RATTLE algorithm Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
- Re: Constraint failure in RATTLE algorithm Axel Kohlmeyer (Wed Jun 18 2014 - 13:23:05 CDT)
- Re: Constraint failure in RATTLE algorithm Aron Broom (Wed Jun 18 2014 - 14:07:04 CDT)
- Re: Constraint failure in RATTLE algorithm Douglas Houston (Thu Jun 19 2014 - 05:26:53 CDT)
- Re: Constraint failure in RATTLE algorithm Aron Broom (Thu Jun 19 2014 - 09:15:49 CDT)
- Re: Constraint failure in RATTLE algorithm Douglas Houston (Thu Jun 19 2014 - 09:51:33 CDT)
- Re: Constraint failure in RATTLE algorithm Aron Broom (Thu Jun 19 2014 - 10:37:59 CDT)
- Re: Constraint failure in RATTLE algorithm Douglas Houston (Fri Jun 20 2014 - 08:31:56 CDT)
- RE: Constraint failure in RATTLE algorithm Tristan Croll (Sat Jun 21 2014 - 18:43:43 CDT)
- Re: Constraint failure in RATTLE algorithm Aron Broom (Sun Jun 22 2014 - 23:02:28 CDT)
- RE: Constraint failure in RATTLE algorithm Douglas Houston (Fri Jun 27 2014 - 09:29:42 CDT)
- Re: Constraint failure in RATTLE algorithm Kenno Vanommeslaeghe (Fri Jun 27 2014 - 10:37:19 CDT)
- Re: Constraint failure in RATTLE algorithm Douglas Houston (Tue Jul 01 2014 - 04:29:38 CDT)
- 2-residue patch for hydrocarbon staple Kenno Vanommeslaeghe (Thu Jul 24 2014 - 15:48:52 CDT)
- Re: Constraint failure in RATTLE algorithm Axel Kohlmeyer (Wed Jun 18 2014 - 13:23:05 CDT)
- is the aMD implementation compatible with AMBER force fields Thomas Evangelidis (Wed Jun 18 2014 - 06:20:06 CDT)
- Inquiry about lipid membrane simulation Mo Chen (Tue Jun 17 2014 - 20:57:59 CDT)
- Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 10:20:24 CDT)
- Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 14:02:52 CDT)
- Re: Inquiry about lipid membrane simulation Mo Chen (Wed Jun 18 2014 - 14:25:16 CDT)
- Re: Inquiry about lipid membrane simulation Sunhwan Jo (Wed Jun 18 2014 - 14:46:56 CDT)
- Re: Inquiry about lipid membrane simulation Wonpil Im (Wed Jun 18 2014 - 14:53:31 CDT)
- Re: Inquiry about lipid membrane simulation JC Gumbart (Wed Jun 18 2014 - 19:48:17 CDT)
- Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 14:02:52 CDT)
- Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 10:20:24 CDT)
- Merging the two files...... Gurpreet Kaur Dhindsa (Tue Jun 17 2014 - 10:00:09 CDT)
- Reg : MD simulation with DMSO instead of water Akshay Bhatnagar (Tue Jun 17 2014 - 06:04:58 CDT)
- alchemical free energy simulations with parmtop Hannes Loeffler (Tue Jun 17 2014 - 04:35:59 CDT)
- Re: alchemical free energy simulations with parmtop Hannes Loeffler (Mon Dec 01 2014 - 03:20:17 CST)
- Re: Re: alchemical free energy simulations with parmtop Jim Phillips (Tue Dec 02 2014 - 12:06:40 CST)
- RE: Re: alchemical free energy simulations with parmtop hannes.loeffler_at_stfc.ac.uk (Tue Dec 02 2014 - 12:39:41 CST)
- RE: Re: alchemical free energy simulations with parmtop Jim Phillips (Thu Dec 04 2014 - 11:09:22 CST)
- RE: Re: alchemical free energy simulations with parmtop hannes.loeffler_at_stfc.ac.uk (Thu Dec 04 2014 - 11:52:49 CST)
- RE: Re: alchemical free energy simulations with parmtop Jim Phillips (Fri Dec 05 2014 - 14:49:55 CST)
- Re: Re: alchemical free energy simulations with parmtop Jim Phillips (Tue Dec 02 2014 - 12:06:40 CST)
- Re: alchemical free energy simulations with parmtop Hannes Loeffler (Mon Dec 01 2014 - 03:20:17 CST)
- improving tclforce efficiency, getting "Signal: segmentation violation" error zeynab mohamad hoseyni (Sun Jun 15 2014 - 20:18:11 CDT)
- unsubscribe Laura (Sun Jun 15 2014 - 12:29:39 CDT)
- The short range nonbonbed force charge after load balancing ¬ (Sun Jun 15 2014 - 04:57:43 CDT)
- New partial charges after patching Sadegh Faramarzi Ganjabad (Sat Jun 14 2014 - 04:15:47 CDT)
- About converting NAMD dcd file into CHARMM dcd file Mo Chen (Fri Jun 13 2014 - 18:41:30 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Fri Jun 13 2014 - 12:17:15 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Mon Jun 16 2014 - 02:19:28 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Jun 18 2014 - 07:24:00 CDT)
- AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Wed Jun 18 2014 - 07:52:29 CDT)
- Re: AW: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Jun 18 2014 - 07:57:59 CDT)
- AW: AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Thu Jun 19 2014 - 02:19:03 CDT)
- Re: AW: AW: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Thu Jun 19 2014 - 04:56:28 CDT)
- AW: AW: AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Thu Jun 19 2014 - 05:09:43 CDT)
- Re: Using nodelist file causes namd to hang Douglas Houston (Thu Jun 19 2014 - 12:25:25 CDT)
- AW: Using nodelist file causes namd to hang Norman Geist (Fri Jun 20 2014 - 02:25:11 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Fri Jun 20 2014 - 05:00:05 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Fri Jun 20 2014 - 05:15:02 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Tue Jun 24 2014 - 08:42:20 CDT)
- AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Tue Jun 24 2014 - 08:50:06 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Aug 27 2014 - 09:30:42 CDT)
- Re: AW: Using nodelist file causes namd to hang Ajasja Ljubetič (Wed Aug 27 2014 - 12:32:53 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Aug 27 2014 - 12:47:24 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Thu Aug 28 2014 - 02:47:58 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Thu Aug 28 2014 - 05:43:48 CDT)
- AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Thu Aug 28 2014 - 06:08:47 CDT)
- Re: AW: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Thu Aug 28 2014 - 07:54:30 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Jun 18 2014 - 07:24:00 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Mon Jun 16 2014 - 02:19:28 CDT)
- AW: Reg: movement of protein outside box Norman Geist (Fri Jun 13 2014 - 03:09:20 CDT)
- How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 00:53:12 CDT)
- RE: How to refer to side-chain via tcl-force scripting? Tristan Croll (Fri Jun 13 2014 - 02:08:51 CDT)
- AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 02:53:41 CDT)
- AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 02:56:03 CDT)
- Re: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 03:21:08 CDT)
- AW: AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 03:26:33 CDT)
- Re: AW: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 23:01:42 CDT)
- RE: AW: AW: How to refer to side-chain via tcl-force scripting? Tristan Croll (Sat Jun 14 2014 - 01:09:39 CDT)
- Re: AW: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Sat Jun 14 2014 - 09:03:09 CDT)
- Re: AW: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Mon Jun 16 2014 - 11:20:46 CDT)
- Re: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 03:21:08 CDT)
- NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Vlastimil Zíma (Wed Jun 11 2014 - 02:36:44 CDT)
- AW: Reg: movement of protein outside box Norman Geist (Tue Jun 10 2014 - 07:26:58 CDT)
- Reg: movement of protein outside box Akshay Bhatnagar (Mon Jun 09 2014 - 20:46:56 CDT)
- NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Shailesh Pandey (Mon Jun 09 2014 - 12:54:03 CDT)
- boron nitride nanotube Z (Mon Jun 09 2014 - 02:58:02 CDT)
- change in pdb.. Gurpreet Kaur Dhindsa (Sat Jun 07 2014 - 18:37:41 CDT)
- NAMD Multicore CUDA usage Ravi Abrol (Fri Jun 06 2014 - 14:20:10 CDT)
- alchElecLambdaStart (Thermodynamic Integration) Javad Noroozi (Fri Jun 06 2014 - 13:55:28 CDT)
- Reg: deformation of water box during equilibration Akshay Bhatnagar (Fri Jun 06 2014 - 11:35:34 CDT)
- Fixed atoms. Gurpreet Kaur Dhindsa (Thu Jun 05 2014 - 16:15:05 CDT)
- NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 12:45:36 CDT)
- non-neutralized system Research Jubilant (Wed Jun 04 2014 - 10:29:47 CDT)
- Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 13:31:40 CDT)
- Re: Ion Au+3 simulation Axel Kohlmeyer (Tue Jun 03 2014 - 14:38:35 CDT)
- Re: Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 15:17:15 CDT)
- Re: Ion Au+3 simulation Axel Kohlmeyer (Tue Jun 03 2014 - 15:49:35 CDT)
- Re: Ion Au+3 simulation Aron Broom (Tue Jun 03 2014 - 16:21:52 CDT)
- Re: Ion Au+3 simulation Kenno Vanommeslaeghe (Wed Jun 04 2014 - 10:32:46 CDT)
- Re: Ion Au+3 simulation Aron Broom (Wed Jun 04 2014 - 16:00:23 CDT)
- Re: Ion Au+3 simulation Kenno Vanommeslaeghe (Thu Jun 05 2014 - 17:27:37 CDT)
- Re: Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 16:17:38 CDT)
- error message Richard Wood (Tue Jun 03 2014 - 19:13:26 CDT)
- Re: Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 15:17:15 CDT)
- Re: Ion Au+3 simulation Axel Kohlmeyer (Tue Jun 03 2014 - 14:38:35 CDT)
- Density of water box Akshay Bhatnagar (Tue Jun 03 2014 - 05:22:00 CDT)
- coordinates in namd Research Jubilant (Mon Jun 02 2014 - 23:34:52 CDT)
- About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:35:50 CDT)
- code implementation based on NAMD source code Teerapong Pirojsirikul (Thu May 29 2014 - 17:39:21 CDT)
- FEP of water molecule in binding pocket Monika Sharma (Wed May 28 2014 - 15:35:33 CDT)
- Rapid and accurate parameterization of new molecules in CHARMM Aaron Larsen (Tue May 27 2014 - 08:21:06 CDT)
- RE: Rapid and accurate parameterization of new molecules in CHARMM JC Gumbart (Tue May 27 2014 - 09:19:40 CDT)
- constraint file from amber prmtop/inpcrd amin_at_imtech.res.in (Sat May 24 2014 - 14:32:55 CDT)
- IMPROPER PARAMETERS FOR CA CA CA CA Z (Sat May 24 2014 - 10:50:49 CDT)
- *** glibc detected *** namd2: invalid fastbin entry (free) Wesley Lay (Thu May 22 2014 - 15:19:11 CDT)
- (no subject) zmhoseyni (Wed May 21 2014 - 04:48:25 CDT)
- building namd on a Cray XE6 with Interlagos procs Giovanni Settanni (Tue May 20 2014 - 09:03:22 CDT)
- (no subject) zmhoseyni (Mon May 19 2014 - 04:18:48 CDT)
- COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Mon May 19 2014 - 03:44:36 CDT)
- Re: Steered MD with the RMSD colvar George Patargias (Mon May 19 2014 - 05:01:12 CDT)
- Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014 David Brandon (Sat May 17 2014 - 18:22:07 CDT)
- running Multiple-replicas metadynamics Osvalds Verners (Fri May 16 2014 - 13:01:08 CDT)
- Polymer Layer/ Cutoff Rawan Al Nsour (Thu May 15 2014 - 11:19:21 CDT)
- NAMD-GPU Ramin Ekhteiari (Wed May 14 2014 - 07:19:10 CDT)
- Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 13:34:13 CDT)
- Re: Scaling solvent-solute intermolecular interactions Axel Kohlmeyer (Tue May 13 2014 - 13:56:02 CDT)
- RE: Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 15:09:06 CDT)
- Re: Scaling solvent-solute intermolecular interactions Axel Kohlmeyer (Tue May 13 2014 - 15:17:53 CDT)
- Re: Scaling solvent-solute intermolecular interactions Jason Swails (Tue May 13 2014 - 16:57:14 CDT)
- RE: Scaling solvent-solute intermolecular interactions Michael Bellucci (Wed May 14 2014 - 08:50:36 CDT)
- Re: Scaling solvent-solute intermolecular interactions Jason Swails (Wed May 14 2014 - 10:20:57 CDT)
- RE: Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 15:09:06 CDT)
- Re: Scaling solvent-solute intermolecular interactions Axel Kohlmeyer (Tue May 13 2014 - 13:56:02 CDT)
- NAMD-SMP-Ibverbs-CUDA assistance Matthew Ralph Adendorff (Tue May 13 2014 - 09:25:44 CDT)
- Dual boost accelerated md energy parameters? Per Larsson (Mon May 12 2014 - 13:54:48 CDT)
- unsubscribe Shalton Evans (Sun May 11 2014 - 19:18:39 CDT)
- Protein solvation farzad kiani (Sat May 10 2014 - 12:28:26 CDT)
- FixedAtoms and Reference group in spinangle colvar nicolas martin (Fri May 09 2014 - 09:01:28 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar Jérôme Hénin (Fri May 09 2014 - 13:53:56 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Sun May 11 2014 - 16:52:42 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar Giacomo Fiorin (Sun May 11 2014 - 17:27:29 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Thu May 22 2014 - 06:21:02 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar Jérôme Hénin (Thu May 22 2014 - 07:00:25 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Thu May 22 2014 - 07:06:08 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Sun May 11 2014 - 16:52:42 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar Jérôme Hénin (Fri May 09 2014 - 13:53:56 CDT)
- error while making psf file for bacteriorhodopsin system Faezeh Mottaghitalab (Thu May 08 2014 - 15:11:26 CDT)
- PMF from ABF simulation not plateauing Riley Workman (Thu May 08 2014 - 12:08:13 CDT)
- Setting up membrane protein simulation from existing conformation? Per Larsson (Wed May 07 2014 - 14:17:41 CDT)
- NAMD and NUMA Joseph Farran (Wed May 07 2014 - 13:54:51 CDT)
- AW: NAMD and NUMA Norman Geist (Thu May 08 2014 - 01:53:12 CDT)
- Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:28:46 CDT)
- AW: AW: NAMD and NUMA Norman Geist (Fri May 09 2014 - 02:11:19 CDT)
- Re: AW: AW: NAMD and NUMA Kenno Vanommeslaeghe (Fri May 09 2014 - 11:45:09 CDT)
- Re: NAMD and NUMA Brunner, Robert Kraemer (Fri May 09 2014 - 12:03:53 CDT)
- AW: NAMD and NUMA Norman Geist (Mon May 12 2014 - 01:12:54 CDT)
- Re: AW: NAMD and NUMA Kenno Vanommeslaeghe (Mon May 12 2014 - 12:06:53 CDT)
- Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:33:25 CDT)
- Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:28:46 CDT)
- AW: NAMD and NUMA Norman Geist (Thu May 08 2014 - 01:53:12 CDT)
- choose the best equilibrium arrangement of water molecules Boshra Moradi (Tue May 06 2014 - 16:55:17 CDT)
- (no subject) Boshra Moradi (Tue May 06 2014 - 16:35:44 CDT)
- TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Norman Geist (Tue May 06 2014 - 05:49:45 CDT)
- Topology for lysine bouding in Epsilon Jean-Patrick Francoia (Mon May 05 2014 - 12:11:23 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Mon May 05 2014 - 15:07:31 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Tue May 06 2014 - 13:06:38 CDT)
- Re: Topology for lysine bouding in Epsilon Jean-Patrick Francoia (Tue May 06 2014 - 13:38:43 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Tue May 06 2014 - 14:04:37 CDT)
- Re: Topology for lysine bouding in Epsilon Jean-Patrick Francoia (Wed May 07 2014 - 04:40:11 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Wed May 07 2014 - 10:33:16 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Tue May 06 2014 - 13:06:38 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Mon May 05 2014 - 15:07:31 CDT)
- Colvars keyword problem Sofya Lushchekina (Mon May 05 2014 - 09:32:11 CDT)
- Empirical force fields: release new version of RED Server Dev/PyRED FyD (Mon May 05 2014 - 06:07:18 CDT)
- Force field for sulfated tyrosines Shaon Chakrabarti (Sun May 04 2014 - 21:35:38 CDT)
- Patch to connect monomers code Rawan Al Nsour (Sun May 04 2014 - 12:15:12 CDT)
- Getting extra atoms by Patching! Sadegh Faramarzi Ganjabad (Fri May 02 2014 - 18:51:31 CDT)
- Re: Teflon New Residue Rawan Al Nsour (Fri May 02 2014 - 11:10:38 CDT)
- Teflon New Residue Rawan Al Nsour (Fri May 02 2014 - 09:57:57 CDT)
- How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory zeynab mohamad hoseyni (Mon Apr 28 2014 - 23:12:57 CDT)
- FEP is in kj/mol Javad Noroozi (Sun Apr 27 2014 - 08:32:33 CDT)
- Using the CHARMM36 forcefield with NAMD Alex Utev (CMP) (Wed Apr 23 2014 - 11:15:08 CDT)
- FATAL ERROR: Setting parameter tclForces from script failed! zeynab mohamad hoseyni (Tue Apr 22 2014 - 02:43:23 CDT)
- TI analysis script Javad Noroozi (Sat Apr 19 2014 - 08:16:18 CDT)
- Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014 David Brandon (Fri Apr 18 2014 - 16:49:02 CDT)
- Collective Variables to Restrain Ions Away From Protein Chris Ing (Thu Apr 17 2014 - 18:36:06 CDT)
- peptide tends to migrate out the water box Francesco Pietra (Thu Apr 17 2014 - 17:02:01 CDT)
- CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 02:41:11 CDT)
- How to setup a system with two pulling directions John Xi (Wed Apr 16 2014 - 19:32:27 CDT)
- RBCG and NAMD 2.9 Raul Araya (Wed Apr 16 2014 - 13:21:43 CDT)
- Step size in FEP calculation Javad Noroozi (Tue Apr 15 2014 - 23:21:35 CDT)
- NAMD-Lite Hassan Kianinejad (Tue Apr 15 2014 - 17:22:56 CDT)
- Altering extrabonds forces during MD Bryan Roessler (Tue Apr 15 2014 - 09:53:02 CDT)
- ABF with the RMSD colvar George Patargias (Tue Apr 15 2014 - 05:22:46 CDT)
- (no subject) manish kesherwani (Tue Apr 15 2014 - 00:02:12 CDT)
- full electrostatics and pairlistdist Jonathan Phillips (Mon Apr 14 2014 - 16:25:04 CDT)
- FEP error using CUDA Sadegh Faramarzi Ganjabad (Sun Apr 13 2014 - 22:42:12 CDT)
- Simulation crash during NPT equilibration James Starlight (Fri Apr 11 2014 - 05:58:17 CDT)
- Nanotube Simulation Miro Hodak (Thu Apr 10 2014 - 18:02:56 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 03:36:44 CDT)
- Re: Nanotube Simulation Miro Hodak (Fri Apr 11 2014 - 11:56:59 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 12:05:50 CDT)
- Re: Nanotube Simulation Miro Hodak (Fri Apr 11 2014 - 13:13:32 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 13:30:47 CDT)
- Re: Nanotube Simulation Thomas C. Bishop (Fri Apr 11 2014 - 14:44:08 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 14:55:16 CDT)
- Re: Nanotube Simulation Thomas C. Bishop (Mon Apr 14 2014 - 08:24:22 CDT)
- Re: Nanotube Simulation MEHRAN MB (Fri Apr 11 2014 - 13:33:31 CDT)
- Re: Nanotube Simulation Kenno Vanommeslaeghe (Fri Apr 11 2014 - 17:18:18 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 17:41:04 CDT)
- Re: Nanotube Simulation Kenno Vanommeslaeghe (Mon Apr 14 2014 - 12:33:58 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Mon Apr 14 2014 - 13:53:53 CDT)
- RE: Nanotube Simulation Samoylova, Olga M. (Tue Apr 15 2014 - 09:49:31 CDT)
- Re: Nanotube Simulation Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:13:14 CDT)
- RE: Nanotube Simulation Samoylova, Olga M. (Tue Apr 15 2014 - 12:50:06 CDT)
- Re: Nanotube Simulation Miro Hodak (Fri Apr 11 2014 - 11:56:59 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 03:36:44 CDT)
- Accelerated MD with transmembrane protein Kevin Kastner (Thu Apr 10 2014 - 13:40:26 CDT)
- Re: Accelerated MD with transmembrane protein Felipe Merino (Fri Apr 11 2014 - 03:27:09 CDT)
- Re: Accelerated MD with transmembrane protein Jeff Wereszczynski (Fri Apr 11 2014 - 07:19:20 CDT)
- Re: Accelerated MD with transmembrane protein Francesco Pietra (Fri Apr 11 2014 - 11:39:10 CDT)
- Re: Accelerated MD with transmembrane protein Jeff Wereszczynski (Fri Apr 11 2014 - 11:50:20 CDT)
- Re: Accelerated MD with transmembrane protein Francesco Pietra (Fri Apr 11 2014 - 12:16:40 CDT)
- Re: Accelerated MD with transmembrane protein Kevin Kastner (Fri Apr 11 2014 - 13:06:28 CDT)
- Re: Accelerated MD with transmembrane protein Francesco Pietra (Sat Apr 12 2014 - 08:24:00 CDT)
- Re: Accelerated MD with transmembrane protein Jeff Wereszczynski (Fri Apr 11 2014 - 07:19:20 CDT)
- Re: Accelerated MD with transmembrane protein Felipe Merino (Fri Apr 11 2014 - 03:27:09 CDT)
- Collective variable module naresh kumar (Thu Apr 10 2014 - 11:36:07 CDT)
- Re: Collective variable module Giacomo Fiorin (Thu Apr 10 2014 - 12:03:27 CDT)
- Re: Collective variable module naresh kumar (Thu Apr 10 2014 - 12:54:02 CDT)
- Re: Collective variable module Giacomo Fiorin (Thu Apr 10 2014 - 14:06:18 CDT)
- Re: Collective variable module naresh kumar (Fri Apr 11 2014 - 12:01:32 CDT)
- Re: Collective variable module Giacomo Fiorin (Fri Apr 11 2014 - 12:49:20 CDT)
- Re: Collective variable module naresh kumar (Mon Apr 14 2014 - 10:11:37 CDT)
- Re: Collective variable module naresh kumar (Thu Apr 10 2014 - 12:54:02 CDT)
- Re: Collective variable module Giacomo Fiorin (Thu Apr 10 2014 - 12:03:27 CDT)
- unsuscribe Cat Chenal (Thu Apr 10 2014 - 09:49:18 CDT)
- MMPBSA Energy Calculations using VMD (Post-Processing) Aditya Ranganathan (Thu Apr 10 2014 - 08:25:41 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Sat Apr 12 2014 - 01:53:35 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Vlad Cojocaru (Sat Apr 12 2014 - 03:46:19 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Jason Swails (Sat Apr 12 2014 - 06:53:32 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Mon Apr 14 2014 - 00:56:50 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Mon Apr 14 2014 - 04:23:01 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Jason Swails (Mon Apr 14 2014 - 07:31:05 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Jason Swails (Mon Apr 14 2014 - 07:26:59 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Kenno Vanommeslaeghe (Mon Apr 14 2014 - 12:24:33 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Jason Swails (Mon Apr 14 2014 - 13:02:08 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Mon Apr 21 2014 - 14:27:38 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Sat Apr 12 2014 - 01:53:35 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
- RE: slice of water box Hongbo Du (Wed Apr 09 2014 - 20:22:04 CDT)
- slice of water box Boshra Moradi (Wed Apr 09 2014 - 17:13:12 CDT)
- Problems with energy minimization James Starlight (Wed Apr 09 2014 - 09:07:28 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 05:53:50 CDT)
- PMETolerance Natalie Esther Smith (Tue Apr 08 2014 - 23:07:52 CDT)
- posting from Yahoo addresses disabled Jim Phillips (Tue Apr 08 2014 - 17:45:15 CDT)
- Point group symmetry bmaiti_at_andrew.cmu.edu (Mon Apr 07 2014 - 18:20:08 CDT)
- the dielectric constant use in pairwise interaction energy calculation of ligand and protein Patrick Chiu (Tue Apr 08 2014 - 08:45:11 CDT)
- Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:33:50 CDT)
- Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:33:58 CDT)
- Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:32:49 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Mon Apr 07 2014 - 19:54:30 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Wed Apr 09 2014 - 11:18:13 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Thu Apr 10 2014 - 08:30:44 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Thu Apr 10 2014 - 08:34:25 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Thu Apr 10 2014 - 08:40:18 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Thu Apr 10 2014 - 08:56:01 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Thu Apr 10 2014 - 09:04:21 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Wed Apr 09 2014 - 11:18:13 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Mon Apr 07 2014 - 19:54:30 CDT)
- Electronic density profile of lipid bilayer. Subbarao Kanchi (Sun Apr 06 2014 - 20:32:54 CDT)
- Movie of a channel trajectory Javier Cceres Delpiano (Sat Apr 05 2014 - 22:26:21 CDT)
- medwater config Hassan Kianinejad (Fri Apr 04 2014 - 19:15:32 CDT)
- SHAKE or RATTLE algorithm Ramin Ekhteiari (Fri Apr 04 2014 - 15:08:04 CDT)
- Re: residue_rmsd.tcl segmentation fault Axel Kohlmeyer (Fri Apr 04 2014 - 03:03:55 CDT)
- residue_rmsd.tcl segmentation fault John Xi (Thu Apr 03 2014 - 21:49:05 CDT)
- "Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014 David Brandon (Thu Apr 03 2014 - 11:17:33 CDT)
- Using position-dependent diffusion to simulate long colvars trajectories Ajasja Ljubetič (Thu Apr 03 2014 - 07:36:28 CDT)
- 6 equilibration steps at charmm gui server Ramin Ekhteiari (Thu Apr 03 2014 - 04:32:58 CDT)
- NAMD Pressure profile calculations Tao Qu (Wed Apr 02 2014 - 15:43:59 CDT)
- Multiple dihedral with multiplicity of 7 greater than max of 6 Rawan Al Nsour (Wed Apr 02 2014 - 13:44:33 CDT)
- Multiple dihedral with multiplicity of 7 greater than max of 6 Rawan Al Nsour (Wed Apr 02 2014 - 13:38:53 CDT)
- Excluding non bonded interactions between segments Fotis Baltoumas (Wed Apr 02 2014 - 07:40:29 CDT)
- Re: Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Wed Apr 02 2014 - 00:42:17 CDT)
- Random segfault for MPI based REMD at startup Norman Geist (Wed Apr 02 2014 - 00:34:20 CDT)
- Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Tue Apr 01 2014 - 15:29:36 CDT)
- question Eifler, Jay Q. (UMKC-Student) (Mon Mar 31 2014 - 11:47:16 CDT)
- accelerated MD log Felipe Merino (Mon Mar 31 2014 - 03:57:30 CDT)
- Re: remd across gpus Francesco Pietra (Mon Mar 31 2014 - 02:41:24 CDT)
- Constraint failure in RATTLE Francesco Pietra (Sun Mar 30 2014 - 02:31:54 CDT)
- Fwd: Constraint failure in RATTLE Francesco Pietra (Sun Mar 30 2014 - 03:07:50 CDT)
- Re: Constraint failure in RATTLE Massimiliano Porrini (Sun Mar 30 2014 - 06:49:34 CDT)
- accelMD on GPUs Francesco Pietra (Sat Mar 29 2014 - 02:38:58 CDT)
- remd across gpus Francesco Pietra (Sat Mar 29 2014 - 02:29:12 CDT)
- Help to solve the error Flora Chettiar (Wed Mar 26 2014 - 04:00:46 CDT)
- hey! you! why did my simulation crash? Edward Lyman (Wed Mar 26 2014 - 10:42:46 CDT)
- Question about accelerated MD Mare Libero (Tue Mar 25 2014 - 17:14:27 CDT)
- Compiling with Open64 4.5.2.1 for AMD Opteron 6378 David Chin (Mon Mar 24 2014 - 10:44:54 CDT)
- coarse-grained simulation: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C5M P5 (ATOMS 1 2) Khaled Barakat (Sun Mar 23 2014 - 22:44:02 CDT)
- PME: The Excluded Coulombic Interactions Hadi (Fri Mar 21 2014 - 22:56:50 CDT)
- wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 21:34:57 CDT)
- Re: Restoring simulation from the previous run James Starlight (Wed Mar 19 2014 - 09:38:18 CDT)
- Restoring simulation from the previous run James Starlight (Wed Mar 19 2014 - 03:32:31 CDT)
- Improve scaling for large amount of fixed atoms Norman Geist (Wed Mar 19 2014 - 03:19:38 CDT)
- changing damping coefficient during simulation Gozde Eskici (Tue Mar 18 2014 - 10:20:25 CDT)
- iDataPlex Francesco Pietra (Mon Mar 17 2014 - 13:12:32 CDT)
- Detection of Internal water along MD trajectory James Starlight (Mon Mar 17 2014 - 04:14:38 CDT)
- Free Energy Calculation Using Thermodynamic Integration Javad Noroozi (Mon Mar 17 2014 - 02:06:08 CDT)
- TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:40:09 CDT)
- running benchmarks on NAMD-Lite Hassan Kianinejad (Fri Mar 14 2014 - 17:35:21 CDT)
- Generalized Born Implicit solvation with implicit membrane Fotis Baltoumas (Fri Mar 14 2014 - 08:28:45 CDT)
- Cross-correlation analysis in multidomain proteins James Starlight (Thu Mar 13 2014 - 05:32:22 CDT)
- RE: RE: Re: RE: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Wed Mar 12 2014 - 09:42:34 CDT)
- COLVAR related quesion Abir Ganguly (Tue Mar 11 2014 - 16:06:20 CDT)
- how to get cell vectors in tcl forces script Thomas Evangelidis (Tue Mar 11 2014 - 15:14:17 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Wed Mar 12 2014 - 02:29:43 CDT)
- RE: how to get cell vectors in tcl forces script Cosseddu, Salvatore (Wed Mar 12 2014 - 07:05:43 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Wed Mar 12 2014 - 07:54:50 CDT)
- RE: how to get cell vectors in tcl forces script Cosseddu, Salvatore (Wed Mar 12 2014 - 09:01:35 CDT)
- Re: how to get cell vectors in tcl forces script Thomas Evangelidis (Wed Mar 12 2014 - 09:26:46 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Wed Mar 12 2014 - 09:59:12 CDT)
- Re: how to get cell vectors in tcl forces script Thomas Evangelidis (Thu Mar 13 2014 - 06:11:48 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Thu Mar 13 2014 - 08:34:58 CDT)
- RE: how to get cell vectors in tcl forces script Hongbo Du (Thu Mar 13 2014 - 11:32:32 CDT)
- Re: how to get cell vectors in tcl forces script Thomas Evangelidis (Thu Mar 13 2014 - 11:47:28 CDT)
- RE: how to get cell vectors in tcl forces script Cosseddu, Salvatore (Thu Mar 13 2014 - 13:11:01 CDT)
- RE: how to get cell vectors in tcl forces script Cosseddu, Salvatore (Wed Mar 12 2014 - 07:05:43 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Wed Mar 12 2014 - 02:29:43 CDT)
- NAMD on Rescale Istvan Jonyer (Mon Mar 10 2014 - 20:22:10 CDT)
- aa_ref-monomer-noh.dcd file in the tutorial of shape-based coarse grained (SBCG) simulation sunyeping (Mon Mar 10 2014 - 20:01:13 CDT)
- Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 Vlad Cojocaru (Mon Mar 10 2014 - 11:38:09 CDT)
- aa_ref-monomer-noh.dcd in shape-based coarse grained simulation sunyeping (Sat Mar 08 2014 - 20:09:26 CST)
- Accelerated Molecular Dynamics logs Johny Telecaster (Sat Mar 08 2014 - 09:37:05 CST)
- Regarding colvar distancez Subbarao Kanchi (Sat Mar 08 2014 - 05:00:28 CST)
- NAMD 2.9 quits early without error message. Ivan Gregoretti (Fri Mar 07 2014 - 11:36:17 CST)
- Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:08:11 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Cosseddu, Salvatore (Fri Mar 07 2014 - 08:21:35 CST)
- Re: Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:52:43 CST)
- Re: Monitoring progress of an ongoing molecular dynamics simulation Douglas Houston (Fri Mar 07 2014 - 08:55:47 CST)
- Re: Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 09:08:44 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Cosseddu, Salvatore (Fri Mar 07 2014 - 10:43:29 CST)
- Re: Monitoring progress of an ongoing molecular dynamics simulation Axel Kohlmeyer (Fri Mar 07 2014 - 10:49:34 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Cosseddu, Salvatore (Fri Mar 07 2014 - 10:57:59 CST)
- Re: Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 10:57:31 CST)
- Re: Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:52:43 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Bennion, Brian (Fri Mar 07 2014 - 11:44:01 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Cosseddu, Salvatore (Fri Mar 07 2014 - 08:21:35 CST)
- force field parameter for graphene oxide Asis Jana (Fri Mar 07 2014 - 07:58:34 CST)
- AW: AW: benchmark info Norman Geist (Fri Mar 07 2014 - 01:40:25 CST)
- compiling namd-lite Hassan Kianinejad (Thu Mar 06 2014 - 19:08:28 CST)
- compiling namd-lite Hassan Kianinejad (Thu Mar 06 2014 - 18:55:54 CST)
- How to maintain Density constant? Roy Fernando (Wed Mar 05 2014 - 15:43:59 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Wed Mar 05 2014 - 16:51:30 CST)
- Re: How to maintain Density constant? Ivan Gregoretti (Thu Mar 06 2014 - 07:23:29 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Thu Mar 06 2014 - 09:57:24 CST)
- Re: How to maintain Density constant? Ivan Gregoretti (Thu Mar 06 2014 - 10:34:43 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Thu Mar 06 2014 - 10:55:28 CST)
- Re: How to maintain Density constant? Roy Fernando (Thu Mar 06 2014 - 11:28:23 CST)
- RE: How to maintain Density constant? Morgan, Brittany (Thu Mar 06 2014 - 11:41:12 CST)
- Re: How to maintain Density constant? Roy Fernando (Thu Mar 06 2014 - 12:03:37 CST)
- RE: How to maintain Density constant? Morgan, Brittany (Thu Mar 06 2014 - 12:26:02 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Thu Mar 06 2014 - 12:39:08 CST)
- RE: How to maintain Density constant? Tristan Croll (Thu Mar 06 2014 - 16:30:43 CST)
- Re: How to maintain Density constant? Ivan Gregoretti (Thu Mar 06 2014 - 07:23:29 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Wed Mar 05 2014 - 16:51:30 CST)
- Restarting an FEP simulation Shyno Mathew (Wed Mar 05 2014 - 12:43:48 CST)
- VDW energy: positive or negative? PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 17:20:53 CST)
- How to stop omega trans-cis switching Alex Utev (CMP) (Mon Mar 03 2014 - 12:10:08 CST)
- FEP result analysis Javad Noroozi (Sat Mar 01 2014 - 03:37:29 CST)
- Generating .psf for amorphous disaccharide Maxwell Wesley Terban (Fri Feb 28 2014 - 13:10:56 CST)
- Apply magnetic field through TCLBC Hongbo Du (Fri Feb 28 2014 - 11:22:04 CST)
- benchmark info Hassan Kianinejad (Thu Feb 27 2014 - 16:34:08 CST)
- solvate plugin watsize value Sridhar Kumar Kannam (Wed Feb 26 2014 - 20:40:46 CST)
- Persistent margin errors Vlastimil Zíma (Wed Feb 26 2014 - 06:38:23 CST)
- Symmetry restraints break IMD handshaking Tristan Croll (Tue Feb 25 2014 - 21:23:26 CST)
- ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Tue Feb 25 2014 - 11:02:24 CST)
- Free Energy Perturbation Javad Noroozi (Tue Feb 25 2014 - 00:36:30 CST)
- problem compiling NAMD Hassan Kianinejad (Mon Feb 24 2014 - 10:48:51 CST)
- 答复:RE: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Mon Feb 24 2014 - 03:37:02 CST)
- RE: Re: RE: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Mon Feb 24 2014 - 03:32:06 CST)
- RE: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Sun Feb 23 2014 - 21:13:52 CST)
- NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Sun Feb 23 2014 - 20:29:02 CST)
- Error when running MIC version of namd on Stampede Chen Wei (Fri Feb 21 2014 - 09:49:38 CST)
- NAMD 2.9 Changing/Replacing atoms in multiple molecules Michal Skoczek (Fri Feb 21 2014 - 08:02:41 CST)
- FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE zeynab mohamad hoseyni (Thu Feb 20 2014 - 13:31:50 CST)
- runaway minimizations Bennion, Brian (Thu Feb 20 2014 - 12:06:54 CST)
- About keep_water_out.tcl zeynab mohamad hoseyni (Thu Feb 20 2014 - 05:21:23 CST)
- tools for Charmm Peter Reinke (Thu Feb 20 2014 - 02:39:59 CST)
- Re: tools for Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:16:40 CST)
- Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 04:29:34 CDT)
- AW: Using nodelist file causes namd to hang Norman Geist (Tue Apr 08 2014 - 05:06:03 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 05:52:52 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Tue Apr 08 2014 - 06:22:41 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 07:13:42 CDT)
- AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Tue Apr 08 2014 - 07:30:15 CDT)
- Re: Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 08:50:15 CDT)
- AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 00:21:40 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Apr 09 2014 - 04:28:37 CDT)
- Re: Using nodelist file causes namd to hang Douglas Houston (Wed Apr 09 2014 - 04:49:17 CDT)
- AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 05:28:51 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 07:21:19 CDT)
- Re: AW: Using nodelist file causes namd to hang Douglas Houston (Thu Sep 18 2014 - 05:35:30 CDT)
- Re: AW: Using nodelist file causes namd to hang Norman Geist (Thu Sep 18 2014 - 12:32:23 CDT)
- Re: Using nodelist file causes namd to hang Douglas Houston (Sat Sep 20 2014 - 06:14:29 CDT)
- Is there any point in running NAMD over an ethernet-linked cluster? Douglas Houston (Sat Sep 20 2014 - 06:18:25 CDT)
- Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 04:29:34 CDT)
- Re: tools for Charmm Gianluca Interlandi (Thu Feb 20 2014 - 12:08:24 CST)
- Re: tools for Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:16:40 CST)
- Charmm Peter Reinke (Thu Feb 20 2014 - 02:31:35 CST)
- (no subject) Boyang Wang (Thu Feb 20 2014 - 00:05:03 CST)
- Require Suggestion amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
- pThr topology СӨ (Tue Feb 18 2014 - 21:05:27 CST)
- protein-membrane interface hydration zeynab mohamad hoseyni (Tue Feb 18 2014 - 13:37:30 CST)
- GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance Pino, James Christopher (Tue Feb 18 2014 - 12:00:34 CST)
- Polarization effect of gold cluster Zhao Lina (Tue Feb 18 2014 - 06:20:20 CST)
- Failure of namd2.10 in keeping trace of cell in t-remd Francesco Pietra (Tue Feb 18 2014 - 05:44:34 CST)
- CHARMM36 and NAMD Douglas Houston (Tue Feb 18 2014 - 04:02:38 CST)
- REMD Boshra Moradi (Tue Feb 18 2014 - 02:08:53 CST)
- ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Miss. State (Mon Feb 17 2014 - 17:05:09 CST)
- atomselect option for extracting protein-ligand complex KK R (Mon Feb 17 2014 - 16:16:43 CST)
- Membrane and NPAT Jos Villalan (Mon Feb 17 2014 - 04:49:08 CST)
- Widom test particle insertion in NAMD Javad Noroozi (Mon Feb 17 2014 - 00:40:08 CST)
- Guideline for selecting water box size. Hyuntae Na (Sun Feb 16 2014 - 18:49:00 CST)
- FAD topology and parameters Tanner, John J. (Sun Feb 16 2014 - 15:30:38 CST)
- Instability in thermodynamic integration Maryam Sayadi (Sun Feb 16 2014 - 14:04:12 CST)
- psf file does not contain cross-terms zeynab mohamad hoseyni (Sun Feb 16 2014 - 12:00:30 CST)
- Adding hydrogen atoms to the crystall structure zeynab mohamad hoseyni (Sun Feb 16 2014 - 09:54:40 CST)
- Re: Adding hydrogen atoms to the crystall structure MEHRAN MB (Tue Feb 18 2014 - 10:10:53 CST)
- Re: Adding hydrogen atoms to the crystall structure Thomas Evangelidis (Tue Feb 18 2014 - 10:44:56 CST)
- Re: Adding hydrogen atoms to the crystall structure zeynab mohamad hoseyni (Tue Feb 18 2014 - 14:30:00 CST)
- Re: Adding hydrogen atoms to the crystall structure Thomas Evangelidis (Tue Feb 18 2014 - 14:56:21 CST)
- Re: Adding hydrogen atoms to the crystall structure MEHRAN MB (Tue Feb 18 2014 - 15:54:55 CST)
- Re: Adding hydrogen atoms to the crystall structure Thomas Evangelidis (Tue Feb 18 2014 - 16:04:23 CST)
- Re: Adding hydrogen atoms to the crystall structure MEHRAN MB (Tue Feb 18 2014 - 10:10:53 CST)
- Non standar solvent Javad Noroozi (Sat Feb 15 2014 - 06:52:17 CST)
- Solvation in non standard solvent Javad Noroozi (Fri Feb 14 2014 - 05:58:59 CST)
- Re: Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 05:22:55 CST)
- Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 04:20:16 CST)
- ABF force distribution Kasra Fattah (Thu Feb 13 2014 - 14:56:42 CST)
- moving out of the box Ariel Talavera Perez (Thu Feb 13 2014 - 09:57:16 CST)
- Re: moving out of the box Ajasja Ljubetič (Thu Feb 13 2014 - 10:08:36 CST)
- AW: moving out of the box Norman Geist (Thu Feb 13 2014 - 14:21:26 CST)
- Re: AW: moving out of the box Ariel Talavera Perez (Fri Feb 14 2014 - 08:38:01 CST)
- Re: AW: moving out of the box Aaron Larsen (Fri Feb 14 2014 - 09:10:36 CST)
- Re: AW: moving out of the box Kenno Vanommeslaeghe (Fri Feb 14 2014 - 13:15:37 CST)
- Re: AW: moving out of the box Aron Broom (Fri Feb 14 2014 - 13:25:54 CST)
- Re: AW: moving out of the box Felipe Merino (Sat Feb 15 2014 - 04:50:15 CST)
- Re: AW: moving out of the box Ariel Talavera Perez (Mon Feb 17 2014 - 04:39:29 CST)
- Re: AW: moving out of the box Ariel Talavera Perez (Mon Feb 17 2014 - 06:51:36 CST)
- Re: AW: moving out of the box MEHRAN MB (Mon Feb 17 2014 - 11:48:44 CST)
- Re: AW: moving out of the box Ariel Talavera Perez (Thu Feb 20 2014 - 07:48:07 CST)
- Re: AW: moving out of the box Ariel Talavera Perez (Fri Feb 14 2014 - 08:38:01 CST)
- AW: moving out of the box Norman Geist (Thu Feb 13 2014 - 14:24:53 CST)
- Dihedrals multiplicity! Anna Borlsky (Thu Feb 13 2014 - 09:24:46 CST)
- Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 10:51:12 CST)
- Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 11:34:16 CST)
- AW: Dihedrals multiplicity! Norman Geist (Thu Feb 13 2014 - 14:23:52 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Thu Feb 13 2014 - 17:53:49 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Thu Feb 13 2014 - 19:48:12 CST)
- Re: AW: Dihedrals multiplicity! Anna Borlsky (Sat Feb 15 2014 - 04:34:49 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Sat Feb 15 2014 - 11:30:42 CST)
- Re: AW: Dihedrals multiplicity! Anna Borlsky (Sat Feb 15 2014 - 11:51:16 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Sat Feb 15 2014 - 22:15:33 CST)
- RE: AW: Dihedrals multiplicity! hannes.loeffler_at_stfc.ac.uk (Sun Feb 16 2014 - 02:34:16 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Sun Feb 16 2014 - 12:45:16 CST)
- Re: AW: Dihedrals multiplicity! Anna Borlsky (Tue Feb 18 2014 - 03:11:42 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:12:14 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:35:55 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:56:29 CST)
- RE: AW: Dihedrals multiplicity! hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 11:43:47 CST)
- Re: AW: Dihedrals multiplicity! Kenno Vanommeslaeghe (Mon Feb 17 2014 - 12:44:19 CST)
- Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 11:34:16 CST)
- Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 10:51:12 CST)
- non-planarity problem! NOE restraints! Anna Borlsky (Thu Feb 13 2014 - 09:22:43 CST)
- chloromethyl ketone patch? Jesper Madsen (Tue Feb 11 2014 - 16:49:21 CST)
- Determining HIS protonation state using PropKa vmd plug-in zeynab mohamad hoseyni (Tue Feb 11 2014 - 06:30:09 CST)
- Questions on calling external program to calculate force with NAMD Wasut Pornpatcharapong (Mon Feb 10 2014 - 15:41:48 CST)
- Volume Entry Rawan Al Nsour (Mon Feb 10 2014 - 10:08:19 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:12:49 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:45:37 CST)
- Re: Volume Entry Rawan Al Nsour (Mon Feb 10 2014 - 11:04:06 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 11:09:18 CST)
- Re: Volume Entry Rawan Al Nsour (Sun Feb 16 2014 - 10:29:18 CST)
- Re: Volume Entry Axel Kohlmeyer (Sun Feb 16 2014 - 10:38:13 CST)
- Re: Volume Entry Rawan Al Nsour (Sun Feb 16 2014 - 13:08:05 CST)
- Re: Volume Entry Axel Kohlmeyer (Sun Feb 16 2014 - 13:51:37 CST)
- Re: Volume Entry Aron Broom (Sun Feb 16 2014 - 13:57:33 CST)
- Re: Volume Entry Rawan Al Nsour (Sun Feb 16 2014 - 15:16:44 CST)
- Re: Volume Entry Aron Broom (Sun Feb 16 2014 - 15:28:27 CST)
- Re: Volume Entry Rawan Al Nsour (Sun Feb 16 2014 - 16:36:04 CST)
- Re: Volume Entry Axel Kohlmeyer (Sun Feb 16 2014 - 17:33:03 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:45:37 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:12:49 CST)
- PREMD in NAMD Matthew Ralph Adendorff (Mon Feb 10 2014 - 09:27:15 CST)
- ABF simulations Abir Ganguly (Sat Feb 08 2014 - 15:38:01 CST)
- Log file is not being updated BATUHAN KAV (Mon Feb 10 2014 - 05:41:07 CST)
- Re: Log file is not being updated Ajasja Ljubetič (Mon Feb 10 2014 - 05:53:39 CST)
- Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Sun Feb 09 2014 - 23:49:41 CST)
- RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 00:20:57 CST)
- RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 18:24:37 CST)
- Re: RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Tue Feb 11 2014 - 15:33:28 CST)
- Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Tristan Croll (Tue Feb 11 2014 - 20:07:59 CST)
- RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Bennion, Brian (Wed Feb 12 2014 - 10:57:12 CST)
- RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Tristan Croll (Wed Feb 12 2014 - 17:51:13 CST)
- RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Tristan Croll (Wed Feb 19 2014 - 17:53:43 CST)
- RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Bennion, Brian (Thu Feb 20 2014 - 11:53:31 CST)
- RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Tristan Croll (Thu Feb 20 2014 - 17:52:22 CST)
- AW: RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Norman Geist (Fri Feb 21 2014 - 01:34:55 CST)
- Re: AW: RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) Tristan Croll (Fri Feb 21 2014 - 01:44:39 CST)
- RE: RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Tue Feb 11 2014 - 18:41:53 CST)
- AW: RE: Strange glitches when performing energy minimization in MDFF simulations Norman Geist (Wed Feb 12 2014 - 01:53:40 CST)
- Re: AW: RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Wed Feb 12 2014 - 02:22:47 CST)
- RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 18:24:37 CST)
- RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 00:20:57 CST)
- Interactive molecular dynamics question Mare Libero (Sun Feb 09 2014 - 15:05:51 CST)
- Specific Heat Calculation Rawan Al Nsour (Fri Feb 07 2014 - 20:56:14 CST)
- Calculating density for a molecule Research Jubilant (Fri Feb 07 2014 - 11:36:41 CST)
- RSMDTT keyword for nucleic acids Aaron Larsen (Wed Feb 05 2014 - 14:43:13 CST)
- PMEGridSizeX (number of grid points) is very small. Rawan Al Nsour (Wed Feb 05 2014 - 12:00:57 CST)
- Umbrella sampling using colvarconfig file with dihedrals Aaron Larsen (Wed Feb 05 2014 - 11:07:23 CST)
- Question regarding loss of translational entropy calculation in FEP tutorial Monika Sharma (Tue Feb 04 2014 - 14:05:49 CST)
- ERROR: CALCULATED VDWA/B FORCES DOES NOT MATCH ENERGY Shalton Evans (Mon Feb 03 2014 - 21:13:41 CST)
- Umbrella Sampling of Sugar Pseudorotation Aaron Larsen (Mon Feb 03 2014 - 13:32:45 CST)
- Hydration of protein-lipid interface zeynab mohamad hoseyni (Mon Feb 03 2014 - 10:27:20 CST)
- problems about new molecule parameterization Tian Li (Thu Jan 30 2014 - 22:28:36 CST)
- Structure size limitation in NAMD Nithyanan Annamalai (Wed Jan 29 2014 - 20:36:54 CST)
- ERROR: Molecule destroyed by fatal error Marlet Martinez (Mon Jan 27 2014 - 13:31:18 CST)
- Steering colvars to defined points in space Tristan Croll (Sun Jan 26 2014 - 18:10:03 CST)
- About Number of atoms in fixed atoms PDB doesn't match coordinate PDB Vidhya Sankar (Sat Jan 25 2014 - 21:01:01 CST)
- How to solvate a protein using C36 and not C27 zeynab mohamad hoseyni (Sat Jan 25 2014 - 11:08:14 CST)
- PMF calculation crashes with constraint failure Magnus Andersson (Sat Jan 25 2014 - 11:02:11 CST)
- How to solvate a protein using C36 and not C27 zeynab mohamad hoseyni (Sat Jan 25 2014 - 10:48:31 CST)
- Liquid Simulation Failure Roy Fernando (Fri Jan 24 2014 - 18:54:44 CST)
- AW: recent comparison of NAMD to other MD engines Norman Geist (Fri Jan 24 2014 - 13:22:51 CST)
- recent comparison of NAMD to other MD engines Bennion, Brian (Wed Jan 22 2014 - 18:22:03 CST)
- Re: recent comparison of NAMD to other MD engines Giacomo Fiorin (Wed Jan 22 2014 - 20:38:29 CST)
- RE: recent comparison of NAMD to other MD engines Tristan Croll (Fri Jan 24 2014 - 02:44:05 CST)
- unsubscribe Zailo Leite (Fri Feb 14 2014 - 11:20:04 CST)
- subscribe namd-l Ana Celia Vila Verde (Tue Jan 21 2014 - 11:22:15 CST)
- Citating colvars module Salvatore Mario Cosseddu (Tue Jan 21 2014 - 11:20:50 CST)
- Various questions Douglas Houston (Tue Jan 21 2014 - 09:42:14 CST)
- Question regarding reverse CG to all-atom parikshit moitra (Tue Jan 21 2014 - 04:42:04 CST)
- Reassure fluctuations in course of simulation James Starlight (Mon Jan 20 2014 - 03:19:51 CST)
- Tct script for energy estimation James Starlight (Mon Jan 20 2014 - 03:16:23 CST)
- Question regarding loss of translational entropy calculation in FEP tutorial Monika Sharma (Sun Jan 19 2014 - 11:32:02 CST)
- About Psfgen error for Lipid molecules Vidhya Sankar (Sun Jan 19 2014 - 07:29:51 CST)
- How to parametrize new atom types in Namd Dian Jiao (Fri Jan 17 2014 - 15:44:50 CST)
- Re: namd-l digest V1 #1282 Istvan Jonyer (Fri Jan 17 2014 - 14:04:39 CST)
- AW: keeping Crystal angles constant Norman Geist (Thu Jan 16 2014 - 02:36:51 CST)
- keeping Crystal angles constant Mohan maruthi sena (Wed Jan 15 2014 - 12:03:58 CST)
- RDF calculation with NAMD Dian Jiao (Tue Jan 14 2014 - 15:05:32 CST)
- colvars with replica exchange molecular dynamics Francesco Pietra (Mon Jan 13 2014 - 14:29:41 CST)
- Re: colvars with replica exchange molecular dynamics Giacomo Fiorin (Mon Jan 13 2014 - 15:17:25 CST)
- Re: colvars with replica exchange molecular dynamics Francesco Pietra (Tue Jan 14 2014 - 02:25:19 CST)
- Fwd: colvars with replica exchange molecular dynamics Francesco Pietra (Wed Jan 29 2014 - 10:40:22 CST)
- Fwd: colvars with replica exchange molecular dynamics Francesco Pietra (Thu Jan 30 2014 - 04:38:47 CST)
- Re: colvars with replica exchange molecular dynamics Giacomo Fiorin (Thu Jan 30 2014 - 17:32:47 CST)
- Re: colvars with replica exchange molecular dynamics Francesco Pietra (Fri Jan 31 2014 - 01:38:21 CST)
- Re: colvars with replica exchange molecular dynamics Francesco Pietra (Tue Jan 14 2014 - 02:25:19 CST)
- Re: colvars with replica exchange molecular dynamics Giacomo Fiorin (Mon Jan 13 2014 - 15:17:25 CST)
- useGroupPressure Anna Borlsky (Fri Jan 10 2014 - 17:09:32 CST)
- periodic boundary conditions Anna Borlsky (Fri Jan 10 2014 - 15:27:34 CST)
- Thermodynamic integration questions Randall Hall (Thu Jan 09 2014 - 12:16:03 CST)
- Difficulties with using the "rescalevels" command every MD timestep Spencer, Jacob (Thu Jan 09 2014 - 09:48:37 CST)
- whidth value of orientation in colvars (Thu Jan 09 2014 - 02:27:59 CST)
- MD simulation Patch grid errors Jiann George Pazhamalil (Tue Jan 07 2014 - 17:33:06 CST)
- CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH Katherine Parra Pulido (Mon Jan 06 2014 - 23:33:49 CST)
- citing SODIUM program Shyno Mathew (Sat Jan 04 2014 - 10:45:36 CST)
- About Warning in compilation of Namd Vidhya Sankar (Sat Jan 04 2014 - 03:41:57 CST)
- question about force constant Lurong Pan (Fri Jan 03 2014 - 09:02:13 CST)
- PBC only along the z axis. Sridhar Kumar Kannam (Thu Jan 02 2014 - 21:46:58 CST)
- About Tcl8.3 error in namd2.8 Vidhya Sankar (Wed Jan 01 2014 - 08:20:20 CST)
- Fwd: Majordomo results Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:19:11 CST)
- error : segmentation fault Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:18:30 CST)
- Temperature reassignment PANAGIOTA KYRIAKOU (Tue Dec 31 2013 - 11:28:12 CST)
- Add acetyle and amin Group to peptide Alireza Mansouri (Mon Dec 30 2013 - 03:30:19 CST)
- About Namd Compilation Vidhya Sankar (Sat Dec 28 2013 - 11:12:02 CST)
- Distance Constraints in ABF Simulation Vince Cho (Wed Dec 25 2013 - 05:31:26 CST)
- obtaining the system force Neelanjana Sengupta (Tue Dec 24 2013 - 00:26:59 CST)
- Trouble loading frames from large DCD files Alex Utev (CMP) (Thu Dec 19 2013 - 16:23:30 CST)
- About Membrane anlysis Vidhya Sankar (Wed Dec 18 2013 - 09:09:22 CST)
- Problem with replica exchange Michal Skoczek (Tue Dec 17 2013 - 04:57:38 CST)
- About Free energy tutorial for Membrane-Protein system Vidhya Sankar (Sun Dec 15 2013 - 03:26:34 CST)
- minimization with symmetry restrain flavio seixas (Fri Dec 13 2013 - 12:31:39 CST)
- Will there be a NAMD2.9 for IBM AIX UNIX? Mengyuan Zhu (Fri Dec 13 2013 - 11:06:48 CST)
- Reverse coarse-graining Error: CG Builder Sanket Avinash Deshmukh (Fri Dec 13 2013 - 00:42:25 CST)
- How to compile NAMD2.9 in IBM AIX UNIX$B!)(B Mengyuan Zhu (Thu Dec 12 2013 - 12:24:42 CST)
- Hi Gurpreet Kaur Dhindsa (Thu Dec 12 2013 - 09:19:31 CST)
- Re: AW: vmd-l: AMD vs. nvidia support Aron Broom (Thu Dec 12 2013 - 09:10:52 CST)
- AW: vmd-l: AMD vs. nvidia support Norman Geist (Thu Dec 12 2013 - 01:05:22 CST)
- membrane bilayer crosses the z axis boundaries of the box and separates into two layers Thomas Evangelidis (Wed Dec 11 2013 - 14:29:33 CST)
- colavrs ABF restart not matching Kasra Fattah (Tue Dec 10 2013 - 11:30:50 CST)
- One Chain Simulation Rawan Al Nsour (Tue Dec 10 2013 - 11:06:10 CST)
- Patch information for 1TUB.pdb in order to use "psfgen" Lili Zhang (Tue Dec 10 2013 - 09:21:39 CST)
- puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Tue Dec 10 2013 - 06:02:25 CST)
- AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Norman Geist (Tue Dec 10 2013 - 08:18:03 CST)
- Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Thu Dec 12 2013 - 19:02:30 CST)
- Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Aron Broom (Thu Dec 12 2013 - 19:25:58 CST)
- Re: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Thu Dec 12 2013 - 23:58:49 CST)
- AW: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Norman Geist (Fri Dec 13 2013 - 00:47:03 CST)
- AW: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Norman Geist (Fri Dec 13 2013 - 01:43:43 CST)
- Re: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Aron Broom (Sun Dec 15 2013 - 00:51:33 CST)
- Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs dbaogen (Thu Dec 12 2013 - 19:02:30 CST)
- Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Axel Kohlmeyer (Tue Dec 10 2013 - 08:22:18 CST)
- AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs Norman Geist (Tue Dec 10 2013 - 08:18:03 CST)
- XY constraints with center of mass movements Peterson J (Mon Dec 09 2013 - 11:29:12 CST)
- PSF file for a metalloprotein Haleh Abdizadeh (Mon Dec 09 2013 - 07:29:55 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Sun Dec 08 2013 - 09:11:31 CST)
- AW: 50% system CPU usage when parallel running NAMD on Rocks cluster Norman Geist (Mon Dec 09 2013 - 01:19:28 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 10 2013 - 06:51:31 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Sat Dec 14 2013 - 07:55:47 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 17 2013 - 08:12:33 CST)
- Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Wed Dec 18 2013 - 06:43:18 CST)
- AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 04:57:18 CST)
- Asking for Free energy calculation advice Kasra Fattah (Thu Dec 05 2013 - 14:18:20 CST)
- AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 04:06:31 CST)
- AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Thu Dec 05 2013 - 02:58:07 CST)
- AW: Running NAMD on SGE cluster - multiple modes and cores Norman Geist (Wed Dec 04 2013 - 07:36:48 CST)
- Runaway cuda-enabled namd2 processes Tim.Ho_at_csiro.au (Tue Dec 03 2013 - 21:31:42 CST)
- zeroMomentum for water droplet Mihaela Drenscko (Tue Dec 03 2013 - 17:38:43 CST)
- what to do with this error Liqun Zhang (Tue Dec 03 2013 - 14:21:34 CST)
- 50% system CPU usage when parallel running NAMD on Rocks cluster (Sat Nov 30 2013 - 21:06:18 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Tue Dec 03 2013 - 09:23:30 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Thu Dec 05 2013 - 05:09:27 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Thu Dec 05 2013 - 04:14:05 CST)
- Re: Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Fri Dec 06 2013 - 07:23:29 CST)
- 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 03 2013 - 07:43:07 CST)
- Running NAMD on SGE cluster - multiple modes and cores Anna Gorska (Tue Dec 03 2013 - 05:25:37 CST)
- Re: : Mamon Hatmal (Tue Dec 03 2013 - 05:14:42 CST)
- restrain noe's in random.inp Vanessa Gameiro (Tue Dec 03 2013 - 04:12:38 CST)
- Reduce percent use of cpu jafar azamat (Tue Dec 03 2013 - 02:31:53 CST)
- Bug in T-REMD with colvars Francesco Pietra (Tue Dec 03 2013 - 01:55:14 CST)
- AW: BUG: TCL coorfile command Norman Geist (Mon Dec 02 2013 - 01:43:41 CST)
- pH calculation Nadia Salami (Sun Dec 01 2013 - 23:31:02 CST)
- charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" Frank Thommen (Sat Nov 30 2013 - 14:51:55 CST)
- Colvars periodic boundary treatment question Kasra Fattah (Sat Nov 30 2013 - 13:12:42 CST)
- Phosphorylating a residue with Amber ff Charles McAnany (Sat Nov 30 2013 - 12:24:19 CST)
- Modify Molecule.C to avoid fatal error? George Patargias (Thu Nov 28 2013 - 02:26:37 CST)
- Drifting water molecules Mihaela Drenscko (Wed Nov 27 2013 - 16:45:10 CST)
- Error with dummy atoms George Patargias (Wed Nov 27 2013 - 11:07:40 CST)
- Problem regarding the Pre-Minimizer Bad Contacts Removal Norman Geist (Wed Nov 27 2013 - 02:24:28 CST)
- xplor psf used for namd Jana, Suvamay (Mon Nov 25 2013 - 20:07:31 CST)
- can i use swap partition to increase ram in namd? k.manzoorolajdad (Mon Nov 25 2013 - 09:18:15 CST)
- inconsistency between "Benchmark" and "Timing" output Vlad Cojocaru (Mon Nov 25 2013 - 09:08:58 CST)
- Sherical BC energy conservation Norman Geist (Mon Nov 25 2013 - 03:18:37 CST)
- diffusion of protein into water box Ramin Ekhteiari (Sun Nov 24 2013 - 08:06:27 CST)
- Fwd: manish kesherwani (Sun Nov 24 2013 - 06:29:35 CST)
- Carma v.1.3 available for download Nicholas M Glykos (Sun Nov 24 2013 - 04:33:05 CST)
- Interaction energy definition nan li (Fri Nov 22 2013 - 14:45:13 CST)
- (no subject) sutapa dutta (Fri Nov 22 2013 - 05:04:36 CST)
- New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python FyD (Fri Nov 22 2013 - 04:18:53 CST)
- pre residues and ligands interaction Ramin Ekhteiari (Thu Nov 21 2013 - 06:48:15 CST)
- How to apply Symmetry boundary on NAMD zhangxing (Tue Nov 19 2013 - 17:52:50 CST)
- How to replace NAMD electrostatics Juba, Derek (Tue Nov 19 2013 - 16:36:20 CST)
- NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION Thomas C. Bishop (Tue Nov 19 2013 - 08:06:31 CST)
- Approaching Deadline December 1st 2013 - Advanced LAMMPS and Scientific Software Development Workshop at ICTP in March 2014 Axel Kohlmeyer (Tue Nov 19 2013 - 03:46:45 CST)
- Compile NAMD with FFTW3 and MPI Chan Tabris C (Tue Nov 19 2013 - 02:45:00 CST)
- ABF calculations in NAMD Johny Telecaster (Mon Nov 18 2013 - 07:36:58 CST)
- Question about how much used from CPU? jafar azamat (Mon Nov 18 2013 - 02:50:14 CST)
- Adaptive tempering exception error Matthew Ralph Adendorff (Sun Nov 17 2013 - 09:52:27 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Thomas Albers (Sat Nov 16 2013 - 09:58:22 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Sun Nov 17 2013 - 04:56:04 CST)
- Fwd: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Sun Nov 17 2013 - 09:06:51 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Johny Telecaster (Sun Nov 17 2013 - 14:23:22 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Mon Nov 18 2013 - 01:31:10 CST)
- Fwd: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Mon Nov 18 2013 - 03:13:05 CST)
- Fwd: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Tue Nov 19 2013 - 02:50:42 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Johny Telecaster (Wed Nov 20 2013 - 10:32:41 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Thu Nov 21 2013 - 05:00:54 CST)
- Fwd: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Sun Nov 17 2013 - 09:06:51 CST)
- Re: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Sun Nov 17 2013 - 04:56:04 CST)
- Steered MD along detected routes Johny Telecaster (Sat Nov 16 2013 - 05:10:40 CST)
- FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 15 2013 - 14:41:13 CST)
- FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 15 2013 - 15:02:06 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 11:44:59 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 12:56:19 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Jérôme Hénin (Mon Nov 18 2013 - 17:32:09 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 23:21:35 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Jérôme Hénin (Tue Nov 19 2013 - 04:25:39 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Thu Nov 21 2013 - 13:33:34 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Jérôme Hénin (Fri Nov 22 2013 - 04:21:54 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 22 2013 - 10:32:44 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Jérôme Hénin (Fri Nov 22 2013 - 10:49:17 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 22 2013 - 11:01:18 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Fri Nov 22 2013 - 12:09:37 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Tue Dec 03 2013 - 17:12:43 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Tue Dec 10 2013 - 10:28:10 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Wed Dec 11 2013 - 15:00:01 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Wed Dec 11 2013 - 15:37:08 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Jérôme Hénin (Thu Dec 12 2013 - 03:05:30 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Thu Dec 12 2013 - 09:37:22 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 12:56:19 CST)
- Re: FEP calculations: optimizing the dlambda, number of steps Shyno Mathew (Mon Nov 18 2013 - 11:44:59 CST)
- problem of using SMD and TclForces keywords simultaneously dbaogen (Fri Nov 15 2013 - 02:42:07 CST)
- Re: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? Axel Kohlmeyer (Thu Nov 14 2013 - 06:52:52 CST)
- AW: Separate water coordinates from graphite Norman Geist (Thu Nov 14 2013 - 06:34:46 CST)
- NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? Nicolas Floquet (Thu Nov 14 2013 - 05:17:48 CST)
- AW: Separate water coordinates from graphite Norman Geist (Thu Nov 14 2013 - 01:26:31 CST)
- Release of ConcatXY Ali Khanlarkhani (Tue Nov 12 2013 - 16:18:36 CST)
- Separate water coordinates from graphite Mihaela Drenscko (Tue Nov 12 2013 - 13:57:01 CST)
- Steered Molecular Dynamics tutorial James Starlight (Tue Nov 12 2013 - 03:40:44 CST)
- Fwd: RE: PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Tue Nov 12 2013 - 01:46:45 CST)
- Re: TclForces and efficient PBC corrections Axel Kohlmeyer (Tue Nov 12 2013 - 01:32:28 CST)
- Why does my volume suddenly expand as I increase temperature. Martin, Erik W (Mon Nov 11 2013 - 17:55:05 CST)
- TclForces and efficient PBC corrections Morgan, Brittany (Mon Nov 11 2013 - 12:02:52 CST)
- PCIexpress 3.0 for MD with NAMD on GPUs Francesco Pietra (Mon Nov 11 2013 - 03:51:02 CST)
- Poor scaling in NAMD simulations Tristan Croll (Fri Nov 08 2013 - 22:11:41 CST)
- BLCR and NAMD Phil Miller (Thu Nov 07 2013 - 22:47:14 CST)
- pairInteractionSelf interaction terms Christopher Von Bargen (Thu Nov 07 2013 - 15:22:58 CST)
- Namd energy plugin James Starlight (Thu Nov 07 2013 - 01:53:52 CST)
- Force Field Parameters for PEG Roy Fernando (Wed Nov 06 2013 - 12:21:46 CST)
- Re: Force Field Parameters for PEG Kenno Vanommeslaeghe (Wed Nov 06 2013 - 13:27:41 CST)
- Re: Force Field Parameters for PEG Roy Fernando (Wed Nov 06 2013 - 13:58:57 CST)
- Re: Force Field Parameters for PEG Roy Fernando (Mon Feb 24 2014 - 10:22:47 CST)
- Re: Force Field Parameters for PEG Aron Broom (Mon Feb 24 2014 - 10:29:42 CST)
- Re: Force Field Parameters for PEG Roy Fernando (Mon Feb 24 2014 - 10:48:08 CST)
- Re: Force Field Parameters for PEG Axel Kohlmeyer (Mon Feb 24 2014 - 10:49:58 CST)
- Re: Force Field Parameters for PEG Roy Fernando (Wed Nov 06 2013 - 13:58:57 CST)
- Re: Force Field Parameters for PEG Kenno Vanommeslaeghe (Wed Nov 06 2013 - 13:27:41 CST)
- MM-PBSA calculation Ramin Ekhteiari (Wed Nov 06 2013 - 02:56:43 CST)
- Re: Accelerated MD in NAMD James Starlight (Wed Nov 06 2013 - 01:29:53 CST)
- Re: Accelerated MD in NAMD Jeff Wereszczynski (Wed Nov 06 2013 - 12:00:29 CST)
- Re: Accelerated MD in NAMD James Starlight (Wed Nov 06 2013 - 12:50:36 CST)
- Re: Accelerated MD in NAMD Jeff Wereszczynski (Wed Nov 06 2013 - 15:03:00 CST)
- Re: Accelerated MD in NAMD Thomas Evangelidis (Wed Nov 06 2013 - 15:21:52 CST)
- Accelerated MD in NAMD Jeff Wereszczynski (Wed Nov 06 2013 - 19:24:58 CST)
- Re: Accelerated MD in NAMD James Starlight (Wed Nov 06 2013 - 23:28:44 CST)
- Re: Accelerated MD in NAMD James Starlight (Thu Nov 07 2013 - 01:09:45 CST)
- Re: Accelerated MD in NAMD Thomas Evangelidis (Thu Nov 07 2013 - 04:32:04 CST)
- Re: Accelerated MD in NAMD James Starlight (Thu Nov 07 2013 - 06:48:45 CST)
- Re: Accelerated MD in NAMD Jeff Wereszczynski (Thu Nov 07 2013 - 08:19:53 CST)
- Re: Accelerated MD in NAMD Thomas Evangelidis (Thu Nov 07 2013 - 09:59:39 CST)
- Re: Accelerated MD in NAMD Jeff Wereszczynski (Thu Nov 07 2013 - 10:46:59 CST)
- Re: Accelerated MD in NAMD James Starlight (Thu Nov 07 2013 - 13:18:47 CST)
- Re: Accelerated MD in NAMD James Starlight (Wed Nov 06 2013 - 12:50:36 CST)
- Re: Accelerated MD in NAMD James Starlight (Fri Nov 08 2013 - 00:53:41 CST)
- Re: Accelerated MD in NAMD Jeff Wereszczynski (Wed Nov 06 2013 - 12:00:29 CST)
- Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Wed Nov 06 2013 - 00:51:22 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI Sunhwan Jo (Wed Nov 06 2013 - 08:07:25 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Wed Nov 06 2013 - 09:02:45 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI Sunhwan Jo (Wed Nov 06 2013 - 09:29:54 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI Kenno Vanommeslaeghe (Wed Nov 06 2013 - 14:03:05 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Fri Nov 08 2013 - 06:38:26 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Thu Nov 14 2013 - 07:32:44 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI James Starlight (Wed Nov 06 2013 - 09:02:45 CST)
- Re: Equilibration of the membrane-protein system done in CHARMM-GUI Sunhwan Jo (Wed Nov 06 2013 - 08:07:25 CST)
- Re: FEP simulation: protein moving out of water box. Niklaus Johner (Tue Nov 05 2013 - 21:21:48 CST)
- FEP simulation: protein moving out of water box. venkata agasthya (Tue Nov 05 2013 - 19:39:51 CST)
- accelerated MD and External Electric Field Thomas Evangelidis (Tue Nov 05 2013 - 07:10:24 CST)
- Potential energy in the boundaries Nadia Salami (Tue Nov 05 2013 - 03:06:50 CST)
- regarding editing protonated glutamate in the pdb file via psfgen Prathit Chatterjee (Tue Nov 05 2013 - 00:53:17 CST)
- Restarting T-REMD with colvars Francesco Pietra (Mon Nov 04 2013 - 10:19:30 CST)
- Re: Using volmap to calculate the water density around certain residues bharat gupta (Mon Nov 04 2013 - 02:25:22 CST)
- Accelerated MD in NAMD James Starlight (Sun Nov 03 2013 - 08:17:51 CST)
- About Psfgen for cyclic peptide Vidhya Sankar (Sun Nov 03 2013 - 00:08:11 CDT)
- simulation crashes frequently with "atoms moving too fast" eprates_at_iqm.unicamp.br (Fri Nov 01 2013 - 16:26:57 CDT)
- Martini RBCG simulation frequently crashing with "atoms moving too fast" eprates_at_iqm.unicamp.br (Sun Nov 03 2013 - 11:57:18 CST)
- AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" Norman Geist (Mon Nov 04 2013 - 01:17:46 CST)
- Re: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" eprates_at_iqm.unicamp.br (Mon Nov 04 2013 - 08:42:53 CST)
- AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" Norman Geist (Mon Nov 04 2013 - 09:02:04 CST)
- Re: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" eprates_at_iqm.unicamp.br (Mon Nov 04 2013 - 09:59:14 CST)
- AW: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" Norman Geist (Tue Nov 05 2013 - 03:04:53 CST)
- Re: AW: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" eprates_at_iqm.unicamp.br (Wed Nov 06 2013 - 11:17:19 CST)
- AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" Norman Geist (Mon Nov 04 2013 - 01:17:46 CST)
- Martini RBCG simulation frequently crashing with "atoms moving too fast" eprates_at_iqm.unicamp.br (Sun Nov 03 2013 - 11:57:18 CST)
- Problem in creating dummy atom Atanu Maity (Fri Nov 01 2013 - 01:43:09 CDT)
- Charge distribution Peterson J (Fri Nov 01 2013 - 00:28:34 CDT)
- Extract KE, PE and total energy from log file Mihaela Drenscko (Thu Oct 31 2013 - 15:15:04 CDT)
- accelerated MD parameters for dual boost mode Huihui Liu (Thu Oct 31 2013 - 10:04:23 CDT)
- HMMM model Tristan Croll (Wed Oct 30 2013 - 22:51:50 CDT)
- HEME B PARAMETERS Sadegh Faramarzi Ganjabad (Wed Oct 30 2013 - 02:30:09 CDT)
- I have a question about pair interaction energy calculations. ȣ (Wed Oct 30 2013 - 02:14:32 CDT)
- reassignTemp question Martin, Erik W (Tue Oct 29 2013 - 15:26:46 CDT)
- FEP Error - TCL Eudes Fileti (Tue Oct 29 2013 - 14:28:17 CDT)
- unsuscribe Rehan Zafar (Tue Oct 29 2013 - 11:30:35 CDT)
- unsuscribe Cat Chenal (Tue Oct 29 2013 - 09:45:33 CDT)
- AW: vmd-l: Creating custom molecule in VMD scripting Norman Geist (Tue Oct 29 2013 - 07:16:46 CDT)
- Re: Namd options from TCL Ajasja Ljubetič (Tue Oct 29 2013 - 04:44:50 CDT)
- Two GPU-based workstation James Starlight (Tue Oct 29 2013 - 00:29:43 CDT)
- Re: Two GPU-based workstation Shubhra Ghosh Dastidar (Tue Oct 29 2013 - 01:53:16 CDT)
- AW: Two GPU-based workstation Norman Geist (Tue Oct 29 2013 - 04:13:17 CDT)
- Re: Two GPU-based workstation Ajasja Ljubetič (Tue Oct 29 2013 - 04:46:23 CDT)
- Re: Two GPU-based workstation James Starlight (Tue Oct 29 2013 - 08:20:22 CDT)
- Re: Two GPU-based workstation James Starlight (Wed Oct 30 2013 - 08:12:58 CDT)
- Re: Two GPU-based workstation James Starlight (Thu Oct 31 2013 - 12:24:16 CDT)
- Re: Two GPU-based workstation Aron Broom (Thu Oct 31 2013 - 12:34:14 CDT)
- Re: Two GPU-based workstation James Starlight (Fri Nov 01 2013 - 02:40:14 CDT)
- Re: Two GPU-based workstation James Starlight (Sun Nov 03 2013 - 02:38:59 CST)
- Re: Two GPU-based workstation Ajasja Ljubetič (Sun Nov 03 2013 - 06:54:26 CST)
- Re: Two GPU-based workstation James Starlight (Sun Nov 03 2013 - 08:04:02 CST)
- AW: Two GPU-based workstation Norman Geist (Mon Nov 04 2013 - 01:04:00 CST)
- Re: Two GPU-based workstation James Starlight (Mon Nov 04 2013 - 01:52:01 CST)
- Re: Two GPU-based workstation James Starlight (Mon Nov 04 2013 - 04:43:09 CST)
- Re: Two GPU-based workstation James Starlight (Wed Nov 06 2013 - 23:32:18 CST)
- AW: Two GPU-based workstation Norman Geist (Thu Nov 07 2013 - 01:51:43 CST)
- Re: Two GPU-based workstation Ajasja Ljubetič (Thu Nov 07 2013 - 09:36:44 CST)
- Re: Two GPU-based workstation James Starlight (Fri Nov 08 2013 - 05:50:30 CST)
- Re: Two GPU-based workstation James Starlight (Sat Nov 09 2013 - 08:53:20 CST)
- AW: Two GPU-based workstation Norman Geist (Mon Nov 11 2013 - 01:09:38 CST)
- Re: Two GPU-based workstation James Starlight (Mon Nov 11 2013 - 02:42:18 CST)
- Re: Two GPU-based workstation James Starlight (Mon Nov 11 2013 - 06:55:01 CST)
- Re: Two GPU-based workstation Shubhra Ghosh Dastidar (Tue Oct 29 2013 - 01:53:16 CDT)
- ABF: Distances in colvars.traj not identical with VMD exported distances Maximilian Ebert (Mon Oct 28 2013 - 16:21:45 CDT)
- PLUMED 2.0 announcement Massimiliano Bonomi (Mon Oct 28 2013 - 06:51:47 CDT)
- Mysterious slow down in parallel Roy Fernando (Sat Oct 26 2013 - 10:05:13 CDT)
- AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Norman Geist (Thu Oct 24 2013 - 11:53:37 CDT)
- Calculating pressure on each direction Bala subramanian (Thu Oct 24 2013 - 07:53:07 CDT)
- Mac OS Binary for NAMD 2.10 Eudes Fileti (Thu Oct 24 2013 - 06:16:31 CDT)
- DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface Norman Geist (Thu Oct 24 2013 - 01:21:19 CDT)
- NAMD and water models Mihaela Drenscko (Wed Oct 23 2013 - 20:13:17 CDT)
- Fwd: Re: [Checkpoint] BLCR and NAMD Joseph Farran (Wed Oct 23 2013 - 13:46:00 CDT)
- Bonds in XPLOR format Mihaela Drenscko (Wed Oct 23 2013 - 13:00:05 CDT)
- Membrane/peptide system. Water moving from one layer to the other ... Villalain Boullon, Jose (Wed Oct 23 2013 - 05:46:00 CDT)
- NAMD Internal energy unit Norman Geist (Wed Oct 23 2013 - 05:16:57 CDT)
- Namd options from TCL Norman Geist (Tue Oct 22 2013 - 10:26:37 CDT)
- AW: Fixed and SMD atoms Norman Geist (Tue Oct 22 2013 - 03:37:09 CDT)
- MMPBSA-like analysis Revthi Sanker (Tue Oct 22 2013 - 02:04:49 CDT)
- Re: MMPBSA-like analysis Peter Jones (Tue Oct 22 2013 - 04:21:24 CDT)
- Re: MMPBSA-like analysis Jason Swails (Tue Oct 22 2013 - 05:01:32 CDT)
- Re: MMPBSA-like analysis Revthi Sanker (Tue Oct 22 2013 - 11:12:52 CDT)
- Re: MMPBSA-like analysis Kenno Vanommeslaeghe (Tue Oct 22 2013 - 11:56:59 CDT)
- Re: MMPBSA-like analysis Revthi Sanker (Wed Oct 23 2013 - 01:19:40 CDT)
- Re: MMPBSA-like analysis Hannes Loeffler (Wed Oct 23 2013 - 02:39:29 CDT)
- Re: MMPBSA-like analysis Kenno Vanommeslaeghe (Fri Oct 25 2013 - 15:05:05 CDT)
- Re: MMPBSA-like analysis Hannes Loeffler (Tue Oct 29 2013 - 04:32:01 CDT)
- Re: MMPBSA-like analysis Hannes Loeffler (Wed Oct 30 2013 - 06:02:54 CDT)
- Re: MMPBSA-like analysis Hannes Loeffler (Wed Oct 30 2013 - 08:24:43 CDT)
- Re: MMPBSA-like analysis Jason Swails (Tue Oct 22 2013 - 05:01:32 CDT)
- Re: MMPBSA-like analysis Peter Jones (Tue Oct 22 2013 - 04:21:24 CDT)
- Method for solvation of protein Xingcheng Lin (Mon Oct 21 2013 - 15:45:16 CDT)
- [OT] A new method for quantifying convergence of MD simulations Nicholas M Glykos (Mon Oct 21 2013 - 12:37:45 CDT)
- Re: vmd-l: fftk-charges rodolfo gonzalez (Mon Oct 21 2013 - 01:57:55 CDT)
- AW: vmd-l: fftk-charges Norman Geist (Mon Oct 21 2013 - 01:23:48 CDT)
- Fixed and SMD atoms Mihaela Drenscko (Sat Oct 19 2013 - 14:16:47 CDT)
- Simulation results from NVT has a cavity Xingcheng Lin (Sat Oct 19 2013 - 13:49:12 CDT)
- Adaptive tempering floating point exception Stober, Spencer T (Fri Oct 18 2013 - 13:21:03 CDT)
- CUDA vd non-CUDA for minimization Francesco Pietra (Fri Oct 18 2013 - 12:13:04 CDT)
- Re: [SUSPICIOUS MESSAGE] Reg System Prepartion namd Kenno Vanommeslaeghe (Thu Oct 17 2013 - 16:15:10 CDT)
- Running NAMD in multiprocessor single machine Roy Fernando (Thu Oct 17 2013 - 16:02:58 CDT)
- Peptide insertion into a membrane Villalain Boullon, Jose (Thu Oct 17 2013 - 07:44:47 CDT)
- Error Mihaela Drenscko (Wed Oct 16 2013 - 20:15:29 CDT)
- get topology and parameter file for the ligand. Ramin Ekhteiari (Wed Oct 16 2013 - 12:14:15 CDT)
- NAMD build problems on PowerPC under Red Hat Enterprise Lane, William (Wed Oct 16 2013 - 11:37:12 CDT)
- Pass a runtime parameter into the configuration file Xingcheng Lin (Tue Oct 15 2013 - 17:55:48 CDT)
- NAMD simulation with flag similar to -maxh in Gromacs Xingcheng Lin (Tue Oct 15 2013 - 11:30:49 CDT)
- About Constraint Failure Vidhya Sankar (Tue Oct 15 2013 - 04:57:04 CDT)
- Combining several proteins of the same type together Lili Zhang (Mon Oct 14 2013 - 13:54:56 CDT)
- question about NAMD on Kraken. Martin, Erik W (Mon Oct 14 2013 - 13:44:10 CDT)
- Protein-ligand affinity James Starlight (Mon Oct 14 2013 - 13:20:17 CDT)
- Re: Protein-ligand affinity Aron Broom (Mon Oct 14 2013 - 22:16:00 CDT)
- Re: Protein-ligand affinity James Starlight (Tue Oct 15 2013 - 12:42:09 CDT)
- Re: Protein-ligand affinity Aron Broom (Tue Oct 15 2013 - 12:44:33 CDT)
- Re: Protein-ligand affinity James Starlight (Tue Oct 15 2013 - 13:43:30 CDT)
- Re: Protein-ligand affinity Thomas Evangelidis (Tue Oct 15 2013 - 14:43:39 CDT)
- Re: Protein-ligand affinity James Starlight (Tue Oct 15 2013 - 15:05:11 CDT)
- Re: Protein-ligand affinity Kenno Vanommeslaeghe (Tue Oct 15 2013 - 15:51:03 CDT)
- Re: Protein-ligand affinity James Starlight (Wed Oct 16 2013 - 14:42:42 CDT)
- Re: Protein-ligand affinity Kenno Vanommeslaeghe (Tue Oct 15 2013 - 15:50:25 CDT)
- Re: Protein-ligand affinity Kenno Vanommeslaeghe (Tue Oct 15 2013 - 14:40:50 CDT)
- Re: Protein-ligand affinity James Starlight (Tue Oct 15 2013 - 12:42:09 CDT)
- Re: Protein-ligand affinity Aron Broom (Mon Oct 14 2013 - 22:16:00 CDT)
- question about setting up FEP calculations Shyno Mathew (Mon Oct 14 2013 - 10:48:46 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Mon Oct 14 2013 - 14:32:34 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Mon Oct 14 2013 - 20:01:48 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Tue Oct 15 2013 - 10:44:51 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Tue Oct 15 2013 - 11:21:51 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Tue Oct 15 2013 - 11:29:51 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Tue Oct 15 2013 - 11:53:12 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Tue Oct 15 2013 - 12:00:58 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Wed Oct 16 2013 - 16:21:09 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Fri Oct 18 2013 - 04:33:54 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Fri Oct 18 2013 - 11:44:41 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Fri Nov 01 2013 - 10:14:36 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Sat Nov 02 2013 - 04:24:49 CDT)
- Re: question about setting up FEP calculations Shyno Mathew (Thu Nov 14 2013 - 15:25:45 CST)
- Re: question about setting up FEP calculations Shyno Mathew (Mon Oct 14 2013 - 20:01:48 CDT)
- Re: question about setting up FEP calculations Jérôme Hénin (Mon Oct 14 2013 - 14:32:34 CDT)
- rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs Thomas C. Bishop (Sun Oct 13 2013 - 22:29:51 CDT)
- About Usage of Topolgy and Parameter Vidhya Sankar (Sun Oct 13 2013 - 06:59:39 CDT)
- BUG Report: NAMD 2.10 Nightly Build from 11.Sep Norman Geist (Fri Oct 11 2013 - 06:23:14 CDT)
- Reg Lack of Lack of VDW parameters Vidhya Sankar (Wed Oct 09 2013 - 10:57:58 CDT)
- AW: vmd-l: Finding particles that are close Norman Geist (Tue Oct 08 2013 - 06:48:07 CDT)
- Simulation of a protein and ions Stephan Matthias Grein (Tue Oct 08 2013 - 03:29:05 CDT)
- Simulation of a protein and calcium ions Stephan Matthias Grein (Tue Oct 08 2013 - 03:15:44 CDT)
- abf integrate on two dimensional pmf Nadeem A. Vellore (Mon Oct 07 2013 - 21:25:11 CDT)
- Accumulating free energy change for applying colvar restraint Randy J. Zauhar (Mon Oct 07 2013 - 08:50:07 CDT)
- How I can to change the force field function in NAMD for protein phi-value analysis Juan Jos Galano Frutos (Mon Oct 07 2013 - 04:55:44 CDT)
- Lennard Jones (LJ) parameters Bachir Aoun (Sun Oct 06 2013 - 15:23:36 CDT)
- problem with Dihedral farzad kiani (Sun Oct 06 2013 - 07:27:01 CDT)
- (no subject) buksanbio_at_gmail.com (Sat Oct 05 2013 - 16:12:07 CDT)
- About restaring Simulation Vidhya Sankar (Sat Oct 05 2013 - 02:56:01 CDT)
- .psf file in VMD Lili Zhang (Thu Oct 03 2013 - 12:10:56 CDT)
- Biotin force field Zack Scholl (Thu Oct 03 2013 - 10:44:25 CDT)
- Problem in SMD "Constant Velocity Pulling" on Ubiquitin example Lili Zhang (Thu Oct 03 2013 - 08:53:48 CDT)
- simultaneous simulation for protein in water and SMD amit banerjee (Thu Oct 03 2013 - 07:33:04 CDT)
- MD- GPU Sagar Gore (Thu Oct 03 2013 - 06:51:02 CDT)
- membrane protein simulation lipid bilayer question Tian Li (Wed Oct 02 2013 - 19:48:35 CDT)
- Problem in running "Constant Velocity Pulling" example Lili Zhang (Wed Oct 02 2013 - 12:25:56 CDT)
- Questions regarding pressure difference houyang chen (Wed Oct 02 2013 - 08:29:43 CDT)
- Extent of Sampling possible using classical all-atom MD Simulations Aditya Ranganathan (Tue Oct 01 2013 - 08:22:42 CDT)
- Same NAMD files give error in Linux but not in Windows .... Villalain Boullon, Jose (Tue Oct 01 2013 - 03:49:55 CDT)
- TOTLAL2, POTENTIAL abd aMD sunyeping (Mon Sep 30 2013 - 03:11:43 CDT)
- questions regarding pressure difference houyang chen (Sun Sep 29 2013 - 22:55:10 CDT)
- reg Parameters Vidhya Sankar (Sun Sep 29 2013 - 08:35:10 CDT)
- Reg Reading of files durin simulation Vidhya Sankar (Sat Sep 28 2013 - 03:52:32 CDT)
- NAMD_multiprocessor Shomesankar Bhunia (Sat Sep 28 2013 - 03:08:23 CDT)
- Reg VDw Parameters Vidhya Sankar (Fri Sep 27 2013 - 11:18:30 CDT)
- Adaptive tempering floating point exception Stober, Spencer T (Fri Sep 27 2013 - 09:56:10 CDT)
- (no subject) Arman Imen (Thu Sep 26 2013 - 05:49:15 CDT)
- AW: vmd-l: non-orthorhombic PBCs Norman Geist (Thu Sep 26 2013 - 00:49:18 CDT)
- AW: Coordinates of Carbon atoms on Graphite Norman Geist (Thu Sep 26 2013 - 00:45:38 CDT)
- Re: cell origin problem Haleh Abdizadeh (Wed Sep 25 2013 - 14:00:49 CDT)
- lone pair velocities Gergely Gyimesi (Wed Sep 25 2013 - 11:27:48 CDT)
- Gold nanoparticle Dr. Eddie (Wed Sep 25 2013 - 11:25:45 CDT)
- Re: Gold nanoparticle Axel Kohlmeyer (Wed Sep 25 2013 - 11:34:39 CDT)
- Re: Gold nanoparticle Dr. Eddie (Wed Sep 25 2013 - 11:52:48 CDT)
- Re: Gold nanoparticle Axel Kohlmeyer (Wed Sep 25 2013 - 12:37:13 CDT)
- Re: Gold nanoparticle Ana Celia Vila Verde (Thu Sep 26 2013 - 03:22:47 CDT)
- Re: Gold nanoparticle lcbllcc_at_gmail.com (Thu Sep 26 2013 - 04:07:26 CDT)
- Re: Gold nanoparticle Dr. Eddie (Thu Sep 26 2013 - 09:42:36 CDT)
- Re: Gold nanoparticle Luca Bellucci (Fri Sep 27 2013 - 03:10:09 CDT)
- Re: Gold nanoparticle Kenno Vanommeslaeghe (Fri Sep 27 2013 - 13:30:35 CDT)
- Re: Gold nanoparticle Dr. Eddie (Wed Sep 25 2013 - 11:52:48 CDT)
- Re: Gold nanoparticle Axel Kohlmeyer (Wed Sep 25 2013 - 11:34:39 CDT)
- NAMD electrostatic interaction Failure MEHRAN MB (Wed Sep 25 2013 - 10:53:25 CDT)
- NAMD electrostatic interaction Failure. Mehran Bagheri (Wed Sep 25 2013 - 08:58:03 CDT)
- AW: Coordinates of Carbon atoms on Graphite Norman Geist (Wed Sep 25 2013 - 09:16:24 CDT)
- AW: Coordinates of Carbon atoms on Graphite Norman Geist (Wed Sep 25 2013 - 08:35:15 CDT)
- Organic molecule and membrane. NAMD gives fatal error: Villalain Boullon, Jose (Wed Sep 25 2013 - 08:27:59 CDT)
- pair interaction energy calculation Behnam Rasti (Wed Sep 25 2013 - 06:20:35 CDT)
- Coordinates of Carbon atoms on Graphite Mihaela Drenscko (Tue Sep 24 2013 - 11:47:28 CDT)
- cell origin problem Haleh Abdizadeh (Tue Sep 24 2013 - 09:53:17 CDT)
- CHARMGUI and ligands parametrisation James Starlight (Tue Sep 24 2013 - 09:38:30 CDT)
- vibrational modes calculation Mortaza Aghtar (Mon Sep 23 2013 - 08:55:27 CDT)
- How to setting tilt component in colvars module (Mon Sep 23 2013 - 01:21:35 CDT)
- Psfgen - bonding terms involving disulfide bridges Reza (Sun Sep 22 2013 - 22:26:33 CDT)
- namd conf file oguz gurbulak (Sat Sep 21 2013 - 05:52:23 CDT)
- About Muticore Linux Ibnstalltion if NAmd Vidhya Sankar (Fri Sep 20 2013 - 22:50:38 CDT)
- FEP failure - FFTW problem? JC Gumbart (Fri Sep 20 2013 - 14:16:37 CDT)
- Regarding Membrane Builder Vidhya Sankar (Fri Sep 20 2013 - 08:40:51 CDT)
- (no subject) rasti_at_ut.ac.ir (Fri Sep 20 2013 - 05:19:37 CDT)
- Re: About the scope of show_replicas.vmd Niklaus Johner (Thu Sep 19 2013 - 09:48:11 CDT)
- Re: About the scope of show_replicas.vmd Francesco Pietra (Thu Sep 19 2013 - 10:53:58 CDT)
- Re: About the scope of show_replicas.vmd Francesco Pietra (Fri Sep 20 2013 - 12:39:16 CDT)
- delta-G calculation rasti_at_ut.ac.ir (Thu Sep 19 2013 - 03:02:33 CDT)
- About the scope of show_replicas.vmd Francesco Pietra (Thu Sep 19 2013 - 01:48:16 CDT)
- Reg Membrane Builder Vidhya Sankar (Wed Sep 18 2013 - 12:08:59 CDT)
- About Psfgen for membrane Vidhya Sankar (Wed Sep 18 2013 - 10:56:30 CDT)
- Energy Correction Term For PME Electrostatics in a Charged Periodic System David Huggins (Wed Sep 18 2013 - 05:02:52 CDT)
- incorrect bond Nadia Salami (Wed Sep 18 2013 - 01:28:59 CDT)
- incorrect bond Nadia Salami (Wed Sep 18 2013 - 01:11:08 CDT)
- Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Anna Chailyan (Tue Sep 17 2013 - 11:10:29 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Niklaus Johner (Tue Sep 17 2013 - 11:35:45 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:20:38 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Anna Chailyan (Wed Sep 18 2013 - 10:01:10 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Niklaus Johner (Wed Sep 18 2013 - 10:29:40 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Teerapong Pirojsirikul (Wed Sep 18 2013 - 12:20:24 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Kenno Vanommeslaeghe (Wed Sep 18 2013 - 13:50:04 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Teerapong Pirojsirikul (Wed Sep 18 2013 - 15:45:54 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Kenno Vanommeslaeghe (Wed Sep 18 2013 - 16:52:41 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Anna Chailyan (Thu Sep 19 2013 - 08:40:58 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Grace Brannigan (Wed Sep 18 2013 - 11:59:02 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:20:38 CDT)
- Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Niklaus Johner (Tue Sep 17 2013 - 11:35:45 CDT)
- Segmentation fault - colvar Peterson J (Mon Sep 16 2013 - 23:02:55 CDT)
- CHAMBER generated .prmtop file is not compatable with namd2 sudipta (Sun Sep 15 2013 - 23:51:48 CDT)
- NAMD PERFORMANCE ON NVIDIA K20 GPU Neeraj Agrawal (Sat Sep 14 2013 - 18:59:08 CDT)
- Replica exchange and colvars - Missing Stage from restart Andrei Tudor (Sat Sep 14 2013 - 10:04:43 CDT)
- How to optimize parameters in command for NAMD CUDA GPU MD calculations? Michael Shokhen (Thu Sep 12 2013 - 14:59:21 CDT)
- Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches Rehan Zafar (Thu Sep 12 2013 - 03:41:08 CDT)
- Does stray PME charges with T-REMD mean insufficient resources and can explicit water abandoned for implicit GB? Francesco Pietra (Wed Sep 11 2013 - 09:24:59 CDT)
- MMPBSA calculation using NAMD sudipta (Wed Sep 11 2013 - 07:37:57 CDT)
- Regarding the Protein-Ligand Free Energy Tutorial Aron Broom (Wed Sep 11 2013 - 00:39:18 CDT)
- NAMD CUDA performance Vlastimil Zíma (Tue Sep 10 2013 - 07:59:41 CDT)
- Stray PME grid charges on increasing number of replicas and T-range with T-REMD Francesco Pietra (Tue Sep 10 2013 - 05:24:58 CDT)
- bilayer creation Richard Wood (Mon Sep 09 2013 - 14:00:43 CDT)
- Equilibration of the membrane bilayers with CUDA-support James Starlight (Mon Sep 09 2013 - 10:16:40 CDT)
- Re: explicit NVT simulation Hailey Bureau (Mon Sep 09 2013 - 08:07:19 CDT)
- Re: explicit NVT simulation Axel Kohlmeyer (Mon Sep 09 2013 - 08:17:45 CDT)
- Re: explicit NVT simulation Jérôme Hénin (Mon Sep 09 2013 - 08:31:03 CDT)
- Re: explicit NVT simulation Axel Kohlmeyer (Mon Sep 09 2013 - 09:06:19 CDT)
- Re: explicit NVT simulation Kenno Vanommeslaeghe (Mon Sep 09 2013 - 12:24:29 CDT)
- Re: explicit NVT simulation Axel Kohlmeyer (Mon Sep 09 2013 - 13:02:37 CDT)
- Re: explicit NVT simulation Kenno Vanommeslaeghe (Mon Sep 09 2013 - 13:46:20 CDT)
- Re: explicit NVT simulation Hailey Bureau (Tue Sep 10 2013 - 10:35:24 CDT)
- Re: explicit NVT simulation Jérôme Hénin (Mon Sep 09 2013 - 08:31:03 CDT)
- Re: explicit NVT simulation Axel Kohlmeyer (Mon Sep 09 2013 - 08:17:45 CDT)
- AW: vmd-l: Error: Maximum number of bonds exceeded Norman Geist (Mon Sep 09 2013 - 01:06:38 CDT)
- explicit NVT simulation Hailey Bureau (Sun Sep 08 2013 - 17:54:26 CDT)
- About a REMD tutorial Francesco Pietra (Sat Sep 07 2013 - 09:35:51 CDT)
- VDW energy is negative but total energy is positive dayanidhi mohanta (Fri Sep 06 2013 - 23:18:51 CDT)
- AW: VDW energy is negative but total energy is positive Norman Geist (Mon Sep 09 2013 - 01:14:20 CDT)
- RE: VDW energy is negative but total energy is positive Bennion, Brian (Mon Sep 09 2013 - 10:25:53 CDT)
- RE: VDW energy is negative but total energy is positive Bennion, Brian (Tue Sep 10 2013 - 10:57:23 CDT)
- Atom indices in collective variable definition Randy J. Zauhar (Fri Sep 06 2013 - 09:40:09 CDT)
- charm-gui membrane builder James Starlight (Fri Sep 06 2013 - 06:21:15 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Fri Sep 06 2013 - 07:39:34 CDT)
- Re: charm-gui membrane builder James Starlight (Fri Sep 06 2013 - 11:24:56 CDT)
- Re: charm-gui membrane builder James Starlight (Fri Sep 06 2013 - 15:03:41 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Fri Sep 06 2013 - 15:13:45 CDT)
- Re: charm-gui membrane builder James Starlight (Sat Sep 07 2013 - 04:04:10 CDT)
- Re: charm-gui membrane builder Emilia Wu (Sat Sep 07 2013 - 09:16:19 CDT)
- Re: charm-gui membrane builder James Starlight (Sat Sep 07 2013 - 23:56:42 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Sun Sep 08 2013 - 08:35:10 CDT)
- Re: charm-gui membrane builder James Starlight (Sun Sep 08 2013 - 11:44:04 CDT)
- Re: charm-gui membrane builder Cesar Millan (Sun Sep 08 2013 - 11:51:56 CDT)
- Re: charm-gui membrane builder Grace Brannigan (Sun Sep 08 2013 - 01:02:31 CDT)
- Re: charm-gui membrane builder James Starlight (Sun Sep 08 2013 - 23:52:00 CDT)
- Re: charm-gui membrane builder James Starlight (Tue Sep 10 2013 - 11:29:17 CDT)
- Re: charm-gui membrane builder James Starlight (Wed Sep 11 2013 - 12:20:59 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Wed Sep 11 2013 - 13:32:58 CDT)
- Re: charm-gui membrane builder James Starlight (Wed Sep 11 2013 - 15:15:23 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Wed Sep 11 2013 - 17:41:02 CDT)
- Re: charm-gui membrane builder James Starlight (Thu Sep 12 2013 - 06:24:51 CDT)
- Re: charm-gui membrane builder Niklaus Johner (Thu Sep 12 2013 - 13:08:53 CDT)
- Re: charm-gui membrane builder James Starlight (Fri Sep 13 2013 - 02:06:07 CDT)
- Re: charm-gui membrane builder Niklaus Johner (Fri Sep 13 2013 - 09:01:51 CDT)
- Re: charm-gui membrane builder James Starlight (Tue Sep 17 2013 - 00:33:30 CDT)
- Re: charm-gui membrane builder Aron Broom (Tue Sep 17 2013 - 00:55:57 CDT)
- Re: charm-gui membrane builder James Starlight (Tue Sep 17 2013 - 12:12:21 CDT)
- Re: charm-gui membrane builder Niklaus Johner (Tue Sep 17 2013 - 13:22:45 CDT)
- Re: charm-gui membrane builder James Starlight (Tue Sep 17 2013 - 14:32:17 CDT)
- Re: charm-gui membrane builder James Starlight (Tue Sep 17 2013 - 15:30:31 CDT)
- Re: charm-gui membrane builder James Starlight (Thu Sep 19 2013 - 01:04:39 CDT)
- Re: charm-gui membrane builder Kenno Vanommeslaeghe (Tue Sep 17 2013 - 14:26:09 CDT)
- Re: charm-gui membrane builder James Starlight (Fri Sep 06 2013 - 11:24:56 CDT)
- Re: charm-gui membrane builder James Starlight (Fri Nov 01 2013 - 04:23:07 CDT)
- Re: charm-gui membrane builder Sunhwan Jo (Fri Sep 06 2013 - 07:39:34 CDT)
- forward minh nhut (Thu Sep 05 2013 - 21:01:00 CDT)
- question on explicit solvent reproducibility Hailey Bureau (Thu Sep 05 2013 - 16:31:52 CDT)
- Re: parallel code in tclforce script Axel Kohlmeyer (Thu Sep 05 2013 - 02:02:36 CDT)
- AW: vmd-l: how to enable multiple core rendering? Norman Geist (Thu Sep 05 2013 - 01:01:40 CDT)
- parallel code in tclforce script Teerapong Pirojsirikul (Wed Sep 04 2013 - 22:03:15 CDT)
- Simulation of the membrane protein James Starlight (Wed Sep 04 2013 - 11:16:35 CDT)
- Fwd: deca-alanin folding by remd parallel tempering Francesco Pietra (Wed Sep 04 2013 - 04:35:45 CDT)
- namd scale-up Revthi Sanker (Wed Sep 04 2013 - 02:43:24 CDT)
- Re: namd scale-up Axel Kohlmeyer (Wed Sep 04 2013 - 03:00:30 CDT)
- AW: namd scale-up Norman Geist (Thu Sep 05 2013 - 01:32:45 CDT)
- Re: namd scale-up Revthi Sanker (Thu Sep 05 2013 - 03:47:19 CDT)
- Re: namd scale-up Revthi Sanker (Thu Sep 05 2013 - 08:30:40 CDT)
- Re: namd scale-up Revthi Sanker (Fri Sep 06 2013 - 01:25:53 CDT)
- Re: namd scale-up Revthi Sanker (Sat Sep 14 2013 - 00:26:51 CDT)
- Re: namd scale-up Axel Kohlmeyer (Wed Sep 04 2013 - 03:00:30 CDT)
- AW: AW: AW: pbc error Norman Geist (Tue Sep 03 2013 - 04:55:03 CDT)
- pbc problem jinxj (Tue Sep 03 2013 - 04:45:06 CDT)
- Error with show_replicas.vmd Francesco Pietra (Tue Sep 03 2013 - 04:44:55 CDT)
- writedcd problem jinxj (Mon Sep 02 2013 - 09:32:00 CDT)
- pbc problem jinxj (Mon Sep 02 2013 - 04:08:28 CDT)
- creating coarse grain model with martini force field (Mon Sep 02 2013 - 01:58:10 CDT)
- pbc error jinxj (Sun Sep 01 2013 - 21:38:48 CDT)
- (no subject) Nadia Salami (Sun Sep 01 2013 - 10:26:51 CDT)
- NAMD job submission on Kraken? Martin, Erik W (Fri Aug 30 2013 - 15:36:03 CDT)
- FW: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 13:14:33 CDT)
- Assigning atom serial number after the first 99999 atoms Shyno Mathew (Fri Aug 30 2013 - 11:07:49 CDT)
- Margin setup Tian Li (Fri Aug 30 2013 - 08:37:03 CDT)
- editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 04:27:19 CDT)
- FW: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 04:31:44 CDT)
- Re: editing the code of the non bonded pair potentials Axel Kohlmeyer (Fri Aug 30 2013 - 04:34:46 CDT)
- RE: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 05:26:41 CDT)
- Re: editing the code of the non bonded pair potentials Axel Kohlmeyer (Fri Aug 30 2013 - 09:10:35 CDT)
- Re: editing the code of the non bonded pair potentials Kenno Vanommeslaeghe (Fri Aug 30 2013 - 13:47:15 CDT)
- RE: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 13:55:21 CDT)
- Re: editing the code of the non bonded pair potentials Axel Kohlmeyer (Fri Aug 30 2013 - 13:59:26 CDT)
- Re: editing the code of the non bonded pair potentials Joshua Adelman (Fri Aug 30 2013 - 14:06:12 CDT)
- Re: editing the code of the non bonded pair potentials Victor (Fri Aug 30 2013 - 14:29:58 CDT)
- Re: editing the code of the non bonded pair potentials Gianluca Interlandi (Fri Aug 30 2013 - 18:00:08 CDT)
- Re: editing the code of the non bonded pair potentials Victor (Fri Aug 30 2013 - 18:19:04 CDT)
- Re: editing the code of the non bonded pair potentials Gianluca Interlandi (Fri Aug 30 2013 - 18:33:06 CDT)
- FW: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 19:54:45 CDT)
- RE: editing the code of the non bonded pair potentials Asaf Farhi (Fri Aug 30 2013 - 05:26:41 CDT)
- AW: vmd-l: SangbaeLee: question about pbc wrap Norman Geist (Fri Aug 30 2013 - 02:15:30 CDT)
- ABF historyFile and distFile Sridhar Kumar Kannam (Thu Aug 29 2013 - 22:58:33 CDT)
- Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field sunyeping (Thu Aug 29 2013 - 21:32:22 CDT)
- problem in determining atom types and charges for ligand atoms to type in the topology file Mamon Hatmal (Thu Aug 29 2013 - 06:03:17 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Kenno Vanommeslaeghe (Thu Aug 29 2013 - 09:00:58 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Mamon Hatmal (Thu Aug 29 2013 - 11:28:27 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Branko (Thu Aug 29 2013 - 12:08:30 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Kenno Vanommeslaeghe (Thu Aug 29 2013 - 16:05:27 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Mamon Hatmal (Sun Sep 01 2013 - 16:16:38 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Mamon Hatmal (Thu Aug 29 2013 - 11:28:27 CDT)
- Re: problem in determining atom types and charges for ligand atoms to type in the topology file Kenno Vanommeslaeghe (Thu Aug 29 2013 - 09:00:58 CDT)
- how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Thu Aug 29 2013 - 04:07:02 CDT)
- eigenvector colvar Steven Mike (Wed Aug 28 2013 - 23:14:49 CDT)
- How to prepare FEP input files for double mutant Aman (Wed Aug 28 2013 - 15:05:19 CDT)
- WG: questions regarding the source code in NAMD Norman Geist (Wed Aug 28 2013 - 10:49:31 CDT)
- error when doing minimization with the charmm Drude FF Frank Haverkort (Wed Aug 28 2013 - 05:23:49 CDT)
- LJcorrection Gianluca Interlandi (Wed Aug 28 2013 - 01:33:39 CDT)
- making patch rasti_at_ut.ac.ir (Tue Aug 27 2013 - 18:41:06 CDT)
- Linear force ramp increments in ABF Matthew Ralph Adendorff (Tue Aug 27 2013 - 12:44:41 CDT)
- excluded interactions (NNB) in psf file for FEP simulations Aman (Tue Aug 27 2013 - 10:16:38 CDT)
- problem in finding atom types for ligand Mamon Hatmal (Tue Aug 27 2013 - 06:54:38 CDT)
- CUDA error memcpy to exclusions: invalid argument Haleh Abdizadeh (Tue Aug 27 2013 - 04:06:29 CDT)
- problem with ptch ... rasti (Mon Aug 26 2013 - 15:21:36 CDT)
- Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms? Bryan Roessler (Mon Aug 26 2013 - 11:24:31 CDT)
- Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? Jose Borreguero (Mon Aug 26 2013 - 08:24:32 CDT)
- AW: vmd-l: matching part of two models Norman Geist (Mon Aug 26 2013 - 04:58:04 CDT)
- a problem about pbc in a namd trajectory (Mon Aug 26 2013 - 02:44:23 CDT)
- (no subject) kaushik chakraborty (Sun Aug 25 2013 - 11:41:34 CDT)
- NAMD with pbs script k.manzoorolajdad (Sun Aug 25 2013 - 09:36:58 CDT)
- problem with using patch LINK ... rasti (Sun Aug 25 2013 - 07:54:50 CDT)
- problem with using patch LINK ... rasti (Sat Aug 24 2013 - 07:50:16 CDT)
- Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA David Brandon (Fri Aug 23 2013 - 14:07:30 CDT)
- Implementation of ELASTIC NETWORK model in NAMD Vibhor Agrawal (Fri Aug 23 2013 - 10:57:17 CDT)
- obtaining cellBasisVectors from SCALE entries in the PDB file Jose Borreguero (Fri Aug 23 2013 - 10:31:28 CDT)
- questions regarding the source code in NAMD Asaf Farhi (Fri Aug 23 2013 - 06:12:59 CDT)
- understanding the lone pair section of psf files Frank Haverkort (Thu Aug 22 2013 - 10:44:17 CDT)
- remd restart Francesco Pietra (Thu Aug 22 2013 - 06:00:40 CDT)
- AW: AW: hi every body, Norman Geist (Thu Aug 22 2013 - 04:39:38 CDT)
- hi every body, rasti (Wed Aug 21 2013 - 17:19:05 CDT)
- Low global exclusion count on parallel tempering, not on MD Francesco Pietra (Wed Aug 21 2013 - 10:45:05 CDT)
- Defining colvars groups of atoms for ABF Maria Pikoula (Wed Aug 21 2013 - 04:13:57 CDT)
- Nvidia GPUs Thomas Albers (Tue Aug 20 2013 - 13:27:28 CDT)
- General query re: symmetry restraints Tristan Croll (Mon Aug 19 2013 - 22:33:02 CDT)
- catdcd error Revthi Sanker (Mon Aug 19 2013 - 07:15:04 CDT)
- apoa1 slow Phase 1 Jan Fredin (Thu Aug 15 2013 - 16:25:11 CDT)
- Normal Mode Analysis in NAMD Vibhor Agrawal (Thu Aug 15 2013 - 09:06:09 CDT)
- RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Thu Aug 15 2013 - 01:05:32 CDT)
- Re: CHARMM-c36, glycans and RATTLE Sunhwan Jo (Thu Aug 15 2013 - 01:09:40 CDT)
- RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Thu Aug 15 2013 - 01:23:50 CDT)
- RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Thu Aug 15 2013 - 04:13:59 CDT)
- Re: CHARMM-c36, glycans and RATTLE Sunhwan Jo (Thu Aug 15 2013 - 09:31:26 CDT)
- RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Fri Aug 16 2013 - 05:51:17 CDT)
- RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Fri Aug 16 2013 - 06:26:33 CDT)
- RE: CHARMM-c36, glycans and RATTLE Tristan Croll (Thu Aug 15 2013 - 01:23:50 CDT)
- Re: CHARMM-c36, glycans and RATTLE Sunhwan Jo (Thu Aug 15 2013 - 01:09:40 CDT)
- CHARMM-c36, glycans and RATTLE Tristan Croll (Wed Aug 14 2013 - 23:50:36 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Wed Aug 14 2013 - 17:09:56 CDT)
- AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Norman Geist (Thu Aug 15 2013 - 00:50:54 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Thu Aug 15 2013 - 01:53:22 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Paul Rigor (Thu Aug 15 2013 - 11:15:40 CDT)
- Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Thu Aug 15 2013 - 17:26:07 CDT)
- All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. Lucas (Tue Aug 13 2013 - 13:06:06 CDT)
- Non-equilibrium effects in ABF runs Matthew Ralph Adendorff (Tue Aug 13 2013 - 11:38:57 CDT)
- Incorporating some ions with specific location Stephan Grein (Tue Aug 13 2013 - 03:04:10 CDT)
- unsubscribe Hamze Rahimi (Mon Aug 12 2013 - 23:37:05 CDT)
- problem with restraining a dihedral angle Sijia (Scarlett) Dong (Mon Aug 12 2013 - 18:55:33 CDT)
- unsuscribe Cat Chenal (Mon Aug 12 2013 - 10:01:42 CDT)
- colvars and parallel-tempering with namd2.10 Francesco Pietra (Mon Aug 12 2013 - 09:54:25 CDT)
- Re: colvars and parallel-tempering with namd2.10 Sunhwan Jo (Mon Aug 12 2013 - 10:29:23 CDT)
- Re: colvars and parallel-tempering with namd2.10 Jérôme Hénin (Tue Aug 13 2013 - 09:51:30 CDT)
- Re: colvars and parallel-tempering with namd2.10 Sunhwan Jo (Tue Aug 13 2013 - 10:29:08 CDT)
- Re: colvars and parallel-tempering with namd2.10 Giacomo Fiorin (Tue Aug 13 2013 - 10:51:39 CDT)
- Re: colvars and parallel-tempering with namd2.10 Sunhwan Jo (Tue Aug 13 2013 - 11:17:44 CDT)
- Re: colvars and parallel-tempering with namd2.10 Giacomo Fiorin (Tue Aug 13 2013 - 12:00:45 CDT)
- Re: colvars and parallel-tempering with namd2.10 Axel Kohlmeyer (Tue Aug 13 2013 - 12:07:52 CDT)
- Re: colvars and parallel-tempering with namd2.10 Francesco Pietra (Sat Aug 17 2013 - 11:51:08 CDT)
- Re: colvars and parallel-tempering with namd2.10 Giacomo Fiorin (Sun Aug 18 2013 - 10:40:59 CDT)
- Re: colvars and parallel-tempering with namd2.10 Francesco Pietra (Mon Aug 19 2013 - 01:41:12 CDT)
- Re: colvars and parallel-tempering with namd2.10 Francesco Pietra (Mon Aug 19 2013 - 01:46:36 CDT)
- Re: colvars and parallel-tempering with namd2.10 Francesco Pietra (Fri Aug 23 2013 - 02:57:53 CDT)
- Re: colvars and parallel-tempering with namd2.10 Jérôme Hénin (Tue Aug 13 2013 - 09:51:30 CDT)
- Re: colvars and parallel-tempering with namd2.10 Sunhwan Jo (Mon Aug 12 2013 - 10:29:23 CDT)
- Re: AW: vmd-l: Occupancy maps Axel Kohlmeyer (Mon Aug 12 2013 - 01:14:52 CDT)
- AW: vmd-l: Occupancy maps Norman Geist (Mon Aug 12 2013 - 00:14:36 CDT)
- ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 Uday Midya (Sun Aug 11 2013 - 07:09:05 CDT)
- ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 Uday Midya (Sun Aug 11 2013 - 02:19:47 CDT)
- replica exchange parallel tempering BlueGene/Q Francesco Pietra (Sun Aug 11 2013 - 01:15:04 CDT)
- Question about loading velocity files on VMD Ganesh Kamath (Fri Aug 09 2013 - 10:01:17 CDT)
- Compile NAMD2.9 on Xeon Phi Devang Jane (Thu Aug 08 2013 - 13:15:38 CDT)
- unsuscribe Cat Chenal (Thu Aug 08 2013 - 12:20:16 CDT)
- NBFIX 1-4 scaling term ignored for CHARMM format parameters Sunhwan Jo (Wed Aug 07 2013 - 15:21:33 CDT)
- AW: Colvar cannot be ran on supercomputer newton Norman Geist (Wed Aug 07 2013 - 02:18:25 CDT)
- Evaluate energy of "protein + two closest ions" Xiaodong Pang (Tue Aug 06 2013 - 17:25:45 CDT)
- Colvar cannot be ran on supercomputer newton Tian Li (Tue Aug 06 2013 - 08:35:44 CDT)
- namd/bluegeneQ Francesco Pietra (Mon Aug 05 2013 - 12:48:07 CDT)
- Special constraint on MD simulation Carlos Navarrro Retamal (Mon Aug 05 2013 - 04:13:33 CDT)
- Problem of ATP mutated to dATP in solution using FEP method dbaogen (Mon Aug 05 2013 - 02:14:24 CDT)
- Question about converting velocities DCD to ascii plain text Joe Janicki (Sat Aug 03 2013 - 13:24:11 CDT)
- BKS potential nadia salami (Sat Aug 03 2013 - 12:54:40 CDT)
- Annealing of SiO nadia salami (Fri Aug 02 2013 - 23:07:58 CDT)
- RMSD calculation Vibhor Agrawal (Fri Aug 02 2013 - 21:44:47 CDT)
- Changing NAMD XY restraint Beaven, Andrew (Fri Aug 02 2013 - 16:29:05 CDT)
- pbc wrap Tugba Nogay (Fri Aug 02 2013 - 14:52:23 CDT)
- Colvars RMSD syntax with a moving reference frame Mayne, Christopher G (Fri Aug 02 2013 - 10:14:47 CDT)
- running namd in parallel Revthi Sanker (Thu Aug 01 2013 - 23:39:02 CDT)
- Help regarding PMF with SMD Katherine Parra Pulido (Thu Aug 01 2013 - 10:06:03 CDT)
- setting the polarizabilities for the Drude force field Frank Haverkort (Thu Aug 01 2013 - 06:48:59 CDT)
- Center of mass motion included in Temperature? Norman Geist (Thu Aug 01 2013 - 04:53:34 CDT)
- bugs in NAMD_TI script? shunzhou Wan (Wed Jul 31 2013 - 11:57:28 CDT)
- replica exchange and colvars Francesco Pietra (Wed Jul 31 2013 - 02:34:05 CDT)
- Replica exchange, colvars & harmonic restraints Andrei Tudor (Mon Jul 29 2013 - 13:36:22 CDT)
- analyzing NAMD trajectory with NAMD Energy Markus Dahlgren (Mon Jul 29 2013 - 10:13:42 CDT)
- Reg loadtotalforces. aravind chandrasekaran (Mon Jul 29 2013 - 06:24:31 CDT)
- thernodynamics integration in NAMD sunyeping_at_aliyun.com (Sat Jul 27 2013 - 11:41:09 CDT)
- Water density in the solvate plugin David Cohen-Tanugi (Fri Jul 26 2013 - 10:50:20 CDT)
- Re: Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction ....... Villalain Boullon, Jose (Thu Jul 25 2013 - 05:52:05 CDT)
- vdwForceSwitching and PME Adrian (Wed Jul 24 2013 - 22:48:20 CDT)
- pmf command Pedro Swagger (Wed Jul 24 2013 - 15:30:40 CDT)
- Minimisation issue venkata agasthya (Wed Jul 24 2013 - 15:12:06 CDT)
- Geometric center of a residue over time Sindu (Wed Jul 24 2013 - 05:33:32 CDT)
- Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Villalain Boullon, Jose (Wed Jul 24 2013 - 03:37:20 CDT)
- Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Kenno Vanommeslaeghe (Wed Jul 24 2013 - 11:07:42 CDT)
- Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Aron Broom (Wed Jul 24 2013 - 12:03:47 CDT)
- Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Niklaus Johner (Wed Jul 24 2013 - 08:45:19 CDT)
- Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... Kenno Vanommeslaeghe (Wed Jul 24 2013 - 11:07:42 CDT)
- vacuum minimisation-reg Revthi Sanker (Wed Jul 24 2013 - 02:37:12 CDT)
- FullDirect Electrostatics Adrian (Tue Jul 23 2013 - 09:51:53 CDT)
- Restart files are empy Alessandro Mascioni (Sun Jul 21 2013 - 12:24:23 CDT)
- FEP simulation on membrane protein Kapil jain (Sun Jul 21 2013 - 22:37:44 CDT)
- CatDCD windows binaries Axel Kohlmeyer (Fri Jul 19 2013 - 04:56:00 CDT)
- Unsubscribe Priyanka Purkayastha (Fri Jul 19 2013 - 01:02:33 CDT)
- Unsubscribe (Thu Jul 18 2013 - 18:42:07 CDT)
- Minimization/Equilibrium problem, atoms moving too fast Adrian (Thu Jul 18 2013 - 15:28:10 CDT)
- Re: Minimization/Equilibrium problem, atoms moving too fast Aron Broom (Thu Jul 18 2013 - 16:12:32 CDT)
- RE: Minimization/Equilibrium problem, atoms moving too fast adrian palacios (Thu Jul 18 2013 - 19:58:47 CDT)
- Re: Minimization/Equilibrium problem, atoms moving too fast Aron Broom (Thu Jul 18 2013 - 20:05:53 CDT)
- RE: Minimization/Equilibrium problem, atoms moving too fast adrian palacios (Thu Jul 18 2013 - 20:12:05 CDT)
- Re: Minimization/Equilibrium problem, atoms moving too fast Aron Broom (Thu Jul 18 2013 - 20:15:47 CDT)
- RE: Minimization/Equilibrium problem, atoms moving too fast Tristan Croll (Thu Jul 18 2013 - 20:23:35 CDT)
- RE: Minimization/Equilibrium problem, atoms moving too fast adrian palacios (Thu Jul 18 2013 - 20:32:57 CDT)
- RE: Minimization/Equilibrium problem, atoms moving too fast Tristan Croll (Thu Jul 18 2013 - 21:08:02 CDT)
- RE: Minimization/Equilibrium problem, atoms moving too fast adrian palacios (Thu Jul 18 2013 - 19:58:47 CDT)
- Re: Minimization/Equilibrium problem, atoms moving too fast Aron Broom (Thu Jul 18 2013 - 16:12:32 CDT)
- Implicit water with explicit ions Adrian (Thu Jul 18 2013 - 13:10:49 CDT)
- Minimisation problem venkata agasthya (Thu Jul 18 2013 - 12:42:08 CDT)
- FW: water layer in membrane protein modeling Kong, Ren (Thu Jul 18 2013 - 09:24:06 CDT)
- question about NVE ensamble Hasan haska (Thu Jul 18 2013 - 01:56:18 CDT)
- Preventing rotation of a protein Thomas Albers (Wed Jul 17 2013 - 21:18:16 CDT)
- Re: Preventing rotation of a protein Giacomo Fiorin (Wed Jul 17 2013 - 21:31:15 CDT)
- Re: Preventing rotation of a protein Peter Jones (Wed Jul 17 2013 - 22:06:10 CDT)
- Retaining conformation Riley Workman (Wed Jul 17 2013 - 14:52:44 CDT)
- Simulation at different time-steps Mare Libero (Tue Jul 16 2013 - 22:02:58 CDT)
- Problem regarding the big DCD file Vibhor Agrawal (Tue Jul 16 2013 - 14:07:40 CDT)
- Re: Problem regarding the big DCD file Axel Kohlmeyer (Tue Jul 16 2013 - 14:12:37 CDT)
- Re: Problem regarding the big DCD file Vibhor Agrawal (Thu Jul 18 2013 - 11:42:23 CDT)
- Re: Problem regarding the big DCD file Ajasja Ljubetič (Thu Jul 18 2013 - 12:08:27 CDT)
- Re: Problem regarding the big DCD file Kenno Vanommeslaeghe (Thu Jul 18 2013 - 12:36:34 CDT)
- Re: Problem regarding the big DCD file Axel Kohlmeyer (Thu Jul 18 2013 - 18:10:51 CDT)
- Re: Problem regarding the big DCD file Axel Kohlmeyer (Fri Jul 19 2013 - 05:03:22 CDT)
- Re: Problem regarding the big DCD file Axel Kohlmeyer (Thu Jul 18 2013 - 12:37:28 CDT)
- Re: Problem regarding the big DCD file Vibhor Agrawal (Thu Jul 18 2013 - 11:42:23 CDT)
- Re: Problem regarding the big DCD file Atanu Maity (Fri Jul 19 2013 - 01:05:08 CDT)
- Re: Problem regarding the big DCD file Nicholas M Glykos (Sat Jul 20 2013 - 07:29:04 CDT)
- Re: Problem regarding the big DCD file Axel Kohlmeyer (Tue Jul 16 2013 - 14:12:37 CDT)
- run NAMD command in GPU Adrian (Tue Jul 16 2013 - 14:05:17 CDT)
- Convergence of Sampling and Deciding on Simulation Length Aditya Ranganathan (Tue Jul 16 2013 - 06:08:15 CDT)
- NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Tue Jul 16 2013 - 00:14:36 CDT)
- Re: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Vibhor Agrawal (Tue Jul 16 2013 - 00:56:33 CDT)
- RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Tue Jul 16 2013 - 01:05:19 CDT)
- RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Vibhor Agrawal (Tue Jul 16 2013 - 01:18:44 CDT)
- Re: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Kenno Vanommeslaeghe (Tue Jul 16 2013 - 11:29:09 CDT)
- RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Wed Jul 17 2013 - 19:02:25 CDT)
- RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Tue Jul 16 2013 - 00:59:49 CDT)
- RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Tue Jul 16 2013 - 02:40:08 CDT)
- RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Tristan Croll (Tue Jul 16 2013 - 01:05:19 CDT)
- Re: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart Vibhor Agrawal (Tue Jul 16 2013 - 00:56:33 CDT)
- ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' Jose Borreguero (Mon Jul 15 2013 - 16:19:31 CDT)
- Resample trajectory files Vibhor Agrawal (Mon Jul 15 2013 - 15:52:58 CDT)
- Umbrella Sampling Replica Exchange Simulations TREIKALIS Antons (Sat Jul 13 2013 - 11:24:12 CDT)
- pressure profile calculation problem P.-L. Chau (Fri Jul 12 2013 - 10:47:05 CDT)
- Coarse grain parameter files JAGODINSKY, JUSTIN (Fri Jul 12 2013 - 09:47:50 CDT)
- (no subject) JAGODINSKY, JUSTIN (Fri Jul 12 2013 - 09:12:51 CDT)
- Free Energy using atomic coordinates as CVs Teerapong Pirojsirikul (Thu Jul 11 2013 - 17:59:31 CDT)
- dcd to pdb for trajectory analysis oguz gurbulak (Thu Jul 11 2013 - 07:40:11 CDT)
- Re: NAMD pressureProfile command P.-L. Chau (Thu Jul 11 2013 - 04:05:45 CDT)
- ABF subdividing the reaction coordinate Pedro Swagger (Wed Jul 10 2013 - 16:00:37 CDT)
- local pressure profile for water liquid-vapor Mashayak, Sikandar Yusufoddin (Wed Jul 10 2013 - 10:43:21 CDT)
- Regarding Production Run in NAMD amit banerjee (Wed Jul 10 2013 - 00:14:34 CDT)
- use of colvars to restrain the absolute positions of all atoms in a large system Abir Ganguly (Tue Jul 09 2013 - 17:01:15 CDT)
- Re: use of colvars to restrain the absolute positions of all atoms in a large system Giacomo Fiorin (Tue Jul 09 2013 - 17:16:19 CDT)
- Re: use of colvars to restrain the absolute positions of all atoms in a large system Aron Broom (Tue Jul 09 2013 - 17:18:35 CDT)
- gromacs to NAMD Peterson J (Tue Jul 09 2013 - 14:55:46 CDT)
- about interaction between protein and its image in namd simulation Liqun Zhang (Tue Jul 09 2013 - 12:16:37 CDT)
- minimization does not converge Revthi Sanker (Mon Jul 08 2013 - 11:43:27 CDT)
- REMD history file and question Martin, Erik W (Mon Jul 08 2013 - 10:23:00 CDT)
- Replica exchange on single physical node Francesco Pietra (Sat Jul 06 2013 - 09:19:42 CDT)
- Launching namd GPU-MPI vs GPU-binary Francesco Pietra (Sat Jul 06 2013 - 02:54:00 CDT)
- Drude polarizable force field Hadi (Sat Jul 06 2013 - 02:06:15 CDT)
- NAMD pressureProfile command P.-L. Chau (Thu Jul 04 2013 - 16:52:00 CDT)
- pressure profile calculations P.-L. Chau (Thu Jul 04 2013 - 16:43:32 CDT)
- REMD-GPU Francesco Pietra (Thu Jul 04 2013 - 02:36:59 CDT)
- Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Vibhor Agrawal (Thu Jul 04 2013 - 02:31:27 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Kenno Vanommeslaeghe (Thu Jul 04 2013 - 19:49:35 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Vibhor Agrawal (Thu Jul 04 2013 - 21:28:54 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Kenno Vanommeslaeghe (Fri Jul 05 2013 - 12:21:20 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Sebastin Gutirrez (Fri Jul 05 2013 - 14:03:08 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Rajan Vatassery (Fri Jul 05 2013 - 14:16:59 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Vibhor Agrawal (Fri Jul 05 2013 - 14:44:31 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Kenno Vanommeslaeghe (Fri Jul 05 2013 - 15:47:58 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Kenno Vanommeslaeghe (Fri Jul 05 2013 - 16:44:06 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Vibhor Agrawal (Thu Jul 04 2013 - 21:28:54 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Kenno Vanommeslaeghe (Thu Jul 04 2013 - 19:49:35 CDT)
- NAMD configuration file Hasan haska (Wed Jul 03 2013 - 17:12:22 CDT)
- Martini 2.2 and ElNeDyn in NAMD XAvier Periole (Wed Jul 03 2013 - 12:29:16 CDT)
- Simulation of Protein with Ions Stephan Grein (Wed Jul 03 2013 - 02:47:03 CDT)
- Uncovering the Elusive HIV Capsid with Kepler GPUs Running NAMD & VMD Devang Sachdev (Tue Jul 02 2013 - 13:25:57 CDT)
- Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Tue Jul 02 2013 - 12:33:45 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Aron Broom (Tue Jul 02 2013 - 12:45:17 CDT)
- RE: Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Tue Jul 02 2013 - 12:57:14 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Aron Broom (Tue Jul 02 2013 - 13:10:49 CDT)
- RE: Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Wed Jul 03 2013 - 05:06:46 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Aron Broom (Wed Jul 03 2013 - 06:12:30 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Axel Kohlmeyer (Wed Jul 03 2013 - 06:19:36 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Wed Jul 03 2013 - 07:28:20 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Aron Broom (Wed Jul 03 2013 - 07:40:54 CDT)
- RE: Slow vacuum/GBIS simulations (time to completion keeps increasing) Ole Juul Andersen (Tue Jul 02 2013 - 12:57:14 CDT)
- Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) Aron Broom (Tue Jul 02 2013 - 12:45:17 CDT)
- Restarting simulation James Starlight (Tue Jul 02 2013 - 00:45:37 CDT)
- FATAL ERROR Unknown parameter in charmm parameter file Cat Chenal (Mon Jul 01 2013 - 13:19:27 CDT)
- bks potential sheida bagherzadeh (Mon Jul 01 2013 - 02:15:13 CDT)
- Topology and parameters for nitrate and nitrite ion amin_at_imtech.res.in (Sat Jun 29 2013 - 12:51:39 CDT)
- Re: Topology and parameters for nitrate and nitrite ion flavio seixas (Sun Jun 30 2013 - 14:02:06 CDT)
- Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Sun Jun 30 2013 - 19:17:40 CDT)
- Re: Topology and parameters for nitrate and nitrite ion amin_at_imtech.res.in (Sun Jun 30 2013 - 23:00:29 CDT)
- Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Sun Jun 30 2013 - 23:47:57 CDT)
- Re: Topology and parameters for nitrate and nitrite ion amin_at_imtech.res.in (Mon Jul 01 2013 - 02:39:44 CDT)
- Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Mon Jul 01 2013 - 02:52:28 CDT)
- Re: Topology and parameters for nitrate and nitrite ion Massimiliano Porrini (Mon Jul 01 2013 - 06:41:12 CDT)
- Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Mon Jul 01 2013 - 14:37:51 CDT)
- Re: Topology and parameters for nitrate and nitrite ion amin_at_imtech.res.in (Tue Jul 02 2013 - 09:01:19 CDT)
- Re: Topology and parameters for nitrate and nitrite ion Kenno Vanommeslaeghe (Sun Jun 30 2013 - 19:17:40 CDT)
- Re: Topology and parameters for nitrate and nitrite ion flavio seixas (Sun Jun 30 2013 - 14:02:06 CDT)
- unsubscribe Patricia Campbell (Sat Jun 29 2013 - 00:21:31 CDT)
- unsubscribe Patricia Campbell (Fri Jun 28 2013 - 15:39:45 CDT)
- Simulation in NPT ensemble James Starlight (Fri Jun 28 2013 - 15:28:40 CDT)
- Reaction field treatment Neelanjana Sengupta (Fri Jun 28 2013 - 01:24:08 CDT)
- sn-1 tail order parameter Mihaela Drenscko (Thu Jun 27 2013 - 16:33:11 CDT)
- analysis of simulation output James Starlight (Thu Jun 27 2013 - 13:25:38 CDT)
- Fwd: Troubles to converge while running bidirectional FEP GALLY Jose Manuel (Thu Jun 27 2013 - 02:12:24 CDT)
- zinc finger with ASP FIDAN SUMBUL (Thu Jun 27 2013 - 09:47:22 CDT)
- Tail order parameter Mihaela Drenscko (Wed Jun 26 2013 - 19:47:11 CDT)
- Problem during TMD Peterson J (Wed Jun 26 2013 - 14:59:50 CDT)
- Solvent Box Jon Kusner (Wed Jun 26 2013 - 12:15:31 CDT)
- About NAMD Dennis Lam (Tue Jun 25 2013 - 11:20:15 CDT)
- Simulation in Collective sub-space James Starlight (Tue Jun 25 2013 - 07:52:41 CDT)
- subscribe Axel Kohlmeyer (Mon Jun 24 2013 - 15:29:29 CDT)
- unsubscribe (Mon Jun 24 2013 - 15:26:49 CDT)
- NAMD exiting on startup phase Bryan Roessler (Mon Jun 24 2013 - 09:52:36 CDT)
- Parameters for prosthetic groups James Starlight (Mon Jun 24 2013 - 06:56:03 CDT)
- Protein-ligand simulation James Starlight (Mon Jun 24 2013 - 06:51:46 CDT)
- Re: Protein-ligand simulation Chris Chipot (Mon Jun 24 2013 - 07:02:24 CDT)
- Re: Protein-ligand simulation James Starlight (Mon Jun 24 2013 - 13:15:51 CDT)
- Re: Protein-ligand simulation Kenno Vanommeslaeghe (Mon Jun 24 2013 - 21:51:34 CDT)
- Re: Protein-ligand simulation James Starlight (Tue Jun 25 2013 - 00:58:51 CDT)
- Re: Protein-ligand simulation Kenno Vanommeslaeghe (Tue Jun 25 2013 - 13:09:27 CDT)
- Re: Protein-ligand simulation James Starlight (Tue Jun 25 2013 - 13:39:02 CDT)
- Re: Protein-ligand simulation Kenno Vanommeslaeghe (Tue Jun 25 2013 - 14:17:17 CDT)
- Re: Protein-ligand simulation James Starlight (Wed Jun 26 2013 - 00:56:38 CDT)
- Re: Protein-ligand simulation Kenno Vanommeslaeghe (Wed Jun 26 2013 - 14:07:09 CDT)
- Re: Protein-ligand simulation JC Gumbart (Wed Jun 26 2013 - 15:21:09 CDT)
- Re: Protein-ligand simulation James Starlight (Thu Jun 27 2013 - 00:16:25 CDT)
- Re: Protein-ligand simulation Kenno Vanommeslaeghe (Thu Jun 27 2013 - 10:50:25 CDT)
- Re: Protein-ligand simulation James Starlight (Thu Jun 27 2013 - 13:18:59 CDT)
- Re: Protein-ligand simulation JC Gumbart (Thu Jun 27 2013 - 18:40:15 CDT)
- Re: Protein-ligand simulation James Starlight (Thu Jun 27 2013 - 23:35:21 CDT)
- Re: Protein-ligand simulation James Starlight (Fri Jun 28 2013 - 04:21:45 CDT)
- Re: Protein-ligand simulation James Starlight (Fri Jun 28 2013 - 14:55:55 CDT)
- Re: Protein-ligand simulation James Starlight (Sat Jun 29 2013 - 00:02:32 CDT)
- Re: Protein-ligand simulation Chris Chipot (Mon Jun 24 2013 - 07:02:24 CDT)
- unsubscribe AYSEGUL TURUPCU (Mon Jun 24 2013 - 04:22:27 CDT)
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- unsubscribe Achani K. Yatawara (Sun Jun 23 2013 - 11:39:20 CDT)
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- Failure with compilation namd2.9-cuda_plumed1.3_recon Francesco Pietra (Sat Jun 22 2013 - 12:15:26 CDT)
- unsubscribe Aysegul Turupcu (Sat Jun 22 2013 - 11:07:04 CDT)
- Atom numbering Felipe Merino (Sat Jun 22 2013 - 05:34:53 CDT)
- About Fiorin-Klein-Henin recent colvar examples Francesco Pietra (Fri Jun 21 2013 - 03:50:35 CDT)
- Insertion of GPCR in the POPC Bilayer Vibhor Agrawal (Thu Jun 20 2013 - 15:29:20 CDT)
- Free Energy Calculation Question Kasra Fattah (Thu Jun 20 2013 - 15:28:28 CDT)
- (no subject) Mihaela Drenscko (Thu Jun 20 2013 - 10:14:07 CDT)
- Re: C++ API Aron Broom (Thu Jun 20 2013 - 01:12:19 CDT)
- Using CosntantArea in membrane simulation Peterson J (Wed Jun 19 2013 - 16:53:06 CDT)
- C++ API Stephan Grein (Wed Jun 19 2013 - 08:20:11 CDT)
- Basic question about impropers Wenhao Liu (Tue Jun 18 2013 - 18:30:12 CDT)
- utilizing mic coprocs on Stampede Edward Lyman (Tue Jun 18 2013 - 14:46:47 CDT)
- collective variables new paper Giacomo Fiorin (Mon Jun 17 2013 - 17:48:11 CDT)
- unsubscribe from mailing list Maria Kopp (Mon Jun 17 2013 - 10:24:13 CDT)
- Overestimated PMF Felipe Merino (Mon Jun 17 2013 - 09:43:07 CDT)
- namdenergy and namd Dr. Eddie (Mon Jun 17 2013 - 08:43:44 CDT)
- About Namd Installation Vidhya Sankar (Sun Jun 16 2013 - 00:14:04 CDT)
- Error in PSF gen Vibhor Agrawal (Sat Jun 15 2013 - 21:18:13 CDT)
- query on constraintScaling in NAMD Peterson J (Fri Jun 14 2013 - 15:47:25 CDT)
- Lipid bilayer tears apart during simulation Peterson J (Fri Jun 14 2013 - 15:14:02 CDT)
- how to apply force SMD method on an anisotropic geometry Anurag Sharma (Wed Jun 12 2013 - 15:39:34 CDT)
- AW: how to apply force SMD method on an anisotropic geometry Norman Geist (Thu Jun 13 2013 - 01:56:48 CDT)
- FATAL ERROR: Bad global bond count! Peterson J (Wed Jun 12 2013 - 11:01:23 CDT)
- Error while running the infiniband version. Shubhra Ghosh Dastidar (Wed Jun 12 2013 - 07:52:36 CDT)
- How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Wed Jun 12 2013 - 03:05:36 CDT)
- Re: How to remove center of mass translation of macromolecule Jérôme Hénin (Wed Jun 12 2013 - 04:00:48 CDT)
- Re: How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Thu Jun 13 2013 - 17:38:07 CDT)
- Re: How to remove center of mass translation of macromolecule Giacomo Fiorin (Thu Jun 13 2013 - 18:17:00 CDT)
- Re: How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Thu Jun 13 2013 - 19:40:23 CDT)
- Re: How to remove center of mass translation of macromolecule Giacomo Fiorin (Thu Jun 13 2013 - 20:09:49 CDT)
- Re: How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Thu Jun 13 2013 - 20:56:29 CDT)
- Re: How to remove center of mass translation of macromolecule Jérôme Hénin (Mon Jun 17 2013 - 08:51:20 CDT)
- Re: How to remove center of mass translation of macromolecule Teerapong Pirojsirikul (Thu Jun 13 2013 - 17:38:07 CDT)
- Re: How to remove center of mass translation of macromolecule Jérôme Hénin (Wed Jun 12 2013 - 04:00:48 CDT)
- 2014 Biophysics Workshop In Aspen Colorado MARK PLUMMER (Tue Jun 11 2013 - 20:39:57 CDT)
- Workshop on GPU Programming for Molecular Modeling, August 2-4, 2013, in Urbana, Illinois David Brandon (Tue Jun 11 2013 - 17:41:43 CDT)
- Re: Nonstandard ligand-DNA system Saaz Sakrikar (Tue Jun 11 2013 - 16:47:13 CDT)
- abf_integrate Kasra Fattah (Tue Jun 11 2013 - 14:54:34 CDT)
- multiple vectors in SMD yp sun (Mon Jun 10 2013 - 22:35:50 CDT)
- Two dimensional ABF Nadeem A. Vellore (Tue Jun 11 2013 - 11:33:02 CDT)
- Re: NAMD related Anilkumar Naik (Tue Jun 11 2013 - 00:16:33 CDT)
- protein schematic representaton francesco oteri (Mon Jun 10 2013 - 13:23:17 CDT)
- ABF simulations with barriers (adsorption) Zachary Ulissi (Mon Jun 10 2013 - 12:26:49 CDT)
- NAMD related Anilkumar Naik (Mon Jun 10 2013 - 06:35:27 CDT)
- PSF files and long atom name Reza (Sun Jun 09 2013 - 14:40:17 CDT)
- DCD writing error on cluster Rehan Zafar (Sun Jun 09 2013 - 14:01:44 CDT)
- Shift (or offset) of the lipid bilayer along Z axis during equilibration 翁林岽 (Fri Jun 07 2013 - 20:36:44 CDT)
- Problem regarding the psfgen Vibhor Agrawal (Fri Jun 07 2013 - 14:55:28 CDT)
- New: Colvars project page Jérôme Hénin (Fri Jun 07 2013 - 11:43:42 CDT)
- ABF with the RMSD colvar George Patargias (Fri Jun 07 2013 - 08:51:22 CDT)
- Re: ABF with the RMSD colvar Jérôme Hénin (Fri Jun 07 2013 - 09:07:57 CDT)
- Re: ABF with the RMSD colvar George Patargias (Fri Jun 07 2013 - 09:43:45 CDT)
- Re: ABF with the RMSD colvar George Patargias (Wed Apr 16 2014 - 05:14:05 CDT)
- Re: ABF with the RMSD colvar George Patargias (Fri Apr 25 2014 - 05:20:31 CDT)
- Re: ABF with the RMSD colvar George Patargias (Wed Sep 17 2014 - 06:43:44 CDT)
- Re: ABF with the RMSD colvar George Patargias (Fri Sep 19 2014 - 10:12:40 CDT)
- Re: ABF with the RMSD colvar George Patargias (Mon Sep 22 2014 - 06:21:45 CDT)
- Re: ABF with the RMSD colvar Jérôme Hénin (Fri Jun 07 2013 - 09:07:57 CDT)
- Nucleic acid-small molecule system Saaz Sakrikar (Fri Jun 07 2013 - 01:45:49 CDT)
- Fwd: NAMD tcouple atoms moving too fast Tao Qu (Thu Jun 06 2013 - 15:04:56 CDT)
- Any alternative to colvars for minimization? Francesco Pietra (Thu Jun 06 2013 - 01:36:40 CDT)
- What does "outputSystemForce" output? Ivan Mikhaylov (Wed Jun 05 2013 - 16:28:48 CDT)
- how to do a vacuum minimization without electrostatics and periodic boundary conditions? Jose Borreguero (Wed Jun 05 2013 - 10:20:27 CDT)
- ABF zCoord analog in colvars ? Arturas (Wed Jun 05 2013 - 08:41:15 CDT)
- Re: fixed atom/Constraint failure in RATTLE algorithm/ MEHRAN MB (Tue Jun 04 2013 - 10:26:47 CDT)
- First meeting with NAMD James Starlight (Tue Jun 04 2013 - 09:46:54 CDT)
- AW: fixed atom/Constraint failure in RATTLE algorithm/ Norman Geist (Tue Jun 04 2013 - 02:01:10 CDT)
- First meeting with NAMD James Starlight (Mon Jun 03 2013 - 09:08:58 CDT)
- Re: First meeting with NAMD Giacomo Fiorin (Mon Jun 03 2013 - 09:16:05 CDT)
- Re: First meeting with NAMD James Starlight (Mon Jun 03 2013 - 13:08:01 CDT)
- Re: First meeting with NAMD James Starlight (Tue Jun 04 2013 - 03:13:10 CDT)
- Re: First meeting with NAMD James Starlight (Tue Jun 04 2013 - 08:25:06 CDT)
- Re: First meeting with NAMD Branko (Tue Jun 04 2013 - 08:46:07 CDT)
- Re: First meeting with NAMD Ajasja Ljubetič (Tue Jun 04 2013 - 08:45:44 CDT)
- Re: First meeting with NAMD James Starlight (Tue Jun 04 2013 - 09:33:19 CDT)
- Re: First meeting with NAMD Giacomo Fiorin (Tue Jun 04 2013 - 09:38:15 CDT)
- Re: First meeting with NAMD James Starlight (Thu Jun 06 2013 - 06:31:42 CDT)
- Re: First meeting with NAMD James Starlight (Fri Jun 07 2013 - 00:13:55 CDT)
- Re: First meeting with NAMD James Starlight (Fri Sep 13 2013 - 08:41:12 CDT)
- AW: First meeting with NAMD Norman Geist (Tue Jun 04 2013 - 02:16:18 CDT)
- Re: First meeting with NAMD Giacomo Fiorin (Mon Jun 03 2013 - 09:16:05 CDT)
- Invitation to connect on LinkedIn Gabriel Jara (Mon Jun 03 2013 - 08:46:22 CDT)
- Does MOLLY really retain bond motion for water? Francesco Pietra (Sun Jun 02 2013 - 08:45:04 CDT)
- fixed atom/Constraint failure in RATTLE algorithm/ MEHRAN MB (Fri May 31 2013 - 11:33:03 CDT)
- Fwd: Pressure in NPT ensamble Cobalto Tetracloruro (Fri May 31 2013 - 11:15:49 CDT)
- A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP Yize Hu (Fri May 31 2013 - 10:20:52 CDT)
- QM-MM Francesco Pietra (Fri May 31 2013 - 01:47:47 CDT)
- AW: NAMD/VMD installation on Linux Clusters with InfiniBand Norman Geist (Thu May 30 2013 - 05:14:55 CDT)
- Re: problem with runiing namd through infiniband Shubhra Ghosh Dastidar (Wed May 29 2013 - 05:13:10 CDT)
- Re: namd with ff99sb Francesco Pietra (Wed May 29 2013 - 01:27:32 CDT)
- Flags for TIP3 water with NAMD/AMBER FF Francesco Pietra (Tue May 28 2013 - 10:46:01 CDT)
- problem with runiing namd through infiniband Shubhra Ghosh Dastidar (Tue May 28 2013 - 02:15:15 CDT)
- Free energy calculations karthik kumar (Mon May 27 2013 - 07:47:33 CDT)
- Suggestions while building a GPU-machine (CUDA) for NAMD use! Aditya Ranganathan (Mon May 27 2013 - 03:14:33 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Axel Kohlmeyer (Mon May 27 2013 - 03:57:15 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Aditya Ranganathan (Mon May 27 2013 - 04:35:32 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Francesco Pietra (Tue May 28 2013 - 00:55:38 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Aditya Ranganathan (Tue May 28 2013 - 02:23:39 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Francesco Pietra (Tue May 28 2013 - 02:54:47 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Aditya Ranganathan (Tue May 28 2013 - 04:04:18 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Axel Kohlmeyer (Tue May 28 2013 - 04:40:00 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Aron Broom (Tue May 28 2013 - 08:26:01 CDT)
- AW: Suggestions while building a GPU-machine (CUDA) for NAMD use! Norman Geist (Wed May 29 2013 - 00:27:44 CDT)
- Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! Axel Kohlmeyer (Mon May 27 2013 - 03:57:15 CDT)
- Should I use a precompiled binary? Andrew DeYoung (Fri May 24 2013 - 15:36:41 CDT)
- 2014 Aspen Center for Physics Workshop MARK PLUMMER (Fri May 24 2013 - 14:50:54 CDT)
- Re: NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Fri May 24 2013 - 04:55:02 CDT)
- Re: NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Fri May 24 2013 - 08:25:10 CDT)
- Re: NAMD/VMD installation on Linux Clusters with InfiniBand Axel Kohlmeyer (Fri May 24 2013 - 22:42:08 CDT)
- NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Fri May 24 2013 - 08:31:09 CDT)
- Aron Broom on NVIDIA CUDA Spotlight Devang Sachdev (Wed May 22 2013 - 19:59:11 CDT)
- NAMD/VMD installation on Linux Clusters with InfiniBand Anilkumar Naik (Wed May 22 2013 - 11:18:22 CDT)
- pressure profile freezing Thomas Brian (Wed May 22 2013 - 11:57:59 CDT)
- modeling missing loops in starting structures Martin, Erik W (Tue May 21 2013 - 17:08:06 CDT)
- Molecular Shape Searching on GPUs MARK (Mon May 20 2013 - 13:13:55 CDT)
- Suggestions on parameterizing a ligand to simulate in NAMD Peterson J (Mon May 20 2013 - 13:03:57 CDT)
- Re: Suggestions on parameterizing a ligand to simulate in NAMD Aron Broom (Mon May 20 2013 - 14:10:21 CDT)
- Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD Jiawei Xu (Mon May 20 2013 - 14:11:50 CDT)
- Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD Mayne, Christopher G (Mon May 20 2013 - 14:32:42 CDT)
- Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Corey Fugate (Mon May 20 2013 - 11:08:07 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Aron Broom (Mon May 20 2013 - 11:16:35 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Corey Fugate (Mon May 20 2013 - 11:57:14 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Aron Broom (Mon May 20 2013 - 14:07:56 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Corey Fugate (Mon May 20 2013 - 17:28:21 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Aron Broom (Mon May 20 2013 - 21:38:01 CDT)
- AW: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Norman Geist (Tue May 21 2013 - 01:02:42 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Corey Fugate (Mon May 20 2013 - 11:57:14 CDT)
- Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" Aron Broom (Mon May 20 2013 - 11:16:35 CDT)
- Protein unfolding and Coarse grained Fugui (Fri May 17 2013 - 06:55:02 CDT)
- Building crystal polymer Shaikh Abdul Rajjak (Fri May 17 2013 - 00:59:09 CDT)
- Linuxtag Gianluca Interlandi (Thu May 16 2013 - 14:38:40 CDT)
- Potential of mean force calculation using colvars in NADM 2.9 package (Thu May 16 2013 - 02:06:53 CDT)
- Re: Potential of mean force calculation using colvars in NADM 2.9 package Aron Broom (Thu May 16 2013 - 07:55:46 CDT)
- Re: Potential of mean force calculation using colvars in NADM 2.9 package Jérôme Hénin (Thu May 16 2013 - 08:19:57 CDT)
- A larger protein data bank for performance benchmark linux freaker (Mon May 13 2013 - 11:49:10 CDT)
- Re: A larger protein data bank for performance benchmark Cesar Millan (Mon May 13 2013 - 11:52:30 CDT)
- Re: A larger protein data bank for performance benchmark Ajasja Ljubetič (Mon May 13 2013 - 12:13:46 CDT)
- Re: A larger protein data bank for performance benchmark linux freaker (Mon May 13 2013 - 19:51:51 CDT)
- Re: A larger protein data bank for performance benchmark Rebecca Swett (Mon May 13 2013 - 20:52:17 CDT)
- Re: A larger protein data bank for performance benchmark linux freaker (Mon May 13 2013 - 21:02:59 CDT)
- Re: A larger protein data bank for performance benchmark Aron Broom (Mon May 13 2013 - 22:56:35 CDT)
- Re: A larger protein data bank for performance benchmark Gianluca Interlandi (Tue May 14 2013 - 00:02:34 CDT)
- AW: A larger protein data bank for performance benchmark Norman Geist (Tue May 14 2013 - 00:46:34 CDT)
- Re: AW: A larger protein data bank for performance benchmark linux freaker (Tue May 14 2013 - 00:58:52 CDT)
- Re: AW: A larger protein data bank for performance benchmark linux freaker (Tue May 14 2013 - 01:28:23 CDT)
- Re: AW: A larger protein data bank for performance benchmark linux freaker (Tue May 14 2013 - 01:30:42 CDT)
- AW: A larger protein data bank for performance benchmark Norman Geist (Tue May 14 2013 - 10:30:08 CDT)
- Re: A larger protein data bank for performance benchmark Cesar Millan (Mon May 13 2013 - 11:52:30 CDT)
- Re: NAMD Tutorial - Water Sphere - Altering size of water sphere Peter Murphy (Mon May 13 2013 - 11:16:20 CDT)
- Coarse-grained reverse transformation Fugui (Sat May 11 2013 - 10:21:04 CDT)
- Can I define a simulation box but turn off the PBC at the same time? (Thu May 09 2013 - 03:49:48 CDT)
- restart files not written. Yarrow Madrona (Thu May 09 2013 - 19:25:57 CDT)
- ABF karthik kumar (Wed May 08 2013 - 23:34:17 CDT)
- Bulk properties of polymers Sindu (Tue May 07 2013 - 23:34:20 CDT)
- fail to guess missing coordinates Liqi Feng (Tue May 07 2013 - 13:30:21 CDT)
- AW: Exploding vdW energies in automatically generated POPC membranes Norman Geist (Tue May 07 2013 - 00:17:36 CDT)
- BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1 dbaogen (Tue May 07 2013 - 00:10:40 CDT)
- catdcd output and .psf file atom count mismatch Izhar Karbat (Mon May 06 2013 - 17:18:53 CDT)
- Exploding vdW energies in automatically generated POPC membranes Lucas (Mon May 06 2013 - 15:33:47 CDT)
- Bad global bond count Fugui (Mon May 06 2013 - 15:26:52 CDT)
- How to converse Coarse-Grained structure into all-atom structure Fugui (Mon May 06 2013 - 05:02:10 CDT)
- Selecting GPU for namd2 Francesco Pietra (Mon May 06 2013 - 02:27:57 CDT)
- AW: AW: Coarse-Grained fatal error! Norman Geist (Mon May 06 2013 - 01:09:08 CDT)
- How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1 dbaogen (Sat May 04 2013 - 02:23:19 CDT)
- Sevoflurane parameters (psf file) Mikhail Suyetin (Fri May 03 2013 - 09:41:19 CDT)
- unsubscribe Patricia Campbell (Fri May 03 2013 - 08:57:21 CDT)
- Patching N- and C-Terms and their parameters Peterson J (Thu May 02 2013 - 18:28:25 CDT)
- MDFF force threshold Ivana (Thu May 02 2013 - 10:07:17 CDT)
- dihedral parameter conversion JC Gumbart (Thu May 02 2013 - 08:17:00 CDT)
- Coarse-Grained fatal error! Fugui (Thu May 02 2013 - 07:49:20 CDT)
- Current bias values Siri Sndergaard (Wed May 01 2013 - 20:39:50 CDT)
- NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. Aaron Cann (Tue Apr 30 2013 - 21:17:02 CDT)
- negative VdW energy and Elect energy 翁林岽 (Tue Apr 30 2013 - 20:50:17 CDT)
- [SOLVED] Charmrun> error x attaching to node Norman Geist (Tue Apr 30 2013 - 05:09:05 CDT)
- WHAM analysis for Umbrella sampling Ada Zhan (Mon Apr 29 2013 - 14:41:37 CDT)
- Re: WHAM analysis for Umbrella sampling Aron Broom (Mon Apr 29 2013 - 15:17:00 CDT)
- Re: WHAM analysis for Umbrella sampling Jérôme Hénin (Tue Apr 30 2013 - 04:07:52 CDT)
- RE: WHAM analysis for Umbrella sampling Ada Zhan (Tue Apr 30 2013 - 17:18:37 CDT)
- Re: WHAM analysis for Umbrella sampling Aron Broom (Tue Apr 30 2013 - 17:27:57 CDT)
- Re: WHAM analysis for Umbrella sampling Chris Chipot (Wed May 01 2013 - 02:01:44 CDT)
- RE: WHAM analysis for Umbrella sampling Ada Zhan (Wed May 01 2013 - 12:20:15 CDT)
- Re: WHAM analysis for Umbrella sampling Chris Chipot (Wed May 01 2013 - 12:58:18 CDT)
- Re: WHAM analysis for Umbrella sampling Aron Broom (Wed May 01 2013 - 13:09:53 CDT)
- RE: WHAM analysis for Umbrella sampling Ada Zhan (Wed May 01 2013 - 13:59:46 CDT)
- Re: WHAM analysis for Umbrella sampling Aron Broom (Wed May 01 2013 - 14:12:23 CDT)
- RE: WHAM analysis for Umbrella sampling Ada Zhan (Wed May 01 2013 - 15:10:03 CDT)
- Re: WHAM analysis for Umbrella sampling Jérôme Hénin (Tue Apr 30 2013 - 04:07:52 CDT)
- Re: WHAM analysis for Umbrella sampling Aron Broom (Mon Apr 29 2013 - 15:17:00 CDT)
- Fe-N bond parameters Francesco Pietra (Sun Apr 28 2013 - 09:55:16 CDT)
- unrecognizable code in the output file of ParseFEP analysis in VMD 1.9.1 under the Linux system dbaogen (Sun Apr 28 2013 - 03:11:52 CDT)
- Conceptual questions about GPU acceleration Andrew DeYoung (Sat Apr 27 2013 - 11:46:49 CDT)
- Free energy calculation of proton transfer with FEP Huihui Liu (Sat Apr 27 2013 - 03:49:10 CDT)
- Are random forces applied at every step (when using the langevin thermostat) ? Ajasja Ljubetič (Fri Apr 26 2013 - 15:21:56 CDT)
- metadynamics Francesco Pietra (Fri Apr 26 2013 - 09:46:12 CDT)
- Build polymer from monomer Sindu (Thu Apr 25 2013 - 23:48:17 CDT)
- (no subject) Ganesh Shahane (Thu Apr 25 2013 - 08:51:59 CDT)
- (no subject) Ganesh Shahane (Thu Apr 25 2013 - 01:25:29 CDT)
- Fwd: vmd-l: HEME acting unplanar Francesco Pietra (Wed Apr 24 2013 - 15:07:54 CDT)
- AW: Link between simulations Norman Geist (Wed Apr 24 2013 - 02:09:13 CDT)
- binding free energy calculation yp sun (Sun Apr 21 2013 - 07:42:52 CDT)
- solvated system for minimization Himani Raina (Mon Apr 22 2013 - 05:31:18 CDT)
- Re: Link between simulations Suresh (Mon Apr 22 2013 - 01:37:00 CDT)
- HEME acting unplanar Yarrow Madrona (Sun Apr 21 2013 - 17:48:43 CDT)
- Link between simulations Mihaela Drenscko (Sat Apr 20 2013 - 15:18:36 CDT)
- Computational Electrostatics for Biological Application (CEBA'13) - July 1-3 2013 - Genoa - Italy Walter Rocchia (Fri Apr 19 2013 - 04:59:23 CDT)
- AW: floating point reproduceability Norman Geist (Fri Apr 19 2013 - 02:09:33 CDT)
- Re: floating point reproduceability Thomas Brian (Thu Apr 18 2013 - 23:28:31 CDT)
- floating point reproduceability Thomas Brian (Wed Apr 17 2013 - 17:08:34 CDT)
- NAMD "tCouple" option Tao Qu (Wed Apr 17 2013 - 15:56:54 CDT)
- grcarma : a graphical user interface to carma Nicholas M Glykos (Wed Apr 17 2013 - 09:33:24 CDT)
- Are coordinates in the tclForces module loaded as wrapped? Salvatore Mario Cosseddu (Tue Apr 16 2013 - 05:12:08 CDT)
- total charge of the system - rounding error ? Fabien Cailliez (Mon Apr 15 2013 - 11:59:33 CDT)
- Minimisation of protein in a water box Gareth Price (Sat Apr 13 2013 - 13:52:01 CDT)
- Re: Minimisation of protein in a water box Rajan Vatassery (Mon Apr 15 2013 - 12:30:46 CDT)
- AW: Minimisation of protein in a water box Norman Geist (Tue Apr 16 2013 - 01:31:31 CDT)
- RE: Minimisation of protein in a water box Price, Gareth (Thu Apr 18 2013 - 19:15:31 CDT)
- AW: Minimisation of protein in a water box Norman Geist (Fri Apr 19 2013 - 02:03:15 CDT)
- Re: AW: Minimisation of protein in a water box Rajan Vatassery (Fri Apr 19 2013 - 18:18:28 CDT)
- AW: AW: Minimisation of protein in a water box Norman Geist (Mon Apr 22 2013 - 01:22:48 CDT)
- AW: Minimisation of protein in a water box Norman Geist (Tue Apr 16 2013 - 01:31:31 CDT)
- Re: Minimisation of protein in a water box Rajan Vatassery (Mon Apr 15 2013 - 12:30:46 CDT)
- restrain ligand to z-interval Magnus Andersson (Mon Apr 15 2013 - 06:29:07 CDT)
- ABF karthik kumar (Mon Apr 15 2013 - 07:38:26 CDT)
- restrain ligand in z-interval Magnus Andersson (Mon Apr 15 2013 - 06:37:26 CDT)
- Problem with running FEP calculations Eric Lang (Sun Apr 14 2013 - 18:51:45 CDT)
- ABF karthik kumar (Sat Apr 13 2013 - 06:45:12 CDT)
- Inconsistency in fast table energy vs force Francesco Pietra (Sat Apr 13 2013 - 02:36:32 CDT)
- minimizer slowly moving atoms with bad contacts downhill Himani Raina (Fri Apr 12 2013 - 02:02:17 CDT)
- Re: namd 2.9 tip4p-2005 Guanglei Cui (Thu Apr 11 2013 - 10:31:33 CDT)
- pump / force application Arturas (Thu Apr 11 2013 - 08:19:46 CDT)
- Unsubscribe Александр Северюхин (Thu Apr 11 2013 - 01:45:51 CDT)
- (no subject) Tina Stokelj (Thu Apr 11 2013 - 00:07:11 CDT)
- Error in distributing the cores for a single processor Priyanka Purkayastha (Wed Apr 10 2013 - 23:36:00 CDT)
- About Bond Deletion Vidhya Sankar (Wed Apr 10 2013 - 22:12:33 CDT)
- (no subject) Mohammad Jomah I Abu Saude (mbusaude) (Wed Apr 10 2013 - 17:30:08 CDT)
- OpenMPI FEP Yields SegFaults and/or infinite dG Andrew Miglino (Wed Apr 10 2013 - 12:51:05 CDT)
- tcf forces and ccordinate wrapping Arturas (Tue Apr 09 2013 - 13:23:21 CDT)
- NAMD Output files Rawan Al Nsour (Tue Apr 09 2013 - 08:02:26 CDT)
- ERROR: Constraint failure in RATTLE algorithm for atom 474! suresh satpati (Tue Apr 09 2013 - 00:54:41 CDT)
- understanding which is which with GPU cards Francesco Pietra (Sat Apr 06 2013 - 17:17:13 CDT)
- CUDA error in cuda_check_remote_progress on Pe 2 Francesco Pietra (Fri Apr 05 2013 - 09:55:44 CDT)
- file for fixed atoms is not found! - but the file exist actually Sridhar Kumar Kannam (Thu Apr 04 2013 - 21:33:52 CDT)
- not fatal error but no more information Wang (Thu Apr 04 2013 - 13:50:17 CDT)
- ABF karthik kumar (Thu Apr 04 2013 - 10:53:58 CDT)
- VDW component: NAMD vs. CHARMM Shubhra Ghosh Dastidar (Thu Apr 04 2013 - 09:20:23 CDT)
- pairInteraction and PME Jason Swails (Wed Apr 03 2013 - 15:58:21 CDT)
- can't run multiple jobs with multiple gpus Gordon Wells (Wed Apr 03 2013 - 15:42:44 CDT)
- colvars configuration file example Martin, Erik W (Wed Apr 03 2013 - 15:04:41 CDT)
- problem with inorganic builder genCompressedPsf Sridhar Kumar Kannam (Wed Apr 03 2013 - 01:05:07 CDT)
- Sutton-Chen potential Zhao Lina (Mon Apr 01 2013 - 03:30:55 CDT)
- Unsubscribe Mark Cheeseman (Fri Mar 29 2013 - 23:05:32 CDT)
- Timeline Mihaela Drenscko (Fri Mar 29 2013 - 19:20:41 CDT)
- cuda error subbarao kanchi (Fri Mar 29 2013 - 12:36:50 CDT)
- Re: strange result using implicit solvent Niklaus Johner (Fri Mar 29 2013 - 08:39:05 CDT)
- strange result using implicit solvent Fugui (Fri Mar 29 2013 - 08:00:04 CDT)
- How to recenter a waterbox with ions around my protein? Maria Bykhovskaia (Thu Mar 28 2013 - 17:44:06 CDT)
- Error in implicit solvent MD Fugui (Wed Mar 27 2013 - 15:08:19 CDT)
- 2d periodic box Pavan G (Wed Mar 27 2013 - 12:51:25 CDT)
- implicit solvent Fugui (Wed Mar 27 2013 - 11:27:55 CDT)
- FFTK Atom types Francesco Pietra (Wed Mar 27 2013 - 02:21:13 CDT)
- NAMD post processing analysis.... linux freaker (Tue Mar 26 2013 - 21:09:31 CDT)
- Accelerated MD parameters Gianluca Interlandi (Tue Mar 26 2013 - 19:37:56 CDT)
- unsubscribe namd-l Bin Zhang (Tue Mar 26 2013 - 13:15:23 CDT)
- (no subject) Mihaela Drenscko (Tue Mar 26 2013 - 12:41:35 CDT)
- Final link of namd2 executable fails under AIX with xlC compiler Mark Cheeseman (Mon Mar 25 2013 - 17:07:05 CDT)
- (no subject) Riley Workman (Mon Mar 25 2013 - 15:07:09 CDT)
- free energy methods cheat-sheet/comparison chart Thomas C. Bishop (Mon Mar 25 2013 - 13:49:16 CDT)
- Re: free energy methods cheat-sheet/comparison chart Aron Broom (Mon Mar 25 2013 - 14:28:00 CDT)
- Re: free energy methods cheat-sheet/comparison chart JC Gumbart (Mon Mar 25 2013 - 14:50:04 CDT)
- Error with NAMD Energy Anurag Sharma (Mon Mar 25 2013 - 13:05:00 CDT)
- Tetraphenylphosphonium Thomas Albers (Mon Mar 25 2013 - 12:19:31 CDT)
- FEP OpenMPI Error Andrew Miglino (Fri Mar 22 2013 - 10:43:43 CDT)
- Ligand in association with water Roy Fernando (Mon Mar 25 2013 - 09:40:44 CDT)
- MARTINI Bad global angle count thomas lemmin (Mon Mar 25 2013 - 04:40:07 CDT)
- Parameter file for DGEBA Sindu (Mon Mar 25 2013 - 03:56:40 CDT)
- Morse potentail with charmm 27 Francesco Pietra (Sun Mar 24 2013 - 11:04:56 CDT)
- Query regarding NAMD linux freaker (Sun Mar 24 2013 - 05:13:43 CDT)
- Simulation at high pressure Rawan Al Nsour (Fri Mar 22 2013 - 14:20:49 CDT)
- Coordinate vs. time plots Mihaela Drenscko (Wed Mar 20 2013 - 17:17:46 CDT)
- Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? somedatta pal (Wed Mar 20 2013 - 00:37:21 CDT)
- AW: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? Norman Geist (Wed Mar 20 2013 - 02:47:06 CDT)
- Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? Grace Brannigan (Wed Mar 20 2013 - 08:45:51 CDT)
- MD crashes at 300K after warm up MD Patricia Campbell (Tue Mar 19 2013 - 13:30:23 CDT)
- how to switch off protein-water electrostatic interaction keeping the protein-water vdw interactions intact somedatta pal (Tue Mar 19 2013 - 02:57:09 CDT)
- Fwd: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? somedatta pal (Tue Mar 19 2013 - 02:54:35 CDT)
- AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Tue Mar 19 2013 - 02:50:33 CDT)
- Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? somedatta pal (Mon Mar 18 2013 - 23:58:43 CDT)
- Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? Axel Kohlmeyer (Tue Mar 19 2013 - 00:04:12 CDT)
- protein-water interactions somedatta pal (Mon Mar 18 2013 - 12:40:31 CDT)
- Locally Enhanced Sampling Melina (Mon Mar 18 2013 - 12:20:09 CDT)
- distanceZ - harmonic restraints Narasimhan LOGANATHAN (Mon Mar 18 2013 - 12:14:46 CDT)
- Restart simulation of an equilibrated bilayer with sugar molecules inserted Keller Wenger (Sun Mar 17 2013 - 09:51:27 CDT)
- smd force is too high Jacqueline Schmidt (Fri Mar 15 2013 - 11:25:58 CDT)
- unsubscribe Van Ngo (Wed Mar 13 2013 - 18:23:14 CDT)
- My calcforces does not work properly after a unknown point of the simulation. Salvatore Mario Cosseddu (Wed Mar 13 2013 - 15:35:11 CDT)
- Effect of phi, psi cross term map (CMAP) correction on result of MD simulation dbaogen (Wed Mar 13 2013 - 04:13:42 CDT)
- AW: LES very slow Norman Geist (Tue Mar 12 2013 - 01:51:40 CDT)
- AW: NAMD 2.9 CUDA compilation Norman Geist (Tue Mar 12 2013 - 02:53:06 CDT)
- Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Mon Mar 11 2013 - 17:18:12 CDT)
- NAMD 2.9 CUDA compilation Francesco Pietra (Mon Mar 11 2013 - 10:40:11 CDT)
- dynamic_cast cannot be done without runtime type information Jérôme Hénin (Mon Mar 11 2013 - 10:16:24 CDT)
- AW: NamdMemoryReduction - genCompressedPsf Norman Geist (Mon Mar 11 2013 - 01:56:40 CDT)
- NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Sun Mar 10 2013 - 16:10:42 CDT)
- Adding HEME parameters Yarrow Madrona (Sat Mar 09 2013 - 17:54:03 CST)
- NAMD with Intel Xeon Phi coprocessors ? Christopher Neale (Fri Mar 08 2013 - 22:32:06 CST)
- psf generation error Vasumathi Velachi (Fri Mar 08 2013 - 13:26:14 CST)
- 'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA David Brandon (Fri Mar 08 2013 - 12:08:25 CST)
- NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Thu Mar 07 2013 - 21:39:20 CST)
- memory demands of REMD Martin, Erik W (Thu Mar 07 2013 - 16:16:00 CST)
- AW: LES very slow Norman Geist (Thu Mar 07 2013 - 00:47:59 CST)
- using stackexchange was: Re: unsubscriber e-mail office pool anybody? Axel Kohlmeyer (Thu Mar 07 2013 - 03:04:16 CST)
- tcl-related segfault in NAMD FX (Wed Mar 06 2013 - 09:32:39 CST)
- AW: LES very slow Norman Geist (Wed Mar 06 2013 - 01:03:39 CST)
- how to convert CHARMM TIP3P to traditional TIP3P subbarao kanchi (Wed Mar 06 2013 - 05:56:27 CST)
- Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?) FX (Wed Mar 06 2013 - 04:43:49 CST)
- unsubscribe JC Gumbart (Tue Mar 05 2013 - 09:44:57 CST)
- unsubscriber e-mail office pool anybody? Axel Kohlmeyer (Tue Mar 05 2013 - 07:11:44 CST)
- unsubscribe karthik s (Tue Mar 05 2013 - 06:54:55 CST)
- AW: LES very slow Norman Geist (Tue Mar 05 2013 - 00:08:42 CST)
- problem in solvating a graphene layer created using VMD-nanotube builder Sridhar Kumar Kannam (Mon Mar 04 2013 - 21:37:15 CST)
- remd run command question Martin, Erik W (Mon Mar 04 2013 - 12:59:56 CST)
- unsubscribe Yihua Zhou (Mon Mar 04 2013 - 11:18:09 CST)
- Very long simulation Mihaela Drenscko (Mon Mar 04 2013 - 05:55:07 CST)
- Re: Very long simulation Axel Kohlmeyer (Mon Mar 04 2013 - 06:10:43 CST)
- Re: Very long simulation flavio seixas (Mon Mar 04 2013 - 17:39:26 CST)
- if{} statements Thomas C. Bishop (Tue Mar 05 2013 - 07:46:29 CST)
- Re: if{} statements Axel Kohlmeyer (Tue Mar 05 2013 - 07:54:53 CST)
- Re: if{} statements Hannes Loeffler (Tue Mar 05 2013 - 07:59:32 CST)
- Re: if{} statements Thomas C. Bishop (Tue Mar 05 2013 - 08:07:02 CST)
- Re: if{} statements Axel Kohlmeyer (Tue Mar 05 2013 - 08:15:21 CST)
- Potential energy as collective variable Austin B. Yongye (Mon Mar 25 2013 - 10:35:30 CDT)
- Re: Potential energy as collective variable Giacomo Fiorin (Mon Mar 25 2013 - 11:55:41 CDT)
- Re: Very long simulation flavio seixas (Mon Mar 04 2013 - 17:39:26 CST)
- Re: Very long simulation Axel Kohlmeyer (Mon Mar 04 2013 - 06:10:43 CST)
- NAMD PBS Parallel Job Error Aditya Ranganathan (Mon Mar 04 2013 - 03:44:15 CST)
- AW: LES very slow Norman Geist (Mon Mar 04 2013 - 01:27:27 CST)
- MDFF - should hydrogens be included? Geoffrey Kwai Wai Kong (Mon Mar 04 2013 - 00:19:26 CST)
- unsubscribe Artem Zhmurov (Sat Mar 02 2013 - 03:12:14 CST)
- Subject: Simulated Annealing/ Cooling Mariana Graterol (Fri Mar 01 2013 - 11:55:21 CST)
- unsubscribe Purushottam Dixit (Fri Mar 01 2013 - 11:01:44 CST)
- unsubscribe Riley Workman (Fri Mar 01 2013 - 10:59:39 CST)
- unsubscribe rukman kesh (Fri Mar 01 2013 - 05:32:54 CST)
- unsubscribe Shubhra Ghosh Dastidar (Fri Mar 01 2013 - 03:27:30 CST)
- Protein Dielectric Constant in GBIS hanif mahboobi (Fri Mar 01 2013 - 02:58:01 CST)
- unsubscribe karthik s (Fri Mar 01 2013 - 02:50:59 CST)
- Fwd: NAMD + PLUMED COMPILATION Francesco Pietra (Fri Mar 01 2013 - 00:52:14 CST)
- Sudden jumps during FEP Lewis Martin (Thu Feb 28 2013 - 23:16:21 CST)
- Amorphous Structure code or builder Rawan Al Nsour (Thu Feb 28 2013 - 14:47:14 CST)
- NAMD + PLUMED COMPILATION Francesco Pietra (Thu Feb 28 2013 - 11:02:28 CST)
- (no subject) Francesco Pietra (Thu Feb 28 2013 - 10:59:57 CST)
- converting dcd files to netcdf or ascii Daniel Abergel (Thu Feb 28 2013 - 07:04:41 CST)
- GPUs silently stop working during simulation when oversubscribed Benjamin Merget (Thu Feb 28 2013 - 02:51:39 CST)
- AW: LES very slow Norman Geist (Thu Feb 28 2013 - 00:37:07 CST)
- colvar keyword ForceNoPBC Nadeem A. Vellore (Wed Feb 27 2013 - 23:46:09 CST)
- ABF - distance between two domains Nadeem A. Vellore (Wed Feb 27 2013 - 15:12:35 CST)
- (no subject) Moema Monteiro (Wed Feb 27 2013 - 15:08:10 CST)
- Re: NAMD on Stampede Niklaus Johner (Wed Feb 27 2013 - 14:27:34 CST)
- NAMD on Stampede hanif mahboobi (Wed Feb 27 2013 - 13:46:29 CST)
- MDFF volumetric map Ivana (Wed Feb 27 2013 - 11:43:03 CST)
- smd simulation Jacqueline Schmidt (Wed Feb 27 2013 - 08:27:43 CST)
- About PLUMED with NAMD VMD Francesco Pietra (Wed Feb 27 2013 - 02:16:28 CST)
- AW: RATTLE algorithm Norman Geist (Wed Feb 27 2013 - 01:24:05 CST)
- AW: LES very slow Norman Geist (Wed Feb 27 2013 - 01:19:51 CST)
- RE: DCD file doubles a monomer JC Gumbart (Tue Feb 26 2013 - 20:58:04 CST)
- DCD file doubles a monomer Patricia Campbell (Tue Feb 26 2013 - 15:01:18 CST)
- DCD file doubles a monomer Patricia Campbell (Tue Feb 26 2013 - 12:09:16 CST)
- Simulated Annealing/ Cooling Rawan Al Nsour (Tue Feb 26 2013 - 09:43:32 CST)
- Regarding installing Namd 2.9 on windows xp 32 bit system Himani Raina (Tue Feb 26 2013 - 04:08:25 CST)
- LES very slow Siri Sndergaard (Mon Feb 25 2013 - 18:00:02 CST)
- RATTLE algorithm Mihaela Drenscko (Mon Feb 25 2013 - 17:56:25 CST)
- ABF thermostats and energy introduced into the system Ajasja Ljubetič (Mon Feb 25 2013 - 07:07:39 CST)
- Re: ABF thermostats and energy introduced into the system Jérôme Hénin (Mon Feb 25 2013 - 08:01:52 CST)
- Re: ABF thermostats and energy introduced into the system JC Gumbart (Mon Feb 25 2013 - 16:32:13 CST)
- Re: Always 24-way SMP? Andrew Pearson (Mon Feb 25 2013 - 06:28:05 CST)
- Calculate binding free energy yp sun (Sun Feb 24 2013 - 19:22:08 CST)
- spectrum simulation francesco oteri (Sun Feb 24 2013 - 14:56:55 CST)
- center of mass calculation in the tcl interface Jacqueline Schmidt (Sun Feb 24 2013 - 13:02:21 CST)
- Single point energy calc with gaussian/namd... log file interpretation Stober, Spencer T (Fri Feb 22 2013 - 16:31:01 CST)
- Always 24-way SMP? Andrew Pearson (Fri Feb 22 2013 - 12:29:58 CST)
- (no subject) Titis Sekar Humani (Fri Feb 22 2013 - 00:05:07 CST)
- Epoxy CHARMM Rawan Al Nsour (Thu Feb 21 2013 - 18:11:41 CST)
- Re: Orientation colvar + metadynamics questions Benjamin Bouvier (Thu Feb 21 2013 - 07:37:06 CST)
- Orientation colvar + metadynamics questions Benjamin Bouvier (Thu Feb 21 2013 - 04:58:48 CST)
- How to write dcd file within Tclforce script Teerapong Pirojsirikul (Wed Feb 20 2013 - 17:56:31 CST)
- Collective variable data analysis using WHAM Narasimhan LOGANATHAN (Wed Feb 20 2013 - 11:55:31 CST)
- Polarizability Question! Sai Kumar Ramadugu (Wed Feb 20 2013 - 11:46:06 CST)
- topology/parameter files for biotin Sridhar Kumar Kannam (Tue Feb 19 2013 - 21:27:48 CST)
- Constant volume energy minimization FX (Tue Feb 19 2013 - 16:06:53 CST)
- NAMD 2.9 jobs hanging. Bhupender Thakur (Mon Feb 18 2013 - 20:40:14 CST)
- transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin Izhar Karbat (Mon Feb 18 2013 - 11:26:30 CST)
- Re: Replica-exchange metadynamics scripts Robert Elder (Thu Feb 14 2013 - 18:29:53 CST)
- namd2 CUDA errors for non-superusers in Debian Blake Mertz (Thu Feb 14 2013 - 16:28:23 CST)
- Scaling on 64 core nodes? Rebecca Swett (Thu Feb 14 2013 - 08:37:44 CST)
- confines volume effects Martin, Erik W (Thu Feb 14 2013 - 12:30:39 CST)
- Re: running NAMD on Amazon EC2? Ajasja Ljubetič (Thu Feb 14 2013 - 02:39:06 CST)
- running NAMD on Amazon EC2? Cloud Computing (Wed Feb 13 2013 - 16:05:03 CST)
- SOLVED: Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help! Jose Borreguero (Wed Feb 13 2013 - 12:34:49 CST)
- Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help! Jose Borreguero (Tue Feb 12 2013 - 17:26:12 CST)
- Simulation continuously crashes after minimization Patricia Campbell (Tue Feb 12 2013 - 15:01:37 CST)
- Simulation continuously crashes after minimization Patricia Campbell (Tue Feb 12 2013 - 14:52:03 CST)
- Namd and CUDA on Debian Wheezy Vlastimil Zíma (Tue Feb 12 2013 - 07:11:38 CST)
- Apply torque with NAMD George Patargias (Tue Feb 12 2013 - 05:30:28 CST)
- Repelling extracellular regions of the protein from membrane in NAMD MD simulation Sahu, Indra (Sat Feb 09 2013 - 14:58:24 CST)
- Generating topology files for crystalline materials FX (Sun Feb 10 2013 - 12:05:26 CST)
- Re: Generating topology files for crystalline materials Axel Kohlmeyer (Sun Feb 10 2013 - 12:22:09 CST)
- Re: Generating topology files for crystalline materials FX (Sun Feb 10 2013 - 14:02:16 CST)
- Re: Generating topology files for crystalline materials Axel Kohlmeyer (Sun Feb 10 2013 - 14:54:45 CST)
- Re: Generating topology files for crystalline materials Axel Kohlmeyer (Sun Feb 10 2013 - 15:11:55 CST)
- Re: Generating topology files for crystalline materials FX (Sun Feb 10 2013 - 15:58:31 CST)
- Re: Generating topology files for crystalline materials Axel Kohlmeyer (Sun Feb 10 2013 - 16:05:16 CST)
- Re: Generating topology files for crystalline materials FX (Sun Feb 10 2013 - 14:02:16 CST)
- Re: Generating topology files for crystalline materials Axel Kohlmeyer (Sun Feb 10 2013 - 12:22:09 CST)
- Repelling extracellular regions of the protein from membrane in NAMD MD simulation Sahu, Indra (Sun Feb 10 2013 - 11:43:43 CST)
- How to get cell information from within calcforces in TclForces Salvatore Mario Cosseddu (Fri Feb 08 2013 - 17:35:52 CST)
- Current CVS broken? (SortedArray.h) Michael Mazack (Tue Feb 05 2013 - 12:52:26 CST)
- Simulated Annealing for a polymer Rawan Al Nsour (Mon Feb 04 2013 - 13:13:54 CST)
- ERROR: Constraint failure in RATTLE algorithm for atom 593! Nutan Preety (Mon Feb 04 2013 - 06:26:44 CST)
- Re: namd-l digest V1 #979 Nutan Preety (Mon Feb 04 2013 - 06:18:55 CST)
- unsubscribe Elif Ozkirimli (Sun Feb 03 2013 - 17:34:25 CST)
- SMD and torque application George Patargias (Sun Feb 03 2013 - 14:42:09 CST)
- NAMD mailing list unsubscribe instructions Ajasja Ljubetič (Sun Feb 03 2013 - 11:28:32 CST)
- unsubscribe Purushottam Dixit (Sun Feb 03 2013 - 07:38:18 CST)
- unsubscribe Tina Stokelj (Sat Feb 02 2013 - 00:02:14 CST)
- unsubscribe Elif Ozkirimli (Fri Feb 01 2013 - 18:37:04 CST)
- Does NAMD read the PDB element field? Albrecht Goez (Fri Feb 01 2013 - 02:52:15 CST)
- Cellulose MD simulations Patriche Simona (Thu Jan 31 2013 - 04:39:33 CST)
- direction of pull in namd raghav singh (Tue Jan 29 2013 - 07:18:49 CST)
- Re: Percentage of Residues in Ramachandran Plot regions versus time of trajectory Aditya Ranganathan (Tue Jan 29 2013 - 04:14:57 CST)
- Problem with psfgen for Carbohydrates Sai Kumar Ramadugu (Mon Jan 28 2013 - 13:28:06 CST)
- Metadynamics pmf restart Riley Workman (Mon Jan 28 2013 - 12:18:48 CST)
- Re: Question about NAMD johan strumpfer (Mon Jan 28 2013 - 02:02:13 CST)
- Percentage of Residues in Ramachandran Plot regions versus time of trajectory Aditya Ranganathan (Sun Jan 27 2013 - 22:45:13 CST)
- not reading improper angle from amber1.5 ff12SB Jorgen Simonsen (Sun Jan 27 2013 - 16:06:20 CST)
- (no subject) forough askari (Sun Jan 27 2013 - 10:06:36 CST)
- suppressing LBD output Jorgen Simonsen (Sat Jan 26 2013 - 21:57:18 CST)
- How to split large NAMD DCD file snoze pa (Thu Jan 24 2013 - 10:49:58 CST)
- Re: How to split large NAMD DCD file Aron Broom (Thu Jan 24 2013 - 11:06:45 CST)
- Re: How to split large NAMD DCD file Michael Purdy (Thu Jan 24 2013 - 11:06:33 CST)
- Re: How to split large NAMD DCD file flavio seixas (Thu Jan 24 2013 - 11:09:31 CST)
- Re: How to split large NAMD DCD file Branko (Thu Jan 24 2013 - 11:15:17 CST)
- question regarding interaction parameters subbarao kanchi (Thu Jan 24 2013 - 09:52:42 CST)
- Assigning Partial Charges to FE in Active Site Superoxide Dismutase. Roy Fernando (Wed Jan 23 2013 - 13:39:04 CST)
- Using CNS parameter file to create NAMD topology and parameter files Roy Fernando (Wed Jan 23 2013 - 13:21:35 CST)
- Re: FEP on an amino acid ligand Thomas Albers (Tue Jan 22 2013 - 16:36:59 CST)
- AW: FEP on an amino acid ligand Norman Geist (Wed Jan 23 2013 - 01:21:09 CST)
- Re: FEP on an amino acid ligand Thomas Albers (Wed Jan 23 2013 - 07:36:36 CST)
- Re: FEP on an amino acid ligand JC Gumbart (Wed Jan 23 2013 - 11:16:32 CST)
- Re: FEP on an amino acid ligand JC Gumbart (Wed Jan 23 2013 - 11:29:57 CST)
- (no subject) forough askari (Tue Jan 22 2013 - 16:32:34 CST)
- FEP on an amino acid ligand Thomas Albers (Mon Jan 21 2013 - 19:44:20 CST)
- (no subject) forough askari (Mon Jan 21 2013 - 18:38:10 CST)
- About "add solvation" Francesco Pietra (Mon Jan 21 2013 - 03:42:54 CST)
- Remove tjwang@iastate.edu from the list pls Norman Geist (Mon Jan 21 2013 - 00:04:57 CST)
- smd tcl script - problem atoms id Branko (Sun Jan 20 2013 - 10:37:56 CST)
- Running namd on linux in cpu+gpu mode James Starlight (Sat Jan 19 2013 - 01:19:53 CST)
- H-bonds cutoff angle criterian Anurag Sharma (Thu Jan 17 2013 - 20:52:40 CST)
- Scaling problem: 4 nodes OK, 5 fails to start Stober, Spencer T (Wed Jan 16 2013 - 13:39:08 CST)
- Scaling problem: 4 nodes OK, 5 nodes fail Stober, Spencer T (Wed Jan 16 2013 - 13:46:07 CST)
- src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target Paraskevi Gkeka (Wed Jan 16 2013 - 10:29:52 CST)
- Re: Re: AW: AW: CUDA problem? Ajasja Ljubetič (Wed Jan 16 2013 - 10:04:02 CST)
- topology file for ligand Maria Saeed (Wed Jan 16 2013 - 01:47:34 CST)
- DNA terminals and charges Siri Sndergaard (Tue Jan 15 2013 - 20:45:40 CST)
- NAMD with NVIDIA Quadro K5000? Martin, Erik W (Tue Jan 15 2013 - 12:15:41 CST)
- Re: AW: AW: CUDA problem? Eric Hill (Tue Jan 15 2013 - 01:12:53 CST)
- namd 2.9 tip4p-2005 Daniele Gentili (Tue Jan 15 2013 - 06:23:14 CST)
- DNA surrounded by a shell of water in a big box with vacuum Bikan Tan (Mon Jan 14 2013 - 11:01:06 CST)
- Martini RBCG DENILSON FERREIRA DE OLIVEIRA (Mon Jan 14 2013 - 09:55:51 CST)
- CNT coarse grain hamid mosaddeghi (Fri Jan 11 2013 - 06:01:51 CST)
- NAMD on Stempede (and other MIC Coprocessor systems) Jeff Wereszczynski (Fri Jan 11 2013 - 13:39:37 CST)
- Charm 6.5.0 compilation issue Dmitry Osolodkin (Fri Jan 11 2013 - 07:17:21 CST)
- Re: secondary structure analysis Nicholas M Glykos (Fri Jan 11 2013 - 02:57:26 CST)
- secondary structure analysis Martin, Erik W (Wed Jan 09 2013 - 14:20:36 CST)
- Switching function while using AMBER force field Sneha Menon (Wed Jan 09 2013 - 04:03:09 CST)
- Charm 6.5.0 compilation issue Dmitry Osolodkin (Sun Jan 06 2013 - 13:28:27 CST)
- How Pressureprofile output are averaged ? namd_chcwaaa_at_yahoo.com.cn (Fri Jan 04 2013 - 23:21:39 CST)
- NAMD 2.9 Replica-exchange. FATAL ERROR: Unknown command-line option +replicas ncskocze_at_cyf-kr.edu.pl (Fri Jan 04 2013 - 07:53:16 CST)
- SOLVED: Issues with the "Keep Water Out" tcl script B Hartzoulakis (Fri Jan 04 2013 - 05:01:08 CST)
- namd-I: sub-routine code in NAMD goldwheel87 (Thu Jan 03 2013 - 16:18:27 CST)
- RE: Issues with the "Keep Water Out" tcl script peter.schmidtke_at_fr.netgrs.com (Thu Jan 03 2013 - 09:09:29 CST)
- RE: reassigning temperatures Martin, Erik W (Thu Jan 03 2013 - 08:19:24 CST)
- Issues with the "Keep Water Out" tcl script B Hartzoulakis (Thu Jan 03 2013 - 06:15:50 CST)
Last message date: Tue Dec 30 2014 - 07:38:36 CST
Archived on: Wed Dec 31 2014 - 23:23:10 CST
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