NAMD-L: By Thread
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About this archive
Starting: Fri Jan 02 2015 - 23:19:01 CST
Ending: Tue Dec 27 2016 - 20:48:03 CST
- NAMD parallelisation / patch grid P.-L. Chau (Tue Dec 27 2016 - 04:37:15 CST)
- Modifying equilibrium distance for part of carbon nanotubes in parameter file jashnvareh 1395 (Tue Dec 27 2016 - 02:55:42 CST)
- NAMD 2.12 released Angelo Rossi (Mon Dec 26 2016 - 15:53:42 CST)
- Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab mohamad hoseyni (Sun Dec 25 2016 - 12:46:28 CST)
- Modifying equilibrium distance for a specific region of carbon nanotube in the parameter file jashnvareh 1395 (Mon Dec 26 2016 - 08:30:59 CST)
- Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 06:57:57 CST)
- Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:17:34 CST)
- Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 10:49:38 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 11:39:48 CST)
- Re: Query regarding colvar distanceZ Giacomo Fiorin (Tue Dec 27 2016 - 13:20:42 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 19:07:07 CST)
- Re: Query regarding colvar distanceZ Vermaas, Joshua (Tue Dec 27 2016 - 19:14:06 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 20:47:16 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
- Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
- Regarding Trajectory files Amit Kumar (Sun Dec 25 2016 - 23:18:26 CST)
- Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Sun Dec 25 2016 - 12:51:46 CST)
- Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Sun Dec 25 2016 - 14:31:53 CST)
- NAMD 2.12 released Jim Phillips (Fri Dec 23 2016 - 12:57:34 CST)
- RMSD based PMF calculation with umbrella sampling Wang, X. Y. (Thu Dec 22 2016 - 04:26:21 CST)
- Constraint bonds that does not include hydrogrens Karteek Bejagam (Wed Dec 21 2016 - 23:00:55 CST)
- Automate QwikMD set up for a large number of NAMD jobs? Danny Xu (Tue Dec 20 2016 - 15:24:36 CST)
- Fw (5): zmhoseyni zmhoseyni (Mon Dec 19 2016 - 13:47:30 CST)
- Studying Folding of 870 Small Peptides. Computationally Feasible? Eric A Brenner (Sat Dec 17 2016 - 12:35:59 CST)
- Re: Studying Folding of 870 Small Peptides. Computationally Feasible? JC Gumbart (Sat Dec 17 2016 - 18:48:50 CST)
- Writing number of atoms in a specific group to a file Hamed Fadaei (Fri Dec 16 2016 - 11:35:24 CST)
- Problem with using autoPSF on TMCL lipid salehesam101 . (Fri Dec 16 2016 - 10:11:47 CST)
- GBIS intrinsic radii set from aber parm7 Norman Geist (Fri Dec 16 2016 - 02:04:15 CST)
- NAMD_CUDA Sana Saeed (Thu Dec 15 2016 - 20:23:18 CST)
- psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:28:56 CST)
- NAMD Energies Chris Goedde (Wed Dec 14 2016 - 13:13:01 CST)
- using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:15:20 CST)
- Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:22:39 CST)
- Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:34:08 CST)
- Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:40:57 CST)
- Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:49:31 CST)
- Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 11:02:37 CST)
- Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 11:11:00 CST)
- Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:34:08 CST)
- Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:22:39 CST)
- A problem in ABF simulation 宋瑞珩 (Wed Dec 14 2016 - 05:45:28 CST)
- NVT and NPT simulationd faride badalkhani (Tue Dec 13 2016 - 23:50:53 CST)
- water permeability calculation using NAMD trajectories Pragya Priyadarshini (Tue Dec 13 2016 - 22:39:41 CST)
- protonating ASP and GLU Nehad Elsalamouny (Tue Dec 13 2016 - 05:58:51 CST)
- NAMD_2.12b1 build on Cray XC40 is failing Ianni, James C CTR USARMY RDECOM ARL (US) (Mon Dec 12 2016 - 14:35:32 CST)
- FATAL ERROR: Duplicate bond when going from nvt to npt Marlon Sidore (Mon Dec 12 2016 - 04:02:17 CST)
- (no subject) Tom King (Fri Dec 09 2016 - 16:43:07 CST)
- Setting up symmetry restraints in a homo-dimer with non-equal number of residues Mark Hilge (Fri Dec 09 2016 - 00:17:19 CST)
- Problem with alpha colvar in NAMD 2.12b1 Amy Rice (Thu Dec 08 2016 - 15:23:16 CST)
- (no subject) Nehir NALINCI (Thu Dec 08 2016 - 01:06:44 CST)
- NAMD How to calculate ns/day Jan Fredin (Wed Dec 07 2016 - 16:02:16 CST)
- Returning energy values from .log file. matthew reeves (Wed Dec 07 2016 - 14:16:44 CST)
- Minimization error Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
- Energy output values matthew reeves (Tue Dec 06 2016 - 13:16:00 CST)
- selectively assign HIE or HID for HIS residues Nehad Elsalamouny (Mon Dec 05 2016 - 20:19:44 CST)
- Getting cluster with defined criteria Peter Mawanga (Sun Dec 04 2016 - 07:05:35 CST)
- How to continue RMSD of previous production simulation Farhad Jahanfar (Fri Dec 02 2016 - 12:21:36 CST)
- FATAL ERROR: cuda_check_progress polled 1000000 times over 101.178648 s on step 6418536 sunyeping (Thu Dec 01 2016 - 17:27:36 CST)
- Low global exclusion count error faride badalkhani (Thu Dec 01 2016 - 15:21:03 CST)
- Spawning too many gpu processes on the first node Robert Sawko (Thu Dec 01 2016 - 13:10:12 CST)
- Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 06:36:24 CST)
- AW: Amber forcefield in namd simulation in parallel version Norman Geist (Thu Dec 01 2016 - 07:58:00 CST)
- Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
- Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Fri Dec 02 2016 - 00:05:35 CST)
- AW: Amber forcefield in namd simulation in parallel version Norman Geist (Fri Dec 02 2016 - 01:59:20 CST)
- Re: Amber forcefield in namd simulation in parallel version Teerapong Pirojsirikul (Fri Dec 02 2016 - 03:30:11 CST)
- Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
- AW: Amber forcefield in namd simulation in parallel version Norman Geist (Thu Dec 01 2016 - 07:58:00 CST)
- DNA not translocating under electric field Athreya, Nagendra Bala Murali (Wed Nov 30 2016 - 21:20:55 CST)
- NAMD 2.11 on CRAY XK with CPU+GPU P.-L. Chau (Wed Nov 30 2016 - 17:47:07 CST)
- query on OuputTotalforce Vs OnesiteTotal force ? Bala subramanian (Tue Nov 29 2016 - 09:39:39 CST)
- A problem in ABF simulation 宋瑞珩 (Tue Nov 29 2016 - 04:28:21 CST)
- How to create 3'-3' phosphodiester linkage for a DNA. Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
- NVE simulations in NAMD - the right choice of timesteps and parameters Harish Srinivasan (Tue Nov 29 2016 - 04:54:32 CST)
- Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 00:30:37 CST)
- AW: Running gromacs in namd Norman Geist (Tue Nov 29 2016 - 01:36:48 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 04:25:06 CST)
- AW: Running gromacs in namd Norman Geist (Wed Nov 30 2016 - 02:45:09 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 00:27:37 CST)
- AW: Running gromacs in namd Norman Geist (Thu Dec 01 2016 - 01:06:23 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 01:42:24 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 04:25:06 CST)
- AW: Running gromacs in namd Norman Geist (Tue Nov 29 2016 - 01:36:48 CST)
- tclBC during SMD and ABF simulations Olya Kravchenko (Mon Nov 28 2016 - 12:36:47 CST)
- A common tool to read the output of NAMD run Harish Srinivasan (Mon Nov 28 2016 - 06:28:00 CST)
- NAMD installation Puneet (Sat Nov 26 2016 - 01:41:14 CST)
- Ligand jump out of the protein through NPT ensemle runs mahdi K (Fri Nov 25 2016 - 06:40:31 CST)
- Low global exclusion count errors! faride badalkhani (Thu Nov 24 2016 - 10:28:53 CST)
- REMD kaushik chakraborty (Wed Nov 23 2016 - 13:58:51 CST)
- Simulation of metalo-binding proteins James Starlight (Wed Nov 23 2016 - 13:52:38 CST)
- Re: Simulation of metalo-binding proteins Jérôme Hénin (Wed Nov 23 2016 - 14:11:44 CST)
- AW: Simulation of metalo-binding proteins Daniel Möller (Wed Nov 23 2016 - 15:52:53 CST)
- Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:01:08 CST)
- Re: Simulation of metalo-binding proteins Francesco Pietra (Thu Nov 24 2016 - 14:41:58 CST)
- Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:44:03 CST)
- Re: Simulation of metalo-binding proteins luca belmonte (Fri Nov 25 2016 - 06:47:10 CST)
- AW: Simulation of metalo-binding proteins Daniel Möller (Wed Nov 23 2016 - 15:52:53 CST)
- Re: Simulation of metalo-binding proteins Jérôme Hénin (Wed Nov 23 2016 - 14:11:44 CST)
- Separate switchdist for electrostatic interactions Peter Mawanga (Mon Nov 21 2016 - 06:17:18 CST)
- “Cannot compile C++ programs with mpicxx" error when compiling charm-6.7 sunyeping (Sun Nov 20 2016 - 13:22:02 CST)
- Charmm++ error matthew reeves (Sun Nov 20 2016 - 11:29:25 CST)
- Query on colvar distanceZ Bala subramanian (Sat Nov 19 2016 - 08:18:57 CST)
- Pressure Profile. msa5 (Thu Nov 17 2016 - 11:06:48 CST)
- Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 06:07:39 CST)
- Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 CST)
- Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
- Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 14:56:01 CST)
- Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 16:59:53 CST)
- Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 18:56:55 CST)
- Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 19:04:06 CST)
- Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
- Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 CST)
- NAMD GPU+ibverbs on multiple nodes: timeout problems Robert Sawko (Thu Nov 17 2016 - 05:51:21 CST)
- K40 benchmark problem in NAMD Atanu Maity (Thu Nov 17 2016 - 01:27:04 CST)
- Hands-On Workshop on Integrative Modeling and Simulations Jodi Ann Hadden (Wed Nov 16 2016 - 11:28:03 CST)
- Crashes with dihedral PC Jiyong Park (Tue Nov 15 2016 - 20:28:32 CST)
- Re: Queries regarding metadynamics and .pmf visualization Giacomo Fiorin (Tue Nov 15 2016 - 10:40:15 CST)
- SMD restraints Allen, Caley R (Mon Nov 14 2016 - 15:14:09 CST)
- Need help with TCL script Nicholus Bhattacharjee (Mon Nov 14 2016 - 13:10:13 CST)
- NPT with graphene Richard Overstreet (Mon Nov 14 2016 - 11:29:27 CST)
- Are there features NOT or POORLY supported on GPU ? sonia ziada (Mon Nov 14 2016 - 04:11:43 CST)
- NAMD2.12b1 and CUDA Jeff Comer (Thu Nov 10 2016 - 09:09:50 CST)
- restraint backbone to keep secondary structure in coarse grain MD Deng, Jinxia (Nancy) (Wed Nov 09 2016 - 10:42:46 CST)
- About pbc Francesco Pietra (Tue Nov 08 2016 - 15:10:56 CST)
- Trigger DCD frame from TCL? Norman Geist (Tue Nov 08 2016 - 09:12:04 CST)
- Re: Trigger DCD frame from TCL? Brian Radak (Tue Nov 08 2016 - 09:22:24 CST)
- AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
- AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:48:33 CST)
- Re: AW: Trigger DCD frame from TCL? Brian Radak (Wed Nov 09 2016 - 07:34:48 CST)
- Re: AW: Trigger DCD frame from TCL? Jim Phillips (Wed Nov 09 2016 - 16:48:00 CST)
- AW: AW: Trigger DCD frame from TCL? Norman Geist (Thu Nov 10 2016 - 02:09:22 CST)
- AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
- Re: Trigger DCD frame from TCL? Brian Radak (Tue Nov 08 2016 - 09:22:24 CST)
- steepest descent Ma'Mon Hatmal (Tue Nov 08 2016 - 08:58:30 CST)
- problem in minimization Ma'Mon Hatmal (Tue Nov 08 2016 - 00:01:28 CST)
- Parameters for determining run time Oscar Bastidas (Mon Nov 07 2016 - 16:10:34 CST)
- performance of GPU calculations Hao Dong (Sun Nov 06 2016 - 21:11:40 CST)
- Dear NAMD users msa5 (Thu Nov 03 2016 - 17:18:00 CDT)
- NAMD 2.12b1 released Jim Phillips (Thu Nov 03 2016 - 17:06:48 CDT)
- multiple run commands freeze when using MTS? Brian Radak (Thu Nov 03 2016 - 15:45:40 CDT)
- Hi All msa5 (Tue Nov 01 2016 - 22:06:01 CDT)
- CHARMM22-STAR force field for NAMD Nicholas M. Glykos (Tue Nov 01 2016 - 13:15:48 CDT)
- CHARMM22-STAR force field for NAMD Nicholas M. Glykos (Tue Nov 01 2016 - 13:07:39 CDT)
- Remembering Klaus Schulten Thomas C. Bishop (Tue Nov 01 2016 - 09:33:31 CDT)
- (no subject) Santanu Santra (Mon Oct 31 2016 - 23:22:58 CDT)
- no response from mail list sunyeping (Mon Oct 31 2016 - 19:23:09 CDT)
- is it possible to restrict the access of ions to certain volume? Olya Kravchenko (Mon Oct 31 2016 - 15:28:40 CDT)
- Diagnosing CUDA (non)performance Chris Goedde (Mon Oct 31 2016 - 07:48:31 CDT)
- NAMD Execution Error Oscar Bastidas (Sun Oct 30 2016 - 18:46:19 CDT)
- AW: vmd-l: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. Norman Geist (Thu Oct 27 2016 - 07:50:19 CDT)
- Problem with minimization Ma'Mon Hatmal (Thu Oct 27 2016 - 05:22:52 CDT)
- Turning off and back on fixed atoms Norman Geist (Thu Oct 27 2016 - 05:14:28 CDT)
- NAMD Question: NAMD Message "364"-What does it mean? Oscar Bastidas (Thu Oct 27 2016 - 03:34:17 CDT)
- NAMD Question: How to run on 2-chain system Oscar Bastidas (Wed Oct 26 2016 - 20:08:18 CDT)
- Switch off rescale temperature after some number of timesteps Harish Srinivasan (Wed Oct 26 2016 - 01:05:50 CDT)
- fix disulfide bond in coarse grain(CG) model for NAMD Deng, Jinxia (Nancy) (Mon Oct 24 2016 - 11:46:11 CDT)
- Using NAMD with NMR structure Oscar Bastidas (Sun Oct 23 2016 - 02:00:14 CDT)
- NAMD breaks with wrong timestep Gtz, Alexander (Fri Oct 21 2016 - 08:23:33 CDT)
- mail reg compilation of mdenergy Vidhya Sankar (Wed Oct 19 2016 - 12:08:12 CDT)
- fix disulfide bridge in coarse grain MD Deng, Jinxia (Nancy) (Wed Oct 19 2016 - 11:54:59 CDT)
- Minimization failing on one machine only Chris Goedde (Fri Oct 14 2016 - 15:34:10 CDT)
- Collecting average energies via Tcl callback? Brian Radak (Thu Oct 13 2016 - 11:19:40 CDT)
- visualizing and analyzing long simulation Dhiraj Srivastava (Mon Oct 10 2016 - 10:41:53 CDT)
- NAMD running on a Cluster of Ubuntu Linux Marisol Oswald (Sun Oct 09 2016 - 18:37:55 CDT)
- Reason: FATAL ERROR: Unknown command-line option ++local 孙业平 (Sun Oct 09 2016 - 14:09:47 CDT)
- Re: Tcl clock Mayne, Christopher G (Wed Oct 05 2016 - 09:51:15 CDT)
- question regarding rmsd Dhiraj Srivastava (Tue Oct 04 2016 - 16:07:43 CDT)
- Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
- Re: question regarding rmsd dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
- Re: question regarding rmsd Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
- RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
- Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
- Re: question regarding rmsd Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
- RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
- Re: question regarding rmsd Leandro Martínez (Wed Oct 05 2016 - 15:58:39 CDT)
- Re: question regarding rmsd dhirajks_at_gmail.com (Thu Oct 06 2016 - 17:37:23 CDT)
- Re: question regarding rmsd dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
- Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
- Tcl clock Laura Joana (Tue Oct 04 2016 - 14:10:12 CDT)
- (no subject) Sourav Pal (Mon Oct 03 2016 - 02:44:00 CDT)
- Switch function equation Faramarz Joodaki (Sun Oct 02 2016 - 23:57:40 CDT)
- stripping off water from DCD file except structural water Dhiraj Srivastava (Sun Oct 02 2016 - 22:57:24 CDT)
- Oxidized cysteine parameters for CHARMM36 Gergely Gyimesi (Fri Sep 30 2016 - 08:40:04 CDT)
- Half of the structure goes out of the simulation box! faride badalkhani (Fri Sep 30 2016 - 05:18:51 CDT)
- dcd file frame number Dhiraj Srivastava (Thu Sep 29 2016 - 22:22:54 CDT)
- Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Thu Sep 29 2016 - 00:27:31 CDT)
- ACS COMP Division awards deadline this week Carlos Simmerling (Wed Sep 28 2016 - 11:34:52 CDT)
- Shrinking a polymer to match its density using pbc Sonu Kumar (Wed Sep 28 2016 - 10:21:11 CDT)
- Wrapall on or off? sunyeping (Tue Sep 27 2016 - 00:14:49 CDT)
- graphene with proteins Zeina Salman (Sun Sep 25 2016 - 19:42:51 CDT)
- FEP double annihilation Carlo Guardiani (Fri Sep 23 2016 - 13:28:30 CDT)
- Martini CG models parameters errors Mahad Gatti (Thu Sep 22 2016 - 10:07:34 CDT)
- NAMD Equil Config Jackson Cavett (Thu Sep 22 2016 - 07:24:53 CDT)
- Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. Zach Bonham (Wed Sep 21 2016 - 15:15:45 CDT)
- Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Fri Sep 16 2016 - 15:35:45 CDT)
- COORDINATE DCD FILE WAS NOT CREATED Mihaela Drenscko (Thu Sep 15 2016 - 15:42:20 CDT)
- NAMD2.11 DCD HEADER PROBLEM Marco Sant (Wed Sep 14 2016 - 05:35:31 CDT)
- Running REMD Nicolas Martin (Wed Sep 14 2016 - 03:10:55 CDT)
- GPU acceleration using K40 and k80 Atanu Maity (Wed Sep 14 2016 - 00:32:00 CDT)
- Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 11:19:08 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 15:16:14 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Sourav Ray (Tue Sep 13 2016 - 15:22:47 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 23:10:21 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Wed Sep 14 2016 - 08:32:43 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
- Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 08:34:30 CDT)
- PMF decompostion Azadeh Alavi (Mon Sep 12 2016 - 06:49:50 CDT)
- AW: REMD and sortreplicas program Norman Geist (Mon Sep 12 2016 - 01:05:39 CDT)
- Shear Stress modelling in NAMD James Starlight (Sun Sep 11 2016 - 05:12:26 CDT)
- Simulated annealing, in solvent or in vacuum? faride badalkhani (Thu Sep 08 2016 - 14:21:26 CDT)
- convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Thu Sep 08 2016 - 10:20:03 CDT)
- query in the equilibration step d.ronika_at_iitg.ernet.in (Thu Sep 08 2016 - 07:32:32 CDT)
- Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 04:54:35 CDT)
- Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 00:12:37 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 CDT)
- RE: Query regarding parameter file generation of non standard residue Bennion, Brian (Thu Sep 08 2016 - 11:07:13 CDT)
- Re: Query regarding parameter file generation of non standard residue Vermaas, Joshua (Thu Sep 08 2016 - 11:19:05 CDT)
- RE: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:22:31 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 CDT)
- REMD and sortreplicas program Horia Jalily Hasani (Wed Sep 07 2016 - 19:10:49 CDT)
- Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Wed Sep 07 2016 - 18:06:53 CDT)
- Query regarding parameter file generation of a non standard residue Mahrukh Imtiaz (Wed Sep 07 2016 - 15:12:14 CDT)
- The needed time for a MD simulation faride badalkhani (Mon Sep 05 2016 - 10:11:08 CDT)
- ION CHANNEL gating mechanism Shambo Hore (Sat Sep 03 2016 - 05:42:46 CDT)
- PDB File of Primary structure and Simulation Emerson Macedo (Fri Sep 02 2016 - 11:19:18 CDT)
- did anyone built NAMD with PLUMED on XSEDE Maksym Korablyov (Thu Sep 01 2016 - 09:36:07 CDT)
- FATAL ERROR CUDA error during equilibration using NAMD Abraham A. Gutierrez Hernandez (Tue Aug 30 2016 - 18:27:38 CDT)
- NAMD Question: Generating ensemble of structures Oscar Bastidas (Wed Aug 31 2016 - 00:52:20 CDT)
- Topology and parameter files for liquid methane Monika Madhavi (Wed Aug 31 2016 - 00:24:24 CDT)
- ion escapes the channel during US simulation Olya Kravchenko (Tue Aug 30 2016 - 16:17:26 CDT)
- (no subject) krishna (Mon Aug 29 2016 - 03:03:21 CDT)
- targetCenters in Umbrella Sampling Olya Kravchenko (Wed Aug 24 2016 - 17:50:36 CDT)
- interpretation of eigenvec colvar? JC Gumbart (Tue Aug 23 2016 - 20:02:37 CDT)
- Shrinking a molecule (Colvars and Constant Pressure not working) Sonu Kumar (Mon Aug 22 2016 - 15:21:48 CDT)
- PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 10:30:28 CDT)
- Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 11:23:58 CDT)
- Re: PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 15:10:57 CDT)
- Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 16:27:34 CDT)
- Re: PMF calculation input files Olya Kravchenko (Tue Aug 23 2016 - 10:01:05 CDT)
- Re: PMF calculation input files Vermaas, Joshua (Tue Aug 23 2016 - 11:02:01 CDT)
- Re: PMF calculation input files Olya Kravchenko (Wed Aug 24 2016 - 16:23:30 CDT)
- Re: PMF calculation input files Jérôme Hénin (Wed Aug 24 2016 - 15:22:47 CDT)
- Re: PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 15:10:57 CDT)
- Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 11:23:58 CDT)
- NAMD equilibrium step d.ronika_at_iitg.ernet.in (Mon Aug 22 2016 - 00:34:01 CDT)
- Graphene Oxide Parameter File Marisol Oswald (Sat Aug 20 2016 - 14:25:38 CDT)
- how to rerun a namd trajectory in order to complement the missing snapshots? sunyeping (Thu Aug 18 2016 - 22:35:51 CDT)
- Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 04:21:07 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 09:47:02 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:16:34 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 10:21:30 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:31:53 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:00:16 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:16:57 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:20:22 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:27:39 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:31:05 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:37:31 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Aug 22 2016 - 07:34:17 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 13:59:31 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Tue Aug 23 2016 - 14:16:28 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 14:28:36 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Sep 05 2016 - 06:03:13 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Sep 06 2016 - 16:43:30 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Wed Sep 07 2016 - 01:14:08 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Wed Sep 07 2016 - 09:17:03 CDT)
- RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Thu Aug 18 2016 - 13:29:40 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 13:50:23 CDT)
- RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Fri Aug 19 2016 - 01:42:03 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Fri Aug 19 2016 - 04:00:59 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:16:34 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 09:47:02 CDT)
- Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Tue Aug 16 2016 - 15:41:22 CDT)
- Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Tue Aug 16 2016 - 15:21:32 CDT)
- Lipid Bilayer Shearing Sachin Natesh (Tue Aug 16 2016 - 12:01:15 CDT)
- Introducing PDBManip Ali Khanlarkhani (Tue Aug 16 2016 - 10:10:05 CDT)
- Energy minimization d.ronika_at_iitg.ernet.in (Mon Aug 15 2016 - 00:05:12 CDT)
- psfgen: creating segments without extra hydrogens? Emerson Macedo (Sat Aug 13 2016 - 13:58:49 CDT)
- PMF Calculation Crystal Liu (Fri Aug 12 2016 - 19:15:46 CDT)
- Is it possible to perform NVT FEP on a fluid system? B.W.J. Irwin (Tue Aug 09 2016 - 05:22:08 CDT)
- Energy minimization in NAMD Faramarz Joodaki (Mon Aug 08 2016 - 11:37:45 CDT)
- how to not overwrite a modified file? (while producing coordinates for ABF/US windows) Olya Kravchenko (Sat Aug 06 2016 - 07:18:56 CDT)
- How to replace NAMD Eletrostatic Forces Emerson Macedo (Thu Aug 04 2016 - 13:15:38 CDT)
- Re: How to replace NAMD Eletrostatic Forces Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
- Re: How to replace NAMD Eletrostatic Forces Jérôme Hénin (Thu Aug 04 2016 - 17:21:40 CDT)
- AW: How to replace NAMD Eletrostatic Forces Norman Geist (Fri Aug 05 2016 - 02:33:51 CDT)
- Re: How to replace NAMD Eletrostatic Forces Ajasja Ljubetič (Fri Aug 05 2016 - 02:46:00 CDT)
- Re: How to replace NAMD Eletrostatic Forces Giacomo Fiorin (Fri Aug 05 2016 - 09:45:05 CDT)
- Re: How to replace NAMD Eletrostatic Forces Emerson Macedo (Fri Aug 05 2016 - 10:45:12 CDT)
- Re: How to replace NAMD Eletrostatic Forces Jérôme Hénin (Thu Aug 04 2016 - 17:21:40 CDT)
- Re: How to replace NAMD Eletrostatic Forces Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
- Fatal Error: vdw atom type CC3161 Allen, Caley R (Wed Aug 03 2016 - 09:53:37 CDT)
- Maximum dihedral angle Mahdi Tavakol (Sun Jul 31 2016 - 03:19:16 CDT)
- performance drop during run Chitrak Gupta (Fri Jul 29 2016 - 10:41:32 CDT)
- Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 10:26:13 CDT)
- Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 10:55:51 CDT)
- Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 11:20:46 CDT)
- Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 12:25:49 CDT)
- Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 13:18:08 CDT)
- Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 14:24:21 CDT)
- Re: Generalized Born solvation models supported by NAMD Chitrak Gupta (Fri Jul 29 2016 - 16:05:02 CDT)
- Re: Generalized Born solvation models supported by NAMD Aron Broom (Tue Aug 02 2016 - 09:41:09 CDT)
- Re: Generalized Born solvation models supported by NAMD Chitrak Gupta (Tue Aug 02 2016 - 17:54:08 CDT)
- Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 11:20:46 CDT)
- Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 10:55:51 CDT)
- water permeation through nanotube in lipid bilayer Nikhil Maroli (Fri Jul 29 2016 - 07:18:45 CDT)
- group selection in TCL script for use in NAMD Allen, Caley R (Wed Jul 27 2016 - 13:35:05 CDT)
- SMD Constant velocity pulling Roshan Shrestha (Wed Jul 27 2016 - 12:59:49 CDT)
- (no subject) krishna (Tue Jul 26 2016 - 00:56:38 CDT)
- Msd Mahdiye Azadpour (Sat Jul 23 2016 - 23:21:09 CDT)
- Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:12:47 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:16:57 CDT)
- Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Fri Jul 22 2016 - 11:05:50 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 02:56:06 CDT)
- Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:08:18 CDT)
- Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:26:05 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 10:44:48 CDT)
- Re: Equivalent of gromacs' "rdd" option Axel Kohlmeyer (Mon Jul 25 2016 - 10:16:08 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 02:56:06 CDT)
- Repulsion of lipid bilayer during equilibration Mahrukh Imtiaz (Fri Jul 22 2016 - 05:00:41 CDT)
- System temperature check of specific atoms , sys temp of only coupled atoms? Karson Bader (Thu Jul 21 2016 - 15:36:13 CDT)
- is there a way to prevent ions from entering the channel? Olya Kravchenko (Thu Jul 21 2016 - 12:56:57 CDT)
- Problems with wrapAll Sonu Kumar (Thu Jul 21 2016 - 00:52:55 CDT)
- NAMD related theoretical questions Kostas Malavazos (Wed Jul 20 2016 - 12:33:11 CDT)
- (no subject) d.ronika_at_iitg.ernet.in (Tue Jul 19 2016 - 22:52:43 CDT)
- aMD doesn't work when some atoms are fixed sunyeping (Mon Jul 18 2016 - 20:41:34 CDT)
- namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ Doug Stetner (Tue Jul 12 2016 - 22:51:40 CDT)
- how to reassign dcdfreq?? Faramarz Joodaki (Mon Jul 11 2016 - 22:17:54 CDT)
- Intramolecular interaction energy of protein in vacuum from NAMD simualtions dayanidhi mohanta (Sat Jul 09 2016 - 08:26:13 CDT)
- The adaptTemp and Temp in Adaptive tempering Chenyi L (Thu Jul 07 2016 - 19:51:03 CDT)
- Possible bug in DCD writer, number of frames not in NSET but in 5-ZEROS Norman Geist (Wed Jul 06 2016 - 07:26:01 CDT)
- Inconsistent atom count Laura Joana (Tue Jul 05 2016 - 12:04:44 CDT)
- metadynamics and pmf file Stefano Guglielmo (Mon Jul 04 2016 - 19:43:23 CDT)
- get seed Laura Joana (Fri Jul 01 2016 - 11:52:46 CDT)
- unbinding free energy using ABF Gabriel Jara (Thu Jun 30 2016 - 13:25:27 CDT)
- MDFF based on known EM maps giulia palermo (Tue Jun 28 2016 - 12:08:12 CDT)
- Potential per TS looks wierd faride badalkhani (Mon Jun 27 2016 - 13:18:33 CDT)
- Tesla K80 vs 3 x GTX 980Ti Nikhil Maroli (Sat Jun 25 2016 - 11:24:25 CDT)
- Tesla K80 vs 3 x GTX 980ti Nikhil Maroli (Sat Jun 25 2016 - 08:02:25 CDT)
- PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Fri Jun 24 2016 - 17:01:13 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Tue Jun 28 2016 - 15:57:14 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 16:20:13 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Tue Jun 28 2016 - 16:37:49 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Fri Jul 01 2016 - 15:50:15 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Fri Jul 01 2016 - 18:42:21 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
- transition metal parameters Francesca Lnstad Bleken (Fri Jun 24 2016 - 02:19:01 CDT)
- Exit Command Failure Sarah Sweger (Thu Jun 23 2016 - 08:01:09 CDT)
- The question about Network calculation ľ (Thu Jun 23 2016 - 03:28:47 CDT)
- LJcorrection option in NAMD Yue Qian (Mon Jun 20 2016 - 17:09:04 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Tue Jun 21 2016 - 07:36:06 CDT)
- Re: LJcorrection option in NAMD Jérôme Hénin (Tue Jun 21 2016 - 09:48:12 CDT)
- Re: LJcorrection option in NAMD Grace Brannigan (Tue Jun 21 2016 - 13:03:24 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:22:07 CDT)
- Re: LJcorrection option in NAMD JC Gumbart (Mon Jun 27 2016 - 00:23:12 CDT)
- Re: LJcorrection option in NAMD Grace Brannigan (Mon Jun 27 2016 - 06:41:33 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:04:02 CDT)
- Re: LJcorrection option in NAMD Jérôme Hénin (Tue Jun 21 2016 - 09:48:12 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Tue Jun 21 2016 - 07:36:06 CDT)
- Coarse Grain Angle Parameter Issue Nisler, Collin R. (Fri Jun 17 2016 - 22:37:42 CDT)
- PME vs. cutoff with switching function Benjamin Brown (Fri Jun 17 2016 - 10:25:44 CDT)
- namd2 or charmrun ++local ? Laura Joana (Fri Jun 17 2016 - 11:35:05 CDT)
- RMSD faride badalkhani (Thu Jun 16 2016 - 12:42:32 CDT)
- Colvar orientation and CoG Nicolas Martin (Thu Jun 16 2016 - 09:02:28 CDT)
- Regarding radial distribution function graph siddharth kamal (Thu Jun 16 2016 - 08:31:23 CDT)
- Free energy calculation using MM-GBSA with NAMD Sneha Menon (Wed Jun 15 2016 - 05:50:41 CDT)
- Missing atom type for hydroperoxide Jean-François Fabre (Tue Jun 14 2016 - 10:48:55 CDT)
- Why does the water box collapse in an aMD sunyeping (Mon Jun 13 2016 - 21:11:00 CDT)
- Drude Prepper error in genic Francesco Pietra (Mon Jun 13 2016 - 01:33:15 CDT)
- Permeation of liquid through Silicon Dioxide Crystal Roshan Shrestha (Fri Jun 10 2016 - 07:30:00 CDT)
- Topology Command in VMD Eric Weine (Thu Jun 09 2016 - 19:27:39 CDT)
- The adaptTemp and Temp in Adaptive tempering henyi (Thu Jun 09 2016 - 15:17:25 CDT)
- Building PSF for the system prepared by Packmol faride badalkhani (Thu Jun 09 2016 - 09:27:31 CDT)
- NBFIX parameters for Calcium ion Azadeh Alavi (Thu Jun 09 2016 - 04:49:04 CDT)
- ATP - CGENFF Benjamin Hill (Tue Jun 07 2016 - 19:34:15 CDT)
- An script for ACF faride badalkhani (Tue Jun 07 2016 - 16:37:13 CDT)
- Help about Drude Prepper Francesco Pietra (Tue Jun 07 2016 - 10:06:48 CDT)
- cgenff Benjamin Hill (Mon Jun 06 2016 - 14:48:30 CDT)
- How can I find the proper number of solvent molecules in the simulation? faride badalkhani (Mon Jun 06 2016 - 09:25:50 CDT)
- Colvars order in the pmf file Marlon Sidore (Mon Jun 06 2016 - 09:14:53 CDT)
- much larger diameter of ssDNA, Aliasghar Alizadeh-Mojarad (Sat Jun 04 2016 - 04:22:41 CDT)
- namdenergy and bigdcd Grant Schauer (Thu Jun 02 2016 - 23:58:23 CDT)
- Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 04:20:29 CDT)
- Is GPU double-precision floating point performance important for NAMD? Mert Gür (Thu Jun 02 2016 - 16:48:07 CDT)
- autocorrelation function faride badalkhani (Thu Jun 02 2016 - 09:06:04 CDT)
- download stmv files for benchmarking Bennion, Brian (Wed Jun 01 2016 - 14:29:22 CDT)
- non-standard solvants faride badalkhani (Wed Jun 01 2016 - 11:55:28 CDT)
- Simulation runs only in background Roshan Shrestha (Wed Jun 01 2016 - 03:44:15 CDT)
- Umbrella sampling of 2 CNT's taking distance as collective variable Kashish Punjani (Wed Jun 01 2016 - 01:16:45 CDT)
- (no subject) Srijita Paul (Tue May 31 2016 - 23:29:11 CDT)
- Using Mergestructs Eric Weine (Tue May 31 2016 - 14:09:46 CDT)
- namd "WARNING: ignoring command" problem Shambo Hore (Tue May 31 2016 - 12:11:35 CDT)
- (no subject) Srijita Paul (Tue May 31 2016 - 05:03:47 CDT)
- Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Mon May 30 2016 - 11:28:24 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 08:41:23 CDT)
- Re: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue May 31 2016 - 11:18:08 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Thu Jun 02 2016 - 01:33:55 CDT)
- Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Thu Jun 02 2016 - 10:59:56 CDT)
- AW: AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Fri Jun 03 2016 - 01:39:54 CDT)
- Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue Jun 07 2016 - 11:21:09 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 08:41:23 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
- SMD simulation problem. Shambo Hore (Sun May 29 2016 - 20:15:57 CDT)
- Conversion from GROMACS .top .itp to CHARMM .psf .par combo Sourav Ray (Sat May 28 2016 - 10:00:54 CDT)
- setting up simulation in vmd using charmm 36 forcefield Rabeta Yeasmin (Fri May 27 2016 - 16:28:38 CDT)
- More FEP using separated topologies David Huggins (Fri May 27 2016 - 15:21:01 CDT)
- Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Fri May 27 2016 - 09:43:28 CDT)
- No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 05:42:02 CDT)
- No parameter for ribose ring, Charmm 27 Benjamin Hill (Thu May 26 2016 - 17:18:43 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Thu May 26 2016 - 18:42:52 CDT)
- Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Fri May 27 2016 - 14:14:17 CDT)
- RE: No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 15:28:43 CDT)
- Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Sun May 29 2016 - 11:12:07 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Mon May 30 2016 - 07:19:44 CDT)
- Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Thu May 26 2016 - 18:42:52 CDT)
- truncated text RE: external computational power for NAMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:59:40 CDT)
- external computational power for NAMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:02:54 CDT)
- Binding energy of organic molecules/small peptides on the surface of Silicon Dioxide Roshan Shrestha (Thu May 26 2016 - 10:29:01 CDT)
- FES analysis Stefano Guglielmo (Tue May 24 2016 - 15:46:21 CDT)
- hyper-branched polymers faride badalkhani (Tue May 24 2016 - 09:24:41 CDT)
- I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 14:41:54 CDT)
- Re: I cannot make MD simulation constant in pressure Jeff Comer (Mon May 23 2016 - 16:06:17 CDT)
- Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 18:29:14 CDT)
- Re: I cannot make MD simulation constant in pressure Peter Freddolino (Mon May 23 2016 - 21:01:23 CDT)
- Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 22:44:21 CDT)
- Re: I cannot make MD simulation constant in pressure Peter Freddolino (Mon May 23 2016 - 22:56:48 CDT)
- Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 18:29:14 CDT)
- Re: I cannot make MD simulation constant in pressure Jeff Comer (Mon May 23 2016 - 16:06:17 CDT)
- namd leaves zombie processes on nodes? JC Gumbart (Mon May 23 2016 - 10:01:45 CDT)
- firstTimestep error message Laura Joana (Mon May 23 2016 - 05:55:51 CDT)
- SMD simulation problem Shambo Hore (Sun May 22 2016 - 10:37:52 CDT)
- Parameters for HS(CH2)11NH2 Natnael Doilicho (Fri May 20 2016 - 19:06:55 CDT)
- H-bonds in charmm36 with namd2.11 Francesco Pietra (Fri May 20 2016 - 16:18:22 CDT)
- Have GPU-accelerated NAMD Questions? Join us for a Live Webinar MARK (Fri May 20 2016 - 13:07:08 CDT)
- Adsorption energy of protein in vacuum Madhulika Gupta (Fri May 20 2016 - 06:01:05 CDT)
- Restart multiple walker ABF Atanu Maity (Thu May 19 2016 - 03:32:24 CDT)
- TIP4P water with flexible bonds Hartling, Kathryn (Wed May 18 2016 - 14:32:24 CDT)
- Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
- MDFF with two symmetry groups Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
- Error associated with protected variable initialization: Nightly Build version Sourav Ray (Tue May 17 2016 - 13:50:54 CDT)
- Postdoc position available Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:05:18 CDT)
- ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
- running simulations in successive steps faride badalkhani (Mon May 16 2016 - 17:31:31 CDT)
- Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 16:29:32 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Jérôme Hénin (Tue May 17 2016 - 14:44:52 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Wed May 18 2016 - 13:25:44 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Thu May 19 2016 - 16:21:08 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Fri May 20 2016 - 07:47:33 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Jérôme Hénin (Fri May 20 2016 - 10:25:03 CDT)
- RE: Excessively high dE_avg values in FEP output (NAMD CVS) Radak, Brian K (Fri May 20 2016 - 11:58:43 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
- Combining Drude structures Jeff Comer (Mon May 16 2016 - 16:25:32 CDT)
- Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 12:42:27 CDT)
- Particle Mesh Ewald with Martini Sourav Ray (Mon May 16 2016 - 10:55:14 CDT)
- Some questions on the Deca-Alanine ABF tutorial sunyeping (Mon May 16 2016 - 04:19:33 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial Jérôme Hénin (Tue May 17 2016 - 10:33:03 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 03:06:08 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 20:29:46 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Thu May 19 2016 - 22:41:05 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial Jérôme Hénin (Fri May 20 2016 - 08:07:03 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial Jérôme Hénin (Tue May 17 2016 - 10:33:03 CDT)
- CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 02:45:55 CDT)
- Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 04:30:29 CDT)
- Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Peter Freddolino (Mon May 16 2016 - 07:46:47 CDT)
- Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 08:54:31 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params JC Gumbart (Tue May 17 2016 - 09:29:52 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Tue May 17 2016 - 11:43:05 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Pardis Tabaee (Fri May 20 2016 - 11:12:24 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 08:54:45 CDT)
- Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Peter Freddolino (Mon May 16 2016 - 07:46:47 CDT)
- Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 04:30:29 CDT)
- Equilibration and production run dhirajks_at_gmail.com (Mon May 16 2016 - 01:25:32 CDT)
- Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 16:34:18 CDT)
- Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 17:08:31 CDT)
- Re: Coarse-grained simulation with Polarizable Water crashing Jeff Comer (Mon May 16 2016 - 12:04:43 CDT)
- Conversion from c6 and c12 = 0 to sigma epsilon Sourav Ray (Sat May 14 2016 - 06:29:49 CDT)
- Output temperature not agreeing with tcouple temperature Karson Bader (Fri May 13 2016 - 12:07:52 CDT)
- Martini polarizable water topology and/or psf file Sourav Ray (Thu May 12 2016 - 17:30:57 CDT)
- PMF calculation using ABF Souvik Sinha (Tue May 10 2016 - 08:57:52 CDT)
- PMEProcessors setting on one node dhirajks_at_gmail.com (Sun May 08 2016 - 21:22:54 CDT)
- gradual heating problem Dhiraj Srivastava (Sun May 08 2016 - 10:27:39 CDT)
- (no subject) Srijita Paul (Sat May 07 2016 - 06:17:48 CDT)
- LJ parameters for Pd surface Madhulika Gupta (Fri May 06 2016 - 08:33:03 CDT)
- Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Pardis Tabaee (Fri May 06 2016 - 08:05:10 CDT)
- heating in NPT ensemble Dhiraj Srivastava (Thu May 05 2016 - 17:39:35 CDT)
- NAMD Recipe for Success with GPUs! MARK (Thu May 05 2016 - 11:35:42 CDT)
- Colvars crossing "upperboundary" limit Sourav Ray (Thu May 05 2016 - 05:33:26 CDT)
- Recipe for Success - GPU accelerated NAMD Mark Berger (Wed May 04 2016 - 19:25:24 CDT)
- excluding non-bonded interactions between two proteins JC Gumbart (Wed May 04 2016 - 18:16:26 CDT)
- parameterization of cations faride badalkhani (Wed May 04 2016 - 11:28:59 CDT)
- parameterizing a new solvent faride badalkhani (Tue May 03 2016 - 08:54:06 CDT)
- TCL Scripting for Force Calculations Allen, Caley R (Mon May 02 2016 - 10:48:56 CDT)
- unix path length limits for namd Chris Goedde (Sun May 01 2016 - 17:10:34 CDT)
- water box and padding Dhiraj Srivastava (Sat Apr 30 2016 - 11:40:53 CDT)
- Compilation of NAMD for CUDA and replica exchange #YEO JINGJIE# (Fri Apr 29 2016 - 13:53:44 CDT)
- Dihedral missing faride badalkhani (Thu Apr 28 2016 - 17:54:15 CDT)
- restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 14:49:45 CDT)
- Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:00:57 CDT)
- Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:13:00 CDT)
- Re: restart file - langevin options removed? Josh Vermaas (Thu Apr 28 2016 - 15:16:41 CDT)
- Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:17:35 CDT)
- Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:28:57 CDT)
- Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:36:52 CDT)
- Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:59:09 CDT)
- Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:13:00 CDT)
- Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:00:57 CDT)
- minimization, heating, equilibration and production run in one script Dhiraj Srivastava (Thu Apr 28 2016 - 10:05:55 CDT)
- Running a test simulation using GPU only (without any CPU core) Sourav Ray (Thu Apr 28 2016 - 09:40:00 CDT)
- Autoionize and topology Dhiraj Srivastava (Tue Apr 26 2016 - 22:07:04 CDT)
- accessing values of 'extendedLagrangian' fictious degree of freedom Prabhakar Bhimalapuram (Tue Apr 26 2016 - 22:01:58 CDT)
- CHARMM36 and TIP3 Dhiraj Srivastava (Tue Apr 26 2016 - 13:37:49 CDT)
- Amino acid as ligand Dhiraj Srivastava (Mon Apr 25 2016 - 12:22:24 CDT)
- Alchemify Possibilities David Huggins (Mon Apr 25 2016 - 11:03:10 CDT)
- Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Mon Apr 25 2016 - 10:42:52 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! Jeff Comer (Tue Apr 26 2016 - 16:14:50 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:22:02 CDT)
- RE: Constraint failure in RATTLE algorithm for atom 6! Radak, Brian K (Tue Apr 26 2016 - 16:26:30 CDT)
- RE: Constraint failure in RATTLE algorithm for atom 6! Bennion, Brian (Tue Apr 26 2016 - 16:29:09 CDT)
- RE: Constraint failure in RATTLE algorithm for atom 6! Radak, Brian K (Tue Apr 26 2016 - 16:40:45 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:46:40 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:47:59 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:22:02 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! Jeff Comer (Tue Apr 26 2016 - 16:14:50 CDT)
- XPLOR format PSF file for small molecules Felix W.-H. Weng (Sun Apr 24 2016 - 11:21:45 CDT)
- Why wrapped and unwrapped trajectories show different energies over the time? zeynab hoseyni (Sat Apr 23 2016 - 21:22:04 CDT)
- Why wrapped and unwrapped trajectories show different energies over time? zeynab mohamad hoseyni (Sat Apr 23 2016 - 09:30:08 CDT)
- SMD in NAMD Madhulika Gupta (Sat Apr 23 2016 - 05:15:34 CDT)
- WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Nicholus Bhattacharjee (Fri Apr 22 2016 - 08:21:46 CDT)
- Re: Replica exchange arpita agarwal (Fri Apr 22 2016 - 02:54:50 CDT)
- (no subject) Srijita Paul (Fri Apr 22 2016 - 01:19:21 CDT)
- Replica exchange arpita agarwal (Thu Apr 21 2016 - 00:43:44 CDT)
- cell basis vectors faride badalkhani (Wed Apr 20 2016 - 13:59:11 CDT)
- rotation angle giulia palermo (Wed Apr 20 2016 - 12:25:16 CDT)
- How to use a proper force constant to decrease computational cost while keeping calculation precision? wliu (Wed Apr 20 2016 - 02:18:01 CDT)
- simulation of hyperbranched polymers faride badalkhani (Tue Apr 19 2016 - 07:54:49 CDT)
- clarification sem ciccioni (Mon Apr 18 2016 - 16:21:08 CDT)
- Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru (Mon Apr 18 2016 - 14:35:38 CDT)
- initial structure faride badalkhani (Mon Apr 18 2016 - 10:17:30 CDT)
- ERROR: ofstream_namd::close() called when file is not open Souvik Sinha (Mon Apr 18 2016 - 02:36:33 CDT)
- (no subject) Srijita Paul (Sat Apr 16 2016 - 00:06:47 CDT)
- initial structure faride badalkhani (Fri Apr 15 2016 - 14:18:03 CDT)
- NAMD Developer Workshop: May 26-27 in Chicago, IL Jodi Ann Hadden (Fri Apr 15 2016 - 13:14:22 CDT)
- Bad initial structure? faride badalkhani (Thu Apr 14 2016 - 13:50:14 CDT)
- Sugar phosphate topology and parameter Dhiraj Srivastava (Thu Apr 14 2016 - 00:32:55 CDT)
- Regarding Bionanotechnology tutorial arpita agarwal (Wed Apr 13 2016 - 20:07:26 CDT)
- Dynamics of an interface Water/Hexane Jean-François Fabre (Wed Apr 13 2016 - 07:54:17 CDT)
- (no subject) Srijita Paul (Wed Apr 13 2016 - 07:08:28 CDT)
- Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 16:49:21 CDT)
- Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Tue Apr 12 2016 - 16:54:35 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 17:02:19 CDT)
- Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Wed Apr 13 2016 - 08:02:36 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 08:32:29 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 12:55:28 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Thu Apr 14 2016 - 09:56:07 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 17:02:19 CDT)
- Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Tue Apr 12 2016 - 16:54:35 CDT)
- Unexpected(?) callback behavior when minimizing before MD Radak, Brian K (Tue Apr 12 2016 - 16:02:34 CDT)
- (no subject) Srijita Paul (Tue Apr 12 2016 - 07:33:41 CDT)
- Few doubt on the numbers implying in REMD simulation Nicholus Bhattacharjee (Tue Apr 12 2016 - 07:06:42 CDT)
- Corrfunc output not generated Sourav Ray (Mon Apr 11 2016 - 12:38:39 CDT)
- Ru surface potential Madhulika Gupta (Mon Apr 11 2016 - 03:52:26 CDT)
- Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Sat Apr 09 2016 - 12:11:53 CDT)
- Metadynamics simulation with Radius of Gyration and RMSD variation - 1 Sourav Ray (Sat Apr 09 2016 - 12:03:36 CDT)
- Running Charmm36 Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri Apr 08 2016 - 19:04:49 CDT)
- (no subject) Srijita Paul (Fri Apr 08 2016 - 08:00:25 CDT)
- LJ Parameters for Au and S and harmonic constraints Madhulika Gupta (Fri Apr 08 2016 - 02:18:29 CDT)
- Simulated annealing error faride badalkhani (Thu Apr 07 2016 - 13:13:38 CDT)
- Packing of different system Srijita Paul (Thu Apr 07 2016 - 10:51:32 CDT)
- simulated annealing faride badalkhani (Thu Apr 07 2016 - 08:14:10 CDT)
- Few doubt on the numbers implying in REMD simulatio Nicholus Bhattacharjee (Thu Apr 07 2016 - 03:34:44 CDT)
- FEP/REMD with NAMD2.11 - missing alchLambda? Nathan Lim (Wed Apr 06 2016 - 20:42:58 CDT)
- water box has a weird shape faride badalkhani (Wed Apr 06 2016 - 13:21:28 CDT)
- restart a job Farideh Badalkhani Khamseh (Wed Apr 06 2016 - 11:57:49 CDT)
- simulated annealing faride badalkhani (Wed Apr 06 2016 - 11:24:30 CDT)
- Post Doctoral Fellow Opening at IBM for Biomolecular Modeling Tien Huynh (Tue Apr 05 2016 - 18:30:43 CDT)
- Few doubt on the numbers implying in REMD simulation Nicholus Bhattacharjee (Tue Apr 05 2016 - 10:00:50 CDT)
- Constraint failure in RATTLE algorithm for atom 538 faride badalkhani (Tue Apr 05 2016 - 09:57:30 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 538 Brian Radak (Tue Apr 05 2016 - 10:04:40 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 538 Chitrak Gupta (Tue Apr 05 2016 - 10:10:44 CDT)
- problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 06:35:23 CDT)
- why does the transition seem to be irreversible in aMD sunyeping (Mon Apr 04 2016 - 22:21:00 CDT)
- AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 02:29:42 CDT)
- Re: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 02:47:39 CDT)
- AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 03:06:43 CDT)
- Re: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 04:10:59 CDT)
- AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 04:31:27 CDT)
- Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Brian Radak (Tue Apr 05 2016 - 09:42:27 CDT)
- Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Mon May 23 2016 - 03:53:37 CDT)
- AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Mon May 23 2016 - 08:42:04 CDT)
- AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue May 24 2016 - 00:57:09 CDT)
- Re: AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Wed May 25 2016 - 00:48:18 CDT)
- Re: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 02:47:39 CDT)
- AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 02:29:42 CDT)
- Dihedral parameter missing faride badalkhani (Mon Apr 04 2016 - 16:26:03 CDT)
- Wrapping molecules in a NAMD simulation Sourav Ray (Mon Apr 04 2016 - 08:23:02 CDT)
- Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Loison Claire (Mon Apr 04 2016 - 07:16:22 CDT)
- Stray PME grid charges detected faride badalkhani (Sun Apr 03 2016 - 12:49:18 CDT)
- Running multi-node jobs on Sun Grid Engine Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
- Steered MD diminishing distances giulia palermo (Sat Apr 02 2016 - 20:29:14 CDT)
- maximum coordinate is negative for z faride badalkhani (Fri Apr 01 2016 - 12:14:17 CDT)
- Occasional performance slow down using NAMD with Xeon Phi Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
- Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 10:11:07 CDT)
- constant velocity pulling Jamal Zanjani (Thu Mar 31 2016 - 06:04:18 CDT)
- segmentation fault (core dumped) faride badalkhani (Wed Mar 30 2016 - 16:24:26 CDT)
- "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:04:07 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:23:46 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:49:01 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 19:33:49 CDT)
- AW: "Jump" in Energy and Volume graphs of my MD Norman Geist (Thu Mar 31 2016 - 01:00:46 CDT)
- Re: AW: "Jump" in Energy and Volume graphs of my MD Brian Radak (Thu Mar 31 2016 - 07:56:32 CDT)
- Re: AW: "Jump" in Energy and Volume graphs of my MD Jeff Comer (Thu Mar 31 2016 - 08:44:50 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Thu Mar 31 2016 - 09:13:46 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Thu Mar 31 2016 - 11:21:03 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD David Hardy (Fri Apr 01 2016 - 12:09:44 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:23:46 CDT)
- problem with angle parameters faride badalkhani (Wed Mar 30 2016 - 09:01:20 CDT)
- size of water box and cellbasisvectors faride badalkhani (Wed Mar 30 2016 - 07:51:14 CDT)
- Mixing all_36_cgenff with all_36_prot Francesco Pietra (Sat Mar 26 2016 - 13:02:27 CDT)
- HBB2-pol R. Charbel MAROUN (Fri Mar 25 2016 - 09:01:46 CDT)
- Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Fri Mar 25 2016 - 08:37:31 CDT)
- varying two colvar distances simultaneously Chitrak Gupta (Thu Mar 24 2016 - 16:49:06 CDT)
- Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Thu Mar 24 2016 - 14:29:02 CDT)
- force units conversion Olya Kravchenko (Thu Mar 24 2016 - 14:15:05 CDT)
- Restarting ABF Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Tue Mar 22 2016 - 13:45:51 CDT)
- instantaneous pressure and temp change for multiple run calls? Radak, Brian K (Tue Mar 22 2016 - 13:21:53 CDT)
- Parameterizing residues of a polymer faride badalkhani (Tue Mar 22 2016 - 12:47:57 CDT)
- Parameterizing residues of a polymer faride badalkhani (Tue Mar 22 2016 - 09:17:46 CDT)
- AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 04:26:39 CDT)
- AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 03:44:44 CDT)
- GPU configuration suggestions Nikhil Maroli (Tue Mar 22 2016 - 00:52:25 CDT)
- Postdoctoral opening in biomolecular modeling at IBM Payel Das (Mon Mar 21 2016 - 16:38:19 CDT)
- Basic validation of CGenFF faride badalkhani (Mon Mar 21 2016 - 07:31:05 CDT)
- Testing NAMD scalability Éric Germaneau (Fri Mar 18 2016 - 20:31:31 CDT)
- CGENFF validation faride badalkhani (Fri Mar 18 2016 - 15:12:56 CDT)
- Manganese force field Taejin Kim (Fri Mar 18 2016 - 14:07:35 CDT)
- dynamic_cast & runtime type information Éric Germaneau (Fri Mar 18 2016 - 11:46:10 CDT)
- charge group faride badalkhani (Fri Mar 18 2016 - 10:56:42 CDT)
- Re: ------------- Processor 0 Exiting: Called CmiAbort ------------ Pardis Tabaee (Thu Mar 17 2016 - 12:09:43 CDT)
- adaptive biasing force with RMSD colvar Haleh a (Thu Mar 17 2016 - 11:39:45 CDT)
- Appropriate FF for a specific solvent faride badalkhani (Thu Mar 17 2016 - 10:48:57 CDT)
- 2016 ISQBP Meeting: early registration / abstract submission deadline approaching Vlad Cojocaru (Thu Mar 17 2016 - 03:49:47 CDT)
- NAMD 2.11 CUDA freezes on windows 8 Ajasja Ljubetič (Wed Mar 16 2016 - 13:08:59 CDT)
- NAMD survey starting Jim Phillips (Tue Mar 15 2016 - 13:34:00 CDT)
- restarting simulation Francesco Pietra (Mon Mar 14 2016 - 09:45:44 CDT)
- WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Mon Mar 14 2016 - 04:47:28 CDT)
- Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
- Tcl script for simulated tempering? Radak, Brian K (Fri Mar 11 2016 - 16:12:21 CST)
- AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
- Re: AW: Tcl script for simulated tempering? Brian Radak (Tue Mar 15 2016 - 08:14:11 CDT)
- AW: AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 10:21:11 CDT)
- RE: AW: Tcl script for simulated tempering? Radak, Brian K (Tue Mar 15 2016 - 13:01:56 CDT)
- AW: AW: Tcl script for simulated tempering? Norman Geist (Wed Mar 16 2016 - 05:10:14 CDT)
- RE: AW: Tcl script for simulated tempering? Radak, Brian K (Wed Mar 16 2016 - 10:17:07 CDT)
- Re: AW: Tcl script for simulated tempering? Brian Radak (Tue Mar 15 2016 - 08:14:11 CDT)
- AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
- Urey-Bradley parameters faride badalkhani (Fri Mar 11 2016 - 09:10:39 CST)
- AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Norman Geist (Thu Mar 10 2016 - 16:43:55 CST)
- problem with bringing down the pressure faride badalkhani (Thu Mar 10 2016 - 11:31:36 CST)
- periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Wed Mar 09 2016 - 21:23:05 CST)
- AW: periodic boundary condition in XY, hard wall in Z - errors Norman Geist (Thu Mar 10 2016 - 01:05:33 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Thu Mar 10 2016 - 15:58:45 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 20:01:12 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:34:35 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 14:57:55 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 15:31:50 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 21:42:23 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Mon Mar 14 2016 - 11:24:35 CDT)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Tue Mar 15 2016 - 14:48:58 CDT)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Tue Mar 15 2016 - 15:50:18 CDT)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:39:06 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
- AW: periodic boundary condition in XY, hard wall in Z - errors Norman Geist (Thu Mar 10 2016 - 01:05:33 CST)
- equilibration error faride badalkhani (Wed Mar 09 2016 - 15:22:25 CST)
- Hands-On Workshop on Computational Biophysics: June 6-10 in Pittsburgh, PA Jodi Ann Hadden (Wed Mar 09 2016 - 14:34:10 CST)
- NAMD Developer Workshop: May 26-27 in Chicago, IL Jodi Ann Hadden (Wed Mar 09 2016 - 14:31:56 CST)
- cellBasisVectors faride badalkhani (Wed Mar 09 2016 - 10:27:53 CST)
- installing NAMD 2.11 faride badalkhani (Wed Mar 09 2016 - 07:32:46 CST)
- Tutorial example of replica exchange Dr. Eddie (Tue Mar 08 2016 - 16:55:34 CST)
- AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 02:03:38 CST)
- Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 09:46:50 CST)
- Re: Tutorial example of replica exchange Josh Vermaas (Thu Mar 10 2016 - 10:04:07 CST)
- Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 12:26:19 CST)
- AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 16:53:22 CST)
- Re: Tutorial example of replica exchange Dr. Eddie (Fri Mar 11 2016 - 09:35:03 CST)
- Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 09:46:50 CST)
- AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 02:03:38 CST)
- selection error in forces script Olya Kravchenko (Mon Mar 07 2016 - 23:02:34 CST)
- segmentation error Stefano Guglielmo (Fri Mar 04 2016 - 04:15:01 CST)
- applying constant force only within certain part of simulation cell? Olya Kravchenko (Thu Mar 03 2016 - 14:00:33 CST)
- Constraint failure in RATTLE algorithm Stefano Guglielmo (Tue Mar 01 2016 - 19:18:05 CST)
- Re: INTERNAL COORDINATES Josh Vermaas (Tue Mar 01 2016 - 08:28:33 CST)
- INTERNAL COORDINATES faride badalkhani (Tue Mar 01 2016 - 07:52:09 CST)
- Combination of top_all36_cgenff with top_all36_prot faride badalkhani (Mon Feb 29 2016 - 15:03:31 CST)
- Energy gradient in colvars.state file Carlo Guardiani (Mon Feb 29 2016 - 13:09:31 CST)
- Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Mon Feb 29 2016 - 02:43:31 CST)
- AW: problem in running targeted MD Norman Geist (Mon Feb 29 2016 - 01:37:21 CST)
- plumed Stefano Guglielmo (Sun Feb 28 2016 - 10:21:32 CST)
- Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Fri Feb 26 2016 - 05:20:03 CST)
- AW: problem in running targeted MD Norman Geist (Fri Feb 26 2016 - 01:57:15 CST)
- test area method to calculate surface tension Yan Shen (Thu Feb 25 2016 - 15:05:45 CST)
- problem in running targeted MD giulia palermo (Wed Feb 24 2016 - 19:56:11 CST)
- AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Mon Feb 22 2016 - 02:04:39 CST)
- AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Fri Feb 19 2016 - 01:47:51 CST)
- external HPC resource Deng, Jinxia (Nancy) (Thu Feb 18 2016 - 10:23:36 CST)
- Should you cap C and N termini? ashika torikora (Thu Feb 18 2016 - 07:09:10 CST)
- Energy increase with fixed atoms in POPC membrane Mihaela Drenscko (Wed Feb 17 2016 - 16:27:15 CST)
- AW: vmd-l: moving atoms and updating distances Norman Geist (Mon Feb 15 2016 - 00:11:47 CST)
- Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
- Non respect of sequence of commands in command file R. Charbel MAROUN (Fri Feb 12 2016 - 05:11:39 CST)
- velocity computation Patrick Welche (Fri Feb 05 2016 - 13:05:25 CST)
- namd on Windows 10 Branko (Thu Feb 04 2016 - 12:24:14 CST)
- About parseFEP error Atsutoshi Okabe (Wed Feb 03 2016 - 08:01:21 CST)
- bond energy high Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
- NAMD Implicit GB Parameters Samuel Bowerman (Mon Feb 01 2016 - 12:41:03 CST)
- Lennard-Jones potential in coarse grained MD Yongcheng Zhou (Sat Jan 30 2016 - 00:36:20 CST)
- Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy yeguoqiao (Fri Jan 29 2016 - 09:05:31 CST)
- tclBC relective boundaries Art (Fri Jan 29 2016 - 13:51:17 CST)
- MD trajectory analysis Deng, Jinxia (Nancy) (Thu Jan 28 2016 - 13:02:14 CST)
- PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Wed Jan 27 2016 - 07:54:34 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand Ajasja Ljubetič (Wed Jan 27 2016 - 09:21:11 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Wed Jan 27 2016 - 09:22:40 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 05:26:33 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Thu Jan 28 2016 - 09:43:21 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 11:03:17 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Thu Jan 28 2016 - 11:09:08 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 11:59:14 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand Jeff Comer (Thu Jan 28 2016 - 12:38:45 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Mon Feb 01 2016 - 10:39:06 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 05:26:33 CST)
- AW: PBC in lipid bilayer: receptor vs. ligand Norman Geist (Wed Jan 27 2016 - 09:35:05 CST)
- (no subject) Srijita Paul (Tue Jan 26 2016 - 23:06:12 CST)
- (no subject) Srijita Paul (Tue Jan 26 2016 - 23:02:28 CST)
- segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 07:58:49 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 08:14:47 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 11:08:22 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:11:58 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 12:23:01 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:31:10 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 12:47:00 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 08:14:47 CST)
- AW: PBC BUG in coorfile + pair interaction Norman Geist (Mon Jan 25 2016 - 02:33:18 CST)
- calculating replica exchange acceptance ratio Chitrak Gupta (Sun Jan 24 2016 - 23:16:09 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 04:37:56 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 05:51:31 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:51:48 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:58:31 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Tue Jan 26 2016 - 08:03:40 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Wed Jan 27 2016 - 04:18:38 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
- compute capability Stefano Guglielmo (Sun Jan 24 2016 - 17:15:43 CST)
- charmc rpath Scott Brozell (Thu Jan 21 2016 - 22:04:41 CST)
- PBC BUG in coorfile + pair interaction Norman Geist (Thu Jan 21 2016 - 03:50:59 CST)
- Enabling GPU for REUS Abhishek TYAGI (Wed Jan 20 2016 - 21:12:50 CST)
- Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
- AW: Re: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:07:59 CST)
- AW: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:09:24 CST)
- Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Mon Jan 25 2016 - 01:49:23 CST)
- Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
- multipld .dcd analysis by VMD Deng, Jinxia (Nancy) (Wed Jan 20 2016 - 13:53:21 CST)
- LSU SuperMIC Jeff Comer (Tue Jan 19 2016 - 16:21:39 CST)
- Replica Exchange Dr. Eddie (Tue Jan 19 2016 - 10:35:00 CST)
- about User-Defined Forces ߾ (Mon Jan 18 2016 - 03:28:31 CST)
- RE: RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 22:02:44 CST)
- Recover the PMF along an unbiased CV Felipe Merino (Thu Jan 14 2016 - 16:11:37 CST)
- 2.11 how to remove charmrun remote-shell options Scott Brozell (Wed Jan 13 2016 - 12:04:54 CST)
- restart namd calculations Bylund, Tatsiana (NIH/NIAID) [F] (Tue Jan 12 2016 - 16:55:09 CST)
- Aoid protein to reach periodic boundary Dharmeshkumar Patel (Mon Jan 11 2016 - 18:15:16 CST)
- Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Mon Jan 11 2016 - 13:10:19 CST)
- AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
- RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
- AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 08:31:52 CST)
- RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 09:44:54 CST)
- AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 13:23:21 CST)
- RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 14:04:36 CST)
- Re: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Brunner, Robert Kraemer (Tue Jan 12 2016 - 14:31:36 CST)
- AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Wed Jan 13 2016 - 02:17:01 CST)
- RE: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Wed Jan 13 2016 - 22:28:53 CST)
- RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
- AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
- Fwd: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
- TIP4P/2005 par file by Jordi Faraudo Monika Madhavi (Sat Jan 09 2016 - 07:16:17 CST)
- PhD and postdoctoral positions in biomolecular simulation Allison, Jane (Thu Jan 07 2016 - 19:01:29 CST)
- Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 06:49:51 CST)
- Re: Regarding system forces in NAMD Jérôme Hénin (Thu Jan 07 2016 - 08:37:07 CST)
- Regarding merging of .grad files obtained from ABF simulations sruthi c k (Thu Jan 07 2016 - 01:49:18 CST)
- (no subject) Srijita Paul (Wed Jan 06 2016 - 22:25:56 CST)
- solvent other than water Deng, Jinxia (Nancy) (Wed Jan 06 2016 - 12:17:11 CST)
- Equilibration fails for long time ,NPT Nikhil Maroli (Sun Jan 03 2016 - 11:42:32 CST)
- GBIS error sunyeping (Sat Jan 02 2016 - 22:55:10 CST)
- Energy decomposition analyse in NAMD sunyzero (Mon Dec 28 2015 - 20:23:28 CST)
- Restraints on the outer solutes Diksha Dubey (Mon Dec 28 2015 - 03:39:00 CST)
- mail reg parameters Vidhya Sankar (Fri Dec 25 2015 - 20:51:57 CST)
- DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1 Srijita Paul (Fri Dec 25 2015 - 00:41:47 CST)
- SMD with PBC Mahdi Tavakol (Thu Dec 24 2015 - 00:22:36 CST)
- Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:01 CST)
- Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Thu Dec 24 2015 - 08:45:43 CST)
- Re: Add ions/molecules different from Autoionize defaults amin_at_imtech.res.in (Fri Dec 25 2015 - 07:16:46 CST)
- Re: Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Fri Dec 25 2015 - 12:28:43 CST)
- Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Sat Dec 26 2015 - 21:12:23 CST)
- Re: Add ions/molecules different from Autoionize defaults Josh Vermaas (Sun Dec 27 2015 - 06:25:50 CST)
- Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Sun Dec 27 2015 - 22:04:00 CST)
- Re: Add ions/molecules different from Autoionize defaults Tristan Croll (Tue Dec 29 2015 - 07:12:10 CST)
- Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Thu Dec 24 2015 - 08:45:43 CST)
- Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Wed Dec 23 2015 - 12:05:36 CST)
- LangevinDamping Coefficient for MARTINI Mahdi Tavakol (Wed Dec 23 2015 - 05:33:48 CST)
- NAMD 2.11 released Jim Phillips (Tue Dec 22 2015 - 10:38:50 CST)
- The script of Umbrella sampling sunyzero (Tue Dec 22 2015 - 03:33:13 CST)
- (no subject) Srijita Paul (Tue Dec 22 2015 - 00:06:49 CST)
- OpenGL Display Window, "Key 2", SMD with NAMD Zeinab Emami (Sun Dec 20 2015 - 11:57:52 CST)
- how to get the restart files from the dcd file? Azadeh Alavi (Sun Dec 20 2015 - 03:02:36 CST)
- MD simulation of Linear Molecules (like 2-butyne ԬС (Fri Dec 18 2015 - 20:26:26 CST)
- RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Jim Phillips (Fri Dec 18 2015 - 09:38:15 CST)
- SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Tom Coles (Thu Dec 17 2015 - 10:26:20 CST)
- ERROR in CUDA run Lara rajam (Thu Dec 17 2015 - 08:50:49 CST)
- "implausibly old time stamp" for charm++ 6.7 in CVS Brian Radak (Wed Dec 16 2015 - 11:42:29 CST)
- Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 09:23:41 CST)
- RATTLE Error During Minimization of Charmm Gui Generated Bilayer begüm alaybeyoğlu (Tue Dec 15 2015 - 10:27:48 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Tue Dec 15 2015 - 12:46:36 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer begüm alaybeyoğlu (Wed Dec 16 2015 - 03:46:10 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Wed Dec 16 2015 - 09:21:07 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer begüm alaybeyoğlu (Wed Dec 16 2015 - 10:21:17 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Wed Dec 16 2015 - 11:23:39 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Jim Phillips (Thu Dec 17 2015 - 19:49:32 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer begüm alaybeyoğlu (Wed Dec 16 2015 - 03:46:10 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Tue Dec 15 2015 - 12:46:36 CST)
- free energy changes via FEP method Haleh a (Tue Dec 15 2015 - 09:59:10 CST)
- Viscosity Calculation using EMD Gaurab Sarkar (Mon Dec 14 2015 - 13:22:02 CST)
- Usage of velDCDfile and forceDCDfile keywords in viscosity calculations Debashis Kundu (Mon Dec 14 2015 - 00:34:56 CST)
- OutputAccumulatedWork...where's the output? Bryan Roessler (Sun Dec 13 2015 - 19:36:26 CST)
- VMD-NAMD and PDB element column Francesco Pietra (Sat Dec 12 2015 - 09:09:55 CST)
- Re: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 14:32:38 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 15:59:37 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Jim Phillips (Mon Dec 14 2015 - 09:04:21 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Victor Ovchinnikov (Mon Dec 14 2015 - 09:47:54 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Mon Dec 14 2015 - 14:42:21 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Mon Dec 14 2015 - 14:52:18 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Victor Ovchinnikov (Mon Dec 14 2015 - 16:27:41 CST)
- Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
- Re: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
- Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 05:07:03 CST)
- PRES and water-ions issues with charmm36 Francesco Pietra (Thu Dec 10 2015 - 15:30:14 CST)
- extendedLagrangian for non-scalar colvar Jerome Karp (Thu Dec 10 2015 - 10:45:27 CST)
- energy output Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 11:39:14 CST)
- NAMD on TACC (Darter) Chitrak Gupta (Tue Dec 08 2015 - 18:16:29 CST)
- buffer overflow with long file paths in psfgen in NAMD 2.11b2? Brian Radak (Tue Dec 08 2015 - 15:54:28 CST)
- anionic cysteine Francesco Pietra (Tue Dec 08 2015 - 08:50:19 CST)
- Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 23:48:55 CST)
- Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 20:02:35 CST)
- multiple output .dcd files?? Deng, Jinxia (Nancy) (Mon Dec 07 2015 - 14:56:53 CST)
- NAMD 2.11b2 released Jim Phillips (Sun Dec 06 2015 - 22:01:09 CST)
- namd2.22b CUDA Phi Francesco Pietra (Sat Dec 05 2015 - 01:06:49 CST)
- modify input file for production phase MD Deng, Jinxia (Nancy) (Fri Dec 04 2015 - 11:31:26 CST)
- Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 15:45:38 CST)
- Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 15:55:30 CST)
- Re: Overflow in LJcorrection? Peter Freddolino (Thu Dec 03 2015 - 15:55:49 CST)
- Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 15:59:27 CST)
- Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:04:28 CST)
- Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 16:10:59 CST)
- Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:15:15 CST)
- Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 16:15:59 CST)
- Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:18:40 CST)
- Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 16:26:19 CST)
- Re: Overflow in LJcorrection? Jason Swails (Sat Dec 05 2015 - 07:54:57 CST)
- Re: Overflow in LJcorrection? Peter Freddolino (Sat Dec 05 2015 - 17:57:22 CST)
- Re: Overflow in LJcorrection? Peter Freddolino (Sat Dec 05 2015 - 21:15:12 CST)
- Re: Overflow in LJcorrection? Jim Phillips (Mon Dec 07 2015 - 16:35:27 CST)
- NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions Jeff Comer (Thu Dec 03 2015 - 14:20:42 CST)
- Re: concerning paratools Mayne, Christopher G (Thu Dec 03 2015 - 14:11:52 CST)
- error when use Charmm_Gui prepared *.inp for NAMD Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 08:37:14 CST)
- Re: error when use Charmm_Gui prepared *.inp for NAMD Chitrak Gupta (Thu Dec 03 2015 - 08:49:59 CST)
- Re: error when use Charmm_Gui prepared *.inp for NAMD Josh Vermaas (Thu Dec 03 2015 - 08:50:36 CST)
- Re: error when use Charmm_Gui prepared *.inp for NAMD Jeffrey Potoff (Thu Dec 03 2015 - 08:44:53 CST)
- concerning paratools luca belmonte (Thu Dec 03 2015 - 04:36:04 CST)
- fructose 1,6 bisphosphate forcefield parameters. Dhiraj Srivastava (Wed Dec 02 2015 - 00:06:45 CST)
- accelerated MD new variant Vlad Cojocaru (Sun Nov 29 2015 - 03:53:20 CST)
- Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 09:17:35 CST)
- Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 09:41:00 CST)
- Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
- Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 10:26:05 CST)
- Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 11:35:25 CST)
- Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 11:37:48 CST)
- Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 15:54:56 CST)
- Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
- Re: Fwd: TIP4P and CHARMM27 Jim Phillips (Mon Nov 30 2015 - 16:21:44 CST)
- Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 09:41:00 CST)
- DOF during alchemical simulations Brian Radak (Wed Nov 25 2015 - 10:31:11 CST)
- Re: DOF during alchemical simulations Jérôme Hénin (Thu Nov 26 2015 - 12:00:01 CST)
- Re: DOF during alchemical simulations Aron Broom (Thu Nov 26 2015 - 12:28:27 CST)
- Re: DOF during alchemical simulations Jérôme Hénin (Fri Nov 27 2015 - 03:31:25 CST)
- Re: DOF during alchemical simulations Brian Radak (Mon Nov 30 2015 - 09:36:55 CST)
- Re: DOF during alchemical simulations Grace Brannigan (Mon Nov 30 2015 - 12:05:36 CST)
- Re: DOF during alchemical simulations Brian Radak (Mon Nov 30 2015 - 12:30:33 CST)
- Re: DOF during alchemical simulations Grace Brannigan (Mon Nov 30 2015 - 14:45:55 CST)
- Re: DOF during alchemical simulations Hannes Loeffler (Tue Dec 01 2015 - 08:19:00 CST)
- Re: DOF during alchemical simulations Brian Radak (Tue Dec 01 2015 - 10:08:08 CST)
- Re: DOF during alchemical simulations Aron Broom (Thu Nov 26 2015 - 12:28:27 CST)
- Re: DOF during alchemical simulations Jérôme Hénin (Thu Nov 26 2015 - 12:00:01 CST)
- Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Wed Nov 25 2015 - 06:39:26 CST)
- recommendations for a fast multicore workstation Jeff Comer (Tue Nov 24 2015 - 11:56:54 CST)
- Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Mon Nov 23 2015 - 09:27:00 CST)
- Which namd to use Maxime Boissonneault (Fri Nov 20 2015 - 07:29:45 CST)
- query for system size in pmf calculation Atanu Maity (Fri Nov 20 2015 - 05:24:47 CST)
- Crazy rigid water molecules Brian Radak (Thu Nov 19 2015 - 15:40:55 CST)
- Changing Boundary conditions from PBC to non-periodic Mahdi Tavakol (Thu Nov 19 2015 - 12:30:23 CST)
- NAMD2.11 source code not compiling Madhulika Gupta (Wed Nov 18 2015 - 02:47:38 CST)
- Fw: "ZOU Changling" <zoucl@ihep.ac.cn>ʼ ZOU Changling (Wed Nov 18 2015 - 00:26:54 CST)
- Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Wed Nov 18 2015 - 00:25:35 CST)
- Can't start SMP NAMD - Problem clearly is in front of the monitor Vogel, Alexander (Tue Nov 17 2015 - 03:18:05 CST)
- ABF calculations - reaction coordinate Mohan maruthi sena (Mon Nov 16 2015 - 19:15:15 CST)
- Free energy profiles in ABF tutorial Haleh a (Mon Nov 16 2015 - 06:35:30 CST)
- Bubble in water during membrane simulations Kevin C Chan (Mon Nov 16 2015 - 02:12:29 CST)
- time per step during GPU-accelerated Implicit Solvent calculations Thomas Albers (Sun Nov 15 2015 - 19:11:26 CST)
- NAMD 2.11 CUDA forces IBverbs Norman Geist (Fri Nov 13 2015 - 06:00:18 CST)
- FATAL ERROR: Unable to access config file ubq_ws_eq.log Hugo Siles (Thu Nov 12 2015 - 16:40:41 CST)
- FEP using separated topologies David Huggins (Thu Nov 12 2015 - 07:46:54 CST)
- Would it be possible to continue a simulation from any snapshot of a trajectory? sunyeping (Thu Nov 12 2015 - 02:45:51 CST)
- Van der Waals and Electrostatic Forces - CUDA Kostas Malavazos (Tue Nov 10 2015 - 11:11:37 CST)
- NAMD 2.11b1 released Jim Phillips (Tue Nov 10 2015 - 09:39:44 CST)
- Re: NAMD 2.11b1 released Tien Huynh (Tue Nov 10 2015 - 11:10:25 CST)
- Re: NAMD 2.11b1 released sunyeping (Thu Nov 12 2015 - 02:39:43 CST)
- Re: Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 06:55:42 CST)
- Re: Re: NAMD 2.11b1 released sunyeping (Thu Nov 12 2015 - 20:29:18 CST)
- Re: Re: Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 22:41:32 CST)
- Re: Re: Re: NAMD 2.11b1 released sunyeping (Thu Nov 26 2015 - 23:26:33 CST)
- AW: Re: Re: Re: NAMD 2.11b1 released Norman Geist (Fri Nov 27 2015 - 01:22:44 CST)
- Re: Re: Re: Re: NAMD 2.11b1 released Jim Phillips (Fri Nov 27 2015 - 20:10:42 CST)
- Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 11:15:27 CST)
- Re: NAMD 2.11b1 released sunyeping (Thu Nov 12 2015 - 02:39:43 CST)
- Re: NAMD 2.11b1 released Jeff Comer (Tue Nov 10 2015 - 13:18:06 CST)
- Re: NAMD 2.11b1 released Tristan Croll (Wed Nov 11 2015 - 20:11:00 CST)
- Re: NAMD 2.11b1 released Tien Huynh (Tue Nov 10 2015 - 11:10:25 CST)
- On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 03:01:19 CST)
- AW: On-the-fly modification of tclforces script? Norman Geist (Tue Nov 10 2015 - 04:18:02 CST)
- Re: On-the-fly modification of tclforces script? Jim Phillips (Tue Nov 10 2015 - 09:53:42 CST)
- Re: On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 16:03:38 CST)
- Re: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 16:48:21 CST)
- Re: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 18:14:28 CST)
- Re: vmd-l: Re: On-the-fly modification of tclforces script? John Stone (Fri Nov 13 2015 - 19:05:34 CST)
- Re: vmd-l: Re: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 19:28:39 CST)
- Re: vmd-l: Re: On-the-fly modification of tclforces script? John Stone (Fri Nov 13 2015 - 20:17:53 CST)
- Re: On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 16:03:38 CST)
- Fw: vmd-l: what is difference between "TOTAL", “TOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot? 孙业平 (Mon Nov 09 2015 - 06:49:42 CST)
- Re: OPLSAA to CHARMM Francesco Pietra (Fri Nov 06 2015 - 00:59:02 CST)
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- OPLSAA to CHARMM Francesco Pietra (Thu Nov 05 2015 - 10:21:42 CST)
- pdb files to dcd Amitkumar Majhi (Tue Nov 03 2015 - 14:33:21 CST)
- Topology and parameters for Sodium dodecanoate Sadegh Faramarzi Ganjabad (Tue Nov 03 2015 - 11:21:45 CST)
- Multiple NAMD calculations on windows Mai Aamer (Mon Nov 02 2015 - 16:40:06 CST)
- about deca alanine tutorial setup Jessen Lucas (Mon Nov 02 2015 - 15:22:16 CST)
- 16 total processes killed (some possibly by mpirun during cleanup) Shalton Evans (Mon Nov 02 2015 - 14:34:13 CST)
- How occupancy relates to force in SMD daneshkaftroody_v_at_mech.sharif.ir (Mon Nov 02 2015 - 10:41:11 CST)
- substrate and membrane protein Lucía Díaz (Mon Nov 02 2015 - 08:03:28 CST)
- ABF error on NAMD 2.10 Haleh a (Mon Nov 02 2015 - 05:55:59 CST)
- Weird psfgen bug? Tristan Croll (Fri Oct 30 2015 - 03:22:06 CDT)
- Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 19:24:53 CDT)
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- namd 2.10 crashes when using more than 1 CPU for FEP simulation Tien Huynh (Tue Oct 27 2015 - 21:58:14 CDT)
- Biasing potential of a Metadynamics Simulation Fidan Sumbul (Tue Oct 27 2015 - 13:05:02 CDT)
- ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 11:12:20 CDT)
- Lennard-Jones and Electrostatic Forces and Energies Kostas Malavazos (Mon Oct 26 2015 - 13:54:28 CDT)
- replica exchange module Jessen Lucas (Mon Oct 26 2015 - 01:29:43 CDT)
- AW: replica exchange module Norman Geist (Mon Oct 26 2015 - 02:11:47 CDT)
- Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 02:25:49 CDT)
- AW: replica exchange module Norman Geist (Mon Oct 26 2015 - 03:21:01 CDT)
- Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 03:25:46 CDT)
- Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 22:49:20 CDT)
- AW: replica exchange module Norman Geist (Tue Oct 27 2015 - 03:08:42 CDT)
- Re: replica exchange module Jessen Lucas (Tue Oct 27 2015 - 03:42:23 CDT)
- Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 02:25:49 CDT)
- AW: replica exchange module Norman Geist (Mon Oct 26 2015 - 02:11:47 CDT)
- constraint failure in Rattle algorithm for atom 54134 Life Sciences Inc (Sun Oct 25 2015 - 19:42:57 CDT)
- global does not work in configuration and callback function jc guo (Sat Oct 24 2015 - 01:46:21 CDT)
- NH4+ params Mikhail Suyetin (Fri Oct 23 2015 - 16:38:55 CDT)
- Dielectric constant of water from MSM and PME simulations Mattia Felice Palermo (Fri Oct 23 2015 - 08:57:37 CDT)
- GPU accelerated MD Nikhil Maroli (Fri Oct 23 2015 - 04:12:24 CDT)
- gromacs to charmm conversion Francesco Pietra (Fri Oct 23 2015 - 02:34:15 CDT)
- aMD and GPU acceleration Thomas Albers (Thu Oct 22 2015 - 13:53:09 CDT)
- Why the computational speed does not increase with the increase of GPUs? sunyeping (Wed Oct 21 2015 - 22:18:17 CDT)
- Error in Metadynamics Simulation Fidan Sumbul (Wed Oct 21 2015 - 16:31:30 CDT)
- Re: Zhe Wu (Wed Oct 21 2015 - 14:16:02 CDT)
- Topology for drugs to do MD after docking Nikhil Maroli (Wed Oct 21 2015 - 11:40:04 CDT)
- ApoA1 simulation Kostas Malavazos (Wed Oct 21 2015 - 05:21:28 CDT)
- (no subject) Mattia Felice Palermo (Wed Oct 21 2015 - 04:07:03 CDT)
- Reverse Coarse Graining using VMD CG Builder Ardavan Mehdizadeh (Wed Oct 21 2015 - 03:15:35 CDT)
- About the TMDInitialRMSD parameter in targeted molecular dynamics sunyeping (Tue Oct 20 2015 - 12:06:22 CDT)
- Regarding FFTW routines usage in NAMD Puneet Singh (Tue Oct 20 2015 - 07:39:50 CDT)
- AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Norman Geist (Tue Oct 20 2015 - 03:53:51 CDT)
- Re: about re install sunyeping (Tue Oct 20 2015 - 02:09:33 CDT)
- about re install jc guo (Tue Oct 20 2015 - 01:20:08 CDT)
- Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Puneet Singh (Tue Oct 20 2015 - 01:01:24 CDT)
- How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Mon Oct 19 2015 - 15:08:27 CDT)
- AW: How to calculate the temperature for a subset of my simulation Norman Geist (Tue Oct 20 2015 - 01:23:57 CDT)
- Re: How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 12:20:46 CDT)
- Re: How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 13:47:53 CDT)
- Re: How to calculate the temperature for a subset of my simulation Josh Vermaas (Tue Oct 20 2015 - 14:03:32 CDT)
- AW: How to calculate the temperature for a subset of my simulation Norman Geist (Wed Oct 21 2015 - 02:24:09 CDT)
- Re: How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 12:20:46 CDT)
- AW: How to calculate the temperature for a subset of my simulation Norman Geist (Tue Oct 20 2015 - 01:23:57 CDT)
- Several questions about targeted molecular dynamics sunyeping (Mon Oct 19 2015 - 04:54:09 CDT)
- about command replicaRecv and replicaSend jc guo (Mon Oct 19 2015 - 02:09:43 CDT)
- stepspercycle Gianluca Interlandi (Sun Oct 18 2015 - 20:20:26 CDT)
- Bias-exchange metadynamics Fidan Sumbul (Sun Oct 18 2015 - 18:16:34 CDT)
- Problem on merging multi-psf files into one wliu (Sun Oct 18 2015 - 07:52:11 CDT)
- Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 14:05:29 CDT)
- Rigid bonds and non-bonded energy Grzegorz Nawrocki (Fri Oct 16 2015 - 16:39:48 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Fri Oct 16 2015 - 17:42:34 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Mon Oct 19 2015 - 14:40:51 CDT)
- Re: Rigid bonds and non-bonded energy Grzegorz Nawrocki (Tue Oct 20 2015 - 10:11:42 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Tue Oct 20 2015 - 10:33:51 CDT)
- Re: Rigid bonds and non-bonded energy Grzegorz Nawrocki (Tue Oct 20 2015 - 11:09:20 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Tue Oct 20 2015 - 12:52:34 CDT)
- Re: Rigid bonds and non-bonded energy Grzegorz Nawrocki (Wed Oct 21 2015 - 08:29:22 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Mon Oct 19 2015 - 14:40:51 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Fri Oct 16 2015 - 17:42:34 CDT)
- about replica exchange jc guo (Fri Oct 16 2015 - 10:43:23 CDT)
- NAMD - wrap atoms, not center of mass Stanislav Q=A0imko?= (Fri Oct 16 2015 - 10:20:28 CDT)
- about replica exchange example in lib of 2.10 NAMD jc guo (Fri Oct 16 2015 - 00:11:18 CDT)
- SMD or moving contraints Kevin C Chan (Thu Oct 15 2015 - 21:50:20 CDT)
- Compile NAMD - Projections Kostas Malavazos (Wed Oct 14 2015 - 11:45:04 CDT)
- keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Tue Oct 13 2015 - 23:39:14 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Jérôme Hénin (Wed Oct 14 2015 - 05:05:54 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Marlon Sidore (Wed Oct 14 2015 - 05:12:16 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Jérôme Hénin (Wed Oct 14 2015 - 05:14:41 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Wed Oct 14 2015 - 05:41:58 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Giacomo Fiorin (Wed Oct 14 2015 - 06:33:28 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Thu Oct 15 2015 - 00:54:00 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Jérôme Hénin (Thu Oct 15 2015 - 01:43:25 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Thu Oct 15 2015 - 02:24:52 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Marlon Sidore (Wed Oct 14 2015 - 05:12:16 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Jérôme Hénin (Wed Oct 14 2015 - 05:05:54 CDT)
- Compilation of NAMD from Source (Cray XC40) Richter, Stefan (Tue Oct 13 2015 - 09:26:06 CDT)
- MD Simulation of accelerated MD using GPU jeevan gc (Mon Oct 12 2015 - 17:19:15 CDT)
- MD Simulation of accelerated MD using GPU jeevan gc (Mon Oct 12 2015 - 17:07:39 CDT)
- simulating TIP5P water Monika Madhavi (Fri Oct 09 2015 - 05:29:35 CDT)
- BONDS vs DOUBLE in topology file Gianluca Interlandi (Fri Oct 09 2015 - 00:42:05 CDT)
- about "small molecules" in OPLS-AAM FF Francesco Pietra (Wed Oct 07 2015 - 16:14:12 CDT)
- Triple-hybrid topology? Tristan Croll (Tue Oct 06 2015 - 19:26:07 CDT)
- Subscribe Vijay L. Roy (Tue Oct 06 2015 - 01:22:14 CDT)
- Regarding biasTemperature used in Well-tempered metadynamics Vijay L. Roy (Tue Oct 06 2015 - 01:49:12 CDT)
- Coarse grained instability: atoms moving too fast Marlon Sidore (Mon Oct 05 2015 - 06:47:41 CDT)
- Output to a file Mahdi Tavakol (Mon Oct 05 2015 - 01:31:55 CDT)
- Segmentation Fault - Debug Kumar, Amit (Mon Oct 05 2015 - 09:13:14 CDT)
- Regarding problem in psfgen of heparin siddharth kamal (Fri Oct 02 2015 - 14:20:15 CDT)
- Ispopetide bond Milica Utješanović (Fri Oct 02 2015 - 14:30:04 CDT)
- Cyclic peptide Nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:52:59 CDT)
- script error Nikhil Maroli (Fri Oct 02 2015 - 08:44:13 CDT)
- PSF for cyclic peptide nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:36:47 CDT)
- simulating tip5p water Monika Madhavi (Thu Oct 01 2015 - 23:36:51 CDT)
- Outward tilting which colvar to use Nicolas Martin (Thu Oct 01 2015 - 05:13:01 CDT)
- Atomselect within radial pair distribution function g(r) Aditya Ranganathan (Wed Sep 30 2015 - 03:55:37 CDT)
- LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 10:20:36 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Peter Freddolino (Tue Sep 29 2015 - 13:25:07 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 14:04:44 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Brian Radak (Tue Sep 29 2015 - 14:52:44 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Peter Freddolino (Wed Sep 30 2015 - 08:14:45 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Wed Sep 30 2015 - 16:39:45 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 14:04:44 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Peter Freddolino (Tue Sep 29 2015 - 13:25:07 CDT)
- Hybrid coarse-grained/all-atom simulation Mahya Hemmat (Mon Sep 28 2015 - 14:25:24 CDT)
- psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring Nikhil Maroli (Sat Sep 26 2015 - 06:50:31 CDT)
- PSF for CYCLIC PEPTIDE : Nikhil Maroli (Sat Sep 26 2015 - 05:45:17 CDT)
- Q=B4=D7=D4"=C2=C0=D0=A1=D3=A8"_<lv-xy11@mail?= s.tsinghua.edu.cn>ʼ СӨ (Fri Sep 25 2015 - 09:19:53 CDT)
- Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Wed Sep 23 2015 - 06:51:28 CDT)
- Re: Adaptive tempering implementation in NAMD differs Nicholas M. Glykos (Wed Sep 23 2015 - 05:45:40 CDT)
- Adaptive tempering implementation in NAMD differs from original paper? Sachin Natesh (Tue Sep 22 2015 - 19:45:22 CDT)
- string method in NAMD 2.10 Jerry Karp (Mon Sep 21 2015 - 10:46:45 CDT)
- string method in NAMD 2.10 Jerome Karp (Mon Sep 21 2015 - 10:49:42 CDT)
- Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:29:16 CDT)
- Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:31:34 CDT)
- Re: string method in NAMD 2.10 Jerome Karp (Tue Sep 22 2015 - 10:05:05 CDT)
- Re: string method in NAMD 2.10 Chris Chipot (Tue Sep 22 2015 - 10:26:53 CDT)
- Re: string method in NAMD 2.10 Jerome Karp (Tue Sep 22 2015 - 10:39:30 CDT)
- Re: string method in NAMD 2.10 Chris Chipot (Tue Sep 22 2015 - 10:46:28 CDT)
- Re: string method in NAMD 2.10 Jerome Karp (Tue Sep 22 2015 - 11:44:37 CDT)
- Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:31:34 CDT)
- Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:29:16 CDT)
- Automatic PSF builder for cyclic peptide Nikhil Maroli (Sun Sep 20 2015 - 07:04:36 CDT)
- Which VMD AND NAMD should install Nikhil Maroli (Sat Sep 19 2015 - 01:57:30 CDT)
- NAMD Anisotropic pressure control Mahdi Tavakol (Fri Sep 18 2015 - 08:50:04 CDT)
- NAMD/VMD: generating psf for Abeta, ACE patch Mona Habibi (Tue Sep 15 2015 - 15:31:37 CDT)
- Can NAMD handle two different LJ cutoffs in a single simulation? Lewis Martin (Mon Sep 14 2015 - 23:17:36 CDT)
- FEP utility for binding estimation HERBERT MAX VENTHUR PE¥A (Mon Sep 14 2015 - 10:35:17 CDT)
- simulating graphene sheets (with bonds across boundaries) with water upayan baul (Mon Sep 14 2015 - 06:59:00 CDT)
- Parameterizing a novel peptide Bryan Roessler (Fri Sep 11 2015 - 17:14:05 CDT)
- Re: Parameterizing a novel peptide Tomek Stępniewski (Fri Sep 11 2015 - 18:16:27 CDT)
- Re: Parameterizing a novel peptide Mayne, Christopher G (Mon Sep 14 2015 - 08:48:57 CDT)
- Re: Parameterizing a novel peptide Peter Freddolino (Mon Sep 14 2015 - 21:08:55 CDT)
- Re: Parameterizing a novel peptide Mayne, Christopher G (Mon Sep 14 2015 - 21:38:04 CDT)
- Re: Parameterizing a novel peptide Peter Freddolino (Mon Sep 14 2015 - 22:00:56 CDT)
- RE: Parameterizing a novel peptide Bennion, Brian (Tue Sep 15 2015 - 11:15:56 CDT)
- Re: Parameterizing a novel peptide Bryan Roessler (Tue Sep 15 2015 - 12:06:12 CDT)
- Re: Parameterizing a novel peptide Mayne, Christopher G (Mon Sep 14 2015 - 08:48:57 CDT)
- Re: Parameterizing a novel peptide Tomek Stępniewski (Fri Sep 11 2015 - 18:16:27 CDT)
- node file for NAMD Parag Khuraswar (Fri Sep 11 2015 - 08:02:54 CDT)
- Error in NAMD Controller Class Reference- Adaptive Tempering Sachin Natesh (Thu Sep 10 2015 - 19:13:41 CDT)
- Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 10:13:31 CDT)
- Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
- Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
- Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Fri Sep 11 2015 - 10:08:07 CDT)
- Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Fri Sep 11 2015 - 11:15:47 CDT)
- Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
- Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
- charm36 for ATP and MG Radhika Anoop (Tue Sep 08 2015 - 00:55:48 CDT)
- Thermodynamic integration question Randall Hall (Sat Sep 05 2015 - 23:28:57 CDT)
- "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file Bryan Roessler (Fri Sep 04 2015 - 00:07:49 CDT)
- patching SO3 group to GAG Lara rajam (Thu Sep 03 2015 - 19:13:21 CDT)
- node file for NAMD Parag Khuraswar (Tue Sep 01 2015 - 23:28:06 CDT)
- parameters problem in sulfated molecules Lara rajam (Tue Sep 01 2015 - 12:12:42 CDT)
- Reducing the amount of work being done on CPU Maxime Boissonneault (Tue Sep 01 2015 - 09:48:24 CDT)
- LJcorrection + switching? Brian Radak (Tue Sep 01 2015 - 09:31:34 CDT)
- Sampling frequency Dr. Eddie (Mon Aug 31 2015 - 14:02:46 CDT)
- Adaptive Tempering - Velocity Rescaling Sachin Natesh (Mon Aug 31 2015 - 09:45:16 CDT)
- Atoms moving too fast; simulation has become unstable Monika Madhavi (Mon Aug 31 2015 - 05:42:48 CDT)
- Re: Atoms moving too fast; simulation has become unstable farzad kiani (Mon Aug 31 2015 - 06:17:38 CDT)
- Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Mon Aug 31 2015 - 08:30:48 CDT)
- Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Thu Sep 17 2015 - 04:42:40 CDT)
- Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Thu Sep 17 2015 - 21:44:09 CDT)
- Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Thu Sep 17 2015 - 22:58:12 CDT)
- Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Thu Sep 17 2015 - 23:01:32 CDT)
- Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Mon Sep 21 2015 - 00:58:32 CDT)
- Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Mon Sep 21 2015 - 07:53:14 CDT)
- Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Thu Sep 17 2015 - 04:42:40 CDT)
- heparin Lara rajam (Sat Aug 29 2015 - 18:48:08 CDT)
- running namd gpu version Sanjana Anil Kumar Nair (Sat Aug 29 2015 - 05:21:41 CDT)
- Problem running REMD simulation Nicholus Bhattacharjee (Tue Aug 25 2015 - 03:01:36 CDT)
- AW: Problem running REMD simulation Norman Geist (Tue Aug 25 2015 - 03:50:15 CDT)
- Re: Problem running REMD simulation Douglas Houston (Tue Aug 25 2015 - 04:16:55 CDT)
- Format of colvars.state Hossein Mohammadiarani (Mon Aug 24 2015 - 12:53:14 CDT)
- Problem with iron ion (FE2+) Daniela Rivas (Mon Aug 24 2015 - 12:51:59 CDT)
- feature request: external initiated clean exit Daniel Mller (Fri Aug 21 2015 - 07:37:02 CDT)
- Problem running REMD simulation Nicholus Bhattacharjee (Thu Aug 20 2015 - 03:47:33 CDT)
- Charm++ warning> fences and atomic operations not available in native assembly Ern Seang Ong (Thu Aug 20 2015 - 02:56:40 CDT)
- Lambda-exchange multiple-copy alchemical free energy calculations 岡部篤俊 (Tue Aug 18 2015 - 09:54:40 CDT)
- Regarding NAMD installation Pragya Priyadarshini (Mon Aug 17 2015 - 02:45:13 CDT)
- Looking for benchmarks on k80's rswett_at_chem.wayne.edu (Thu Aug 13 2015 - 10:40:45 CDT)
- PME Seg Fault Richard Overstreet (Mon Aug 10 2015 - 09:11:27 CDT)
- Verification of NAMD Results Kanzliersch, Lukas (Wed Aug 05 2015 - 15:32:38 CDT)
- OPLS/AA force field oguz gurbulak (Wed Aug 05 2015 - 09:00:01 CDT)
- eBiothon platform eBiothon Admin Team (Mon Aug 03 2015 - 10:07:36 CDT)
- Re: namd-l digest V1 #1726 nader zabarjad (Sun Aug 02 2015 - 10:41:55 CDT)
- how to create two namd jobs in a single script with 2 x dual cuda gpus? nam kim (Sat Aug 01 2015 - 16:36:15 CDT)
- Re: how to create two namd jobs in a single script with 2 x dual cuda gpus? nam kim (Sat Aug 01 2015 - 16:33:04 CDT)
- sausage plot for a namd trajectory in vmd luca belmonte (Fri Jul 31 2015 - 05:01:02 CDT)
- Metadynamics: writeHillsTrajectory Chola Regmi (Thu Jul 30 2015 - 16:37:53 CDT)
- run NAMD 2.10 on Xeon Phi machine Xiaoge Wang (Tue Jul 28 2015 - 12:50:23 CDT)
- The 2 NAMD tests "Alanin" and "tclforces" fail to run with "Atoms moving too fast" error Sriram Adhyapak (Mon Jul 27 2015 - 20:36:14 CDT)
- "missing operator at _@_ in expression" for if statement Simon Kit Sang Chu (Mon Jul 27 2015 - 19:39:51 CDT)
- Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 10:32:29 CDT)
- Re: Interrupted Molecular Dynamics Simulation Chitrak Gupta (Mon Jul 27 2015 - 12:29:25 CDT)
- Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 19:21:00 CDT)
- Re: Interrupted Molecular Dynamics Simulation Felipe Merino (Tue Jul 28 2015 - 02:03:00 CDT)
- Re: Interrupted Molecular Dynamics Simulation Chitrak Gupta (Tue Jul 28 2015 - 09:34:21 CDT)
- Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Tue Jul 28 2015 - 09:45:07 CDT)
- Re: Interrupted Molecular Dynamics Simulation Purushottam Dixit (Tue Jul 28 2015 - 09:51:22 CDT)
- Re: Interrupted Molecular Dynamics Simulation Felipe Merino (Tue Jul 28 2015 - 10:34:17 CDT)
- Re: Interrupted Molecular Dynamics Simulation Axel Kohlmeyer (Tue Jul 28 2015 - 10:53:28 CDT)
- Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Wed Jul 29 2015 - 10:25:29 CDT)
- Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 19:21:00 CDT)
- Re: Interrupted Molecular Dynamics Simulation Chitrak Gupta (Mon Jul 27 2015 - 12:29:25 CDT)
- NAMD hybrid configuration: Atoms moving too fast error Puneet Singh (Mon Jul 27 2015 - 06:41:38 CDT)
- Instability in harmonic restraints when equilibrating large systems Tristan Croll (Fri Jul 24 2015 - 16:52:05 CDT)
- Patch-size Error (not like the other ones) Merrill, Dante (Fri Jul 24 2015 - 13:14:28 CDT)
- segmentation fault when running with mpirun Puneet Singh (Fri Jul 24 2015 - 08:05:23 CDT)
- Tilt angle clockwise rotation Nicolas Martin (Wed Jul 22 2015 - 08:34:47 CDT)
- FEP method- Free energy of solvation of ligand Mohan maruthi sena (Wed Jul 22 2015 - 02:25:40 CDT)
- wrapping in NVT Abhishek TYAGI (Tue Jul 21 2015 - 22:59:52 CDT)
- Error in TI derivatives for staggered lambda scaling? Brian Radak (Tue Jul 21 2015 - 13:41:28 CDT)
- restart error Lara rajam (Mon Jul 20 2015 - 10:15:23 CDT)
- Debugging and Force Checking? Brian Radak (Mon Jul 20 2015 - 09:32:44 CDT)
- Compilation with OpenMPI Kevin C Chan (Mon Jul 20 2015 - 05:02:10 CDT)
- VDW energy diverged & VMD functions applied on cluster Simon Kit Sang Chu (Sat Jul 18 2015 - 16:37:54 CDT)
- what exactly is the form of the cosine angle potential? Charlesworth, Henry (Fri Jul 17 2015 - 08:08:50 CDT)
- Minimization without MD Simon Kit Sang Chu (Thu Jul 16 2015 - 15:37:39 CDT)
- Minimization without MD Simon Kit Sang Chu (Thu Jul 16 2015 - 16:21:40 CDT)
- Controlling water diffusion Evandro Semighini (Thu Jul 16 2015 - 14:21:50 CDT)
- Re: Controlling water diffusion Peter Freddolino (Thu Jul 16 2015 - 21:54:49 CDT)
- Re: Controlling water diffusion Evandro Semighini (Fri Jul 17 2015 - 07:44:36 CDT)
- nvt input file Urszula Uciechowska (Fri Jul 17 2015 - 08:25:21 CDT)
- Re: nvt input file Branko (Fri Jul 17 2015 - 08:44:24 CDT)
- nvt run error Urszula Uciechowska (Tue Jul 21 2015 - 02:54:10 CDT)
- Re: nvt run error Felipe Merino (Tue Jul 21 2015 - 03:28:40 CDT)
- Re: Controlling water diffusion Peter Freddolino (Sun Jul 19 2015 - 21:13:15 CDT)
- Re: Controlling water diffusion Evandro Semighini (Sun Jul 19 2015 - 21:42:17 CDT)
- Re: Controlling water diffusion Evandro Semighini (Fri Jul 17 2015 - 07:44:36 CDT)
- Re: Controlling water diffusion Peter Freddolino (Thu Jul 16 2015 - 21:54:49 CDT)
- namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 12:59:50 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 15:31:34 CDT)
- Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 15:50:36 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 15:56:14 CDT)
- Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 15:59:19 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 16:06:37 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 16:20:34 CDT)
- Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 16:43:06 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 17:09:40 CDT)
- Re: namd ibverbs Kevin C Chan (Thu Jul 23 2015 - 05:38:49 CDT)
- Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 15:50:36 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 15:31:34 CDT)
- Fwd: Regarding problem in generating psf file of heparin and heparan sulfate siddharth kamal (Thu Jul 16 2015 - 07:44:46 CDT)
- Compilation with OpenMPI Kevin C Chan (Tue Jul 14 2015 - 00:11:38 CDT)
- UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Anjela Manandhar (Mon Jul 13 2015 - 15:58:55 CDT)
- Compilation with OpenMPI Kevin C Chan (Sun Jul 12 2015 - 01:13:30 CDT)
- Running constant pH molecular dynamics (CpHMD) Leonardo Herrera (Thu Jul 09 2015 - 19:00:02 CDT)
- call "NAMD" from another program Ma'Mon Hatmal (Thu Jul 09 2015 - 17:53:24 CDT)
- model.conf Mai Aamer (Thu Jul 09 2015 - 17:09:01 CDT)
- NAMD 2.10 Building from Source Kumar, Amit (Thu Jul 09 2015 - 15:28:07 CDT)
- polymerization simulations L. Signorile (Thu Jul 09 2015 - 13:06:51 CDT)
- does fixedAtoms modify velocities? Brian Radak (Tue Jul 07 2015 - 12:25:32 CDT)
- -xHost Gianluca Interlandi (Mon Jul 06 2015 - 13:08:37 CDT)
- Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD Mahya Hemmat (Mon Jul 06 2015 - 11:06:39 CDT)
- Generating solvent models. VINAYAK BHAT (Sun Jul 05 2015 - 04:06:27 CDT)
- running multicore version on a 2-CPU node Gianluca Interlandi (Sat Jul 04 2015 - 15:33:25 CDT)
- multicore vs ibverbs Gianluca Interlandi (Sat Jul 04 2015 - 12:52:40 CDT)
- extra bonds Lara rajam (Thu Jul 02 2015 - 09:20:59 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Wed Jul 01 2015 - 11:01:50 CDT)
- RE: replica exchange and GPU acceleration Norman Geist (Fri Jul 03 2015 - 03:16:17 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Sat Jul 04 2015 - 10:49:22 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Sun Jul 12 2015 - 22:36:54 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Mon Jul 13 2015 - 01:32:14 CDT)
- statistical error of mean force in (NAMD) ABF calculations Branko (Wed Jul 01 2015 - 05:09:48 CDT)
- replica exchange and GPU acceleration Mitchell Gleed (Tue Jun 30 2015 - 18:09:27 CDT)
- Attempting modification to accumulate "Langevin heat" Brian Radak (Tue Jun 30 2015 - 10:43:40 CDT)
- Re: I can not run fixed protein in membrane with NAMD R.L. Ma (Sat Jun 27 2015 - 21:27:18 CDT)
- applying a force to some atoms jing liang (Sat Jun 27 2015 - 06:22:02 CDT)
- Pressure coupling options Kevin C Chan (Fri Jun 26 2015 - 23:32:05 CDT)
- not able to view trajectory in VMD Lara rajam (Fri Jun 26 2015 - 12:55:01 CDT)
- Minimisation goes to several values Kevin C Chan (Thu Jun 25 2015 - 11:32:10 CDT)
- NAMD 2.10 on IBM POWER(8) machines Baker D.J. (Thu Jun 25 2015 - 07:00:49 CDT)
- free energy calculation along image index in us СӨ (Wed Jun 24 2015 - 02:27:35 CDT)
- bond lengths and angles constraints oguz gurbulak (Tue Jun 23 2015 - 10:04:53 CDT)
- Getting Infinity in Calculation of Free Energy using SMD Ebru Çetin (Tue Jun 23 2015 - 00:23:19 CDT)
- Re: Create psf file Mayne, Christopher G (Mon Jun 22 2015 - 10:01:23 CDT)
- Create psf file Fransiska Kurniawan (Sat Jun 20 2015 - 17:56:52 CDT)
- OPLS force field in NAMD oguz gurbulak (Sat Jun 20 2015 - 11:43:02 CDT)
- Weird Bond In Non-Polar Tail Danielle Grodi (Thu Jun 18 2015 - 10:15:53 CDT)
- Remembering resid Kevin C Chan (Thu Jun 18 2015 - 08:42:34 CDT)
- Second Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Tue Jun 16 2015 - 12:04:27 CDT)
- Fwd: Re: Combining parameter files from CHARMM Branko (Mon Jun 15 2015 - 05:12:57 CDT)
- Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015) Lela Vukovic (Fri Jun 12 2015 - 21:06:22 CDT)
- Multiple-replicas metadynamics / Well-tempered metadynamics Yerko Escalona (Fri Jun 12 2015 - 14:15:39 CDT)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) Danielle Grodi (Fri Jun 12 2015 - 13:39:30 CDT)
- non-bonded energy of individual atoms Brwinkel, Tom (Fri Jun 12 2015 - 09:17:46 CDT)
- Using a different potential with NAMD Wade, Alex (Fri Jun 12 2015 - 09:08:48 CDT)
- Recomposing the system splitted by periodicity Francesco Pietra (Thu Jun 11 2015 - 04:34:57 CDT)
- Constant velocity SMD maral hassani (Tue Jun 09 2015 - 07:14:16 CDT)
- FFTK - error Mayne, Christopher G (Mon Jun 08 2015 - 11:56:34 CDT)
- Postdoc in Theoretical and Computational Biophysics Aksimentiev, Oleksii (Mon Jun 08 2015 - 11:51:11 CDT)
- electrostatics cutoff parameters Z (Mon Jun 08 2015 - 09:06:00 CDT)
- FFTK - error Mohan maruthi sena (Sat Jun 06 2015 - 18:35:44 CDT)
- Combining parameter files from CHARMM Kevin C Chan (Fri Jun 05 2015 - 04:51:13 CDT)
- error in writing colvars state file Bennion, Brian (Thu Jun 04 2015 - 16:24:44 CDT)
- Colvars Boundary potentials do not look harmonic Panel Nicolas (M.) (Wed Jun 03 2015 - 10:00:53 CDT)
- Using the multi-copy version of NAMD on a linux workstation Avisek Das (Fri May 29 2015 - 14:43:18 CDT)
- NAMD-Replica exchange ZOU Changling (Wed May 27 2015 - 04:31:28 CDT)
- Can 'nonbonded interaction parameters' be ignored in the parameter file? (Tue May 26 2015 - 20:43:52 CDT)
- the method to move freely in one direction like a rigid body Xiaokang Liu (Mon May 25 2015 - 05:46:40 CDT)
- running with replica exchange on stampede Peter Freddolino (Sun May 24 2015 - 21:40:09 CDT)
- where can I find the parameter file for chlorophenols? (Sun May 24 2015 - 08:30:15 CDT)
- Force-field for DOPI lipid Kevin C Chan (Sat May 23 2015 - 13:58:30 CDT)
- atom types in PSF/PRM/RTF Hannes Loeffler (Fri May 22 2015 - 04:42:45 CDT)
- Error during Opt. Charges while using FF Took Kit Aaron Larsen (Wed May 20 2015 - 16:38:19 CDT)
- Restarting trajectories Michael Feig (Wed May 20 2015 - 02:47:08 CDT)
- RE: Restarting trajectories Bennion, Brian (Wed May 20 2015 - 10:42:46 CDT)
- Re: Restarting trajectories Axel Kohlmeyer (Wed May 20 2015 - 10:49:11 CDT)
- RE: Restarting trajectories Michael Feig (Wed May 20 2015 - 10:59:07 CDT)
- Re: Restarting trajectories Axel Kohlmeyer (Wed May 20 2015 - 11:07:56 CDT)
- RE: Restarting trajectories Michael Feig (Wed May 20 2015 - 11:18:12 CDT)
- Re: Restarting trajectories Emad Tajkhorshid (Wed May 20 2015 - 12:32:12 CDT)
- Re: Restarting trajectories Grzegorz Nawrocki (Wed May 20 2015 - 14:24:08 CDT)
- RE: Restarting trajectories Bennion, Brian (Wed May 20 2015 - 14:38:43 CDT)
- Re: Restarting trajectories Grzegorz Nawrocki (Thu May 21 2015 - 09:10:28 CDT)
- Re: Restarting trajectories Josh Vermaas (Wed May 20 2015 - 11:07:42 CDT)
- Re: Restarting trajectories Maxim Belkin (Wed May 20 2015 - 11:11:33 CDT)
- RE: Restarting trajectories Michael Feig (Wed May 20 2015 - 10:59:07 CDT)
- Best Practices for Nucleobase Parameterization Mayne, Christopher G (Wed May 20 2015 - 08:12:55 CDT)
- Restarting trajectories Michael Feig (Wed May 20 2015 - 03:01:37 CDT)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Wed May 20 2015 - 00:06:46 CDT)
- Best Practices for Nucleobase Parameterization Aaron Larsen (Mon May 18 2015 - 11:30:22 CDT)
- Re: optimising namd ibverb runs Aaron Larsen (Mon May 18 2015 - 08:48:18 CDT)
- optimising namd ibverb runs Thanassis Silis (Mon May 18 2015 - 06:48:03 CDT)
- Different trajectories with and without restarting Grzegorz Nawrocki (Fri May 15 2015 - 18:09:57 CDT)
- Re: Different trajectories with and without restarting btreece_at_andrew.cmu.edu (Fri May 15 2015 - 18:26:09 CDT)
- Re: Different trajectories with and without restarting Axel Kohlmeyer (Fri May 15 2015 - 18:26:53 CDT)
- +p option on Windows 7 Kukol, Andreas (Fri May 15 2015 - 05:07:55 CDT)
- Re: Error applying PME to simulation set up Sourav Ray (Wed May 13 2015 - 06:02:51 CDT)
- Error applying PME to simulation set up Sourav Ray (Wed May 13 2015 - 04:24:41 CDT)
- startup phase 1 for benchmark Branko (Tue May 12 2015 - 09:29:28 CDT)
- NAMD Repeated failures launching tasks Kumar, Amit (Mon May 11 2015 - 13:47:40 CDT)
- Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 03:51:38 CDT)
- Processing 64-window FEP Matthew Ralph Adendorff (Sun May 10 2015 - 08:44:08 CDT)
- School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015 Axel Kohlmeyer (Fri May 08 2015 - 11:28:54 CDT)
- OPLS force-field in NAMD AnkiReddy katha (Thu May 07 2015 - 02:12:03 CDT)
- output files are not stored when running namd-2.10 ibverbs Thanassis Silis (Thu May 07 2015 - 10:29:26 CDT)
- atoms sequence in improper, OPLS, TOPOTOOLS, CHARMM AnkiReddy katha (Thu May 07 2015 - 06:17:27 CDT)
- Re: OPLS in NAMD AnkiReddy katha (Thu May 07 2015 - 04:40:47 CDT)
- OPLS in NAMD AnkiReddy katha (Thu May 07 2015 - 04:17:23 CDT)
- PSFgen with RNA-like nucleotide monophosphates Aaron Larsen (Wed May 06 2015 - 11:01:26 CDT)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015) Lela Vukovic (Wed May 06 2015 - 01:39:55 CDT)
- Simulation Box Rescaling Phillips, Carolyn L. (Tue May 05 2015 - 18:02:28 CDT)
- atom ID in VMD and NAMD Maxim Igaev (Mon May 04 2015 - 03:16:09 CDT)
- RE: namd-l digest V1 #1668 Ern Seang Ong (Sun May 03 2015 - 23:14:28 CDT)
- mail reg DCD error Vidhya Sankar (Sun May 03 2015 - 09:44:50 CDT)
- proper order for par files in namd Mayne, Christopher G (Fri May 01 2015 - 09:21:11 CDT)
- Problems in running AutoIMD Ern Seang Ong (Thu Apr 30 2015 - 23:33:47 CDT)
- Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Thu Apr 30 2015 - 18:51:19 CDT)
- Re: Simulated Annealing with many frequent restarts Francesco Pietra (Fri May 01 2015 - 01:21:28 CDT)
- Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 09:46:21 CDT)
- Re: Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Fri May 01 2015 - 10:16:43 CDT)
- Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 11:18:21 CDT)
- Re: Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Fri May 01 2015 - 11:24:13 CDT)
- Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 11:49:41 CDT)
- Re: Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Fri May 01 2015 - 10:16:43 CDT)
- performance question Thomas C. Bishop (Mon Apr 27 2015 - 15:54:10 CDT)
- question about restart conf file oguz gurbulak (Sun Apr 26 2015 - 07:10:44 CDT)
- RE: proper order for par files in namd (solved) Bennion, Brian (Fri Apr 24 2015 - 18:21:22 CDT)
- proper order for par files in namd Bennion, Brian (Fri Apr 24 2015 - 17:05:16 CDT)
- Patches for namd 2.10 Åke Sandgren (Fri Apr 24 2015 - 01:09:35 CDT)
- Which Binary to use? Arijit Ghosh (Fri Apr 24 2015 - 00:10:49 CDT)
- How to output CCC per residue from MDFF Michael Yuchi (Thu Apr 23 2015 - 21:48:11 CDT)
- How to save a structure after minimizing for 1000 steps? Arijit Ghosh (Thu Apr 23 2015 - 16:15:40 CDT)
- energy minimization in namd Hasan haska (Thu Apr 23 2015 - 11:29:43 CDT)
- Equilibration for a reverse FEP run Matthew Ralph Adendorff (Thu Apr 23 2015 - 09:54:41 CDT)
- restart simulation oguz gurbulak (Thu Apr 23 2015 - 09:22:38 CDT)
- polarizable carbon nanotubes ibrahim khalil (Tue Apr 21 2015 - 11:00:36 CDT)
- energy minimization Dhiraj Srivastava (Mon Apr 20 2015 - 21:57:55 CDT)
- Calculating RMSF per residue Abir Ganguly (Mon Apr 20 2015 - 12:58:24 CDT)
- Mail reg Parameter file Vidhya Sankar (Mon Apr 20 2015 - 07:57:34 CDT)
- TIP4P topology and parameter files oguz gurbulak (Sun Apr 19 2015 - 05:18:41 CDT)
- slow heating of system Dhiraj Srivastava (Sun Apr 19 2015 - 00:55:58 CDT)
- Calculation of PMF between protein domains NAMD Chola Regmi (Fri Apr 17 2015 - 17:26:03 CDT)
- Re: Calculation of PMF between protein domains NAMD Josh Vermaas (Fri Apr 17 2015 - 17:43:49 CDT)
- Re: Calculation of PMF between protein domains NAMD Jeff Comer (Fri Apr 17 2015 - 18:22:17 CDT)
- Problems when running FEP for mutation ASP to GLY Yunhui Peng (Fri Apr 17 2015 - 13:53:03 CDT)
- Re: Is there any point in running NAMD over an ethernet-linked cluster? Douglas Houston (Thu Apr 16 2015 - 05:10:12 CDT)
- Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:39:18 CDT)
- Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:51:29 CDT)
- Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 09:05:43 CDT)
- Re: Running two molecule coarse-grained simulation Prathit Chatterjee (Wed Apr 15 2015 - 09:24:32 CDT)
- Re: Running two molecule coarse-grained simulation Sourav Ray (Thu Apr 16 2015 - 06:27:30 CDT)
- Re: Running two molecule coarse-grained simulation Prathit Chatterjee (Thu Apr 16 2015 - 11:37:21 CDT)
- Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 09:05:43 CDT)
- Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:51:29 CDT)
- CHARMM parameter file Fransiska Kurniawan (Wed Apr 15 2015 - 04:11:00 CDT)
- Problems to parametrize molecules Evandro Semighini (Tue Apr 14 2015 - 15:30:03 CDT)
- RE: Problems to parametrize molecules Bennion, Brian (Tue Apr 14 2015 - 15:45:41 CDT)
- Re: Problems to parametrize molecules Evandro Semighini (Tue Apr 14 2015 - 15:51:17 CDT)
- RE: Problems to parametrize molecules Bennion, Brian (Wed Apr 15 2015 - 13:04:21 CDT)
- Re: Problems to parametrize molecules Evandro Semighini (Wed Apr 15 2015 - 15:37:12 CDT)
- RE: Problems to parametrize molecules Bennion, Brian (Wed Apr 15 2015 - 15:44:53 CDT)
- Re: Problems to parametrize molecules Evandro Semighini (Thu Apr 16 2015 - 14:53:54 CDT)
- Re: Problems to parametrize molecules Evandro Semighini (Thu Apr 16 2015 - 15:28:23 CDT)
- Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 17 2015 - 11:16:16 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Sun Apr 19 2015 - 18:47:21 CDT)
- Re: Re: Problems to parametrize molecules Mayne, Christopher G (Sun Apr 19 2015 - 18:59:20 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 10:04:37 CDT)
- RE: Re: Problems to parametrize molecules Bennion, Brian (Fri Apr 24 2015 - 12:27:51 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 12:49:31 CDT)
- RE: Re: Problems to parametrize molecules Bennion, Brian (Fri Apr 24 2015 - 13:46:52 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 13:54:33 CDT)
- Re: Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 24 2015 - 13:53:01 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 13:58:25 CDT)
- RE: Re: Problems to parametrize molecules Bennion, Brian (Fri Apr 24 2015 - 14:02:59 CDT)
- Re: Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 24 2015 - 14:22:55 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 14:26:50 CDT)
- Re: Re: Problems to parametrize molecules Evandro Semighini (Sun Apr 19 2015 - 18:47:21 CDT)
- RE: Problems to parametrize molecules Bennion, Brian (Tue Apr 14 2015 - 15:45:41 CDT)
- bilayer simulation keeps crashing Chitrak Gupta (Tue Apr 14 2015 - 10:00:27 CDT)
- NetworkView plugin for the non-namd trajectories James Starlight (Tue Apr 14 2015 - 09:34:57 CDT)
- Re: REMD on GPU cluster Michael Feig (Tue Apr 14 2015 - 08:00:16 CDT)
- strange behavior of ABF Danilo Di Maio (Tue Apr 14 2015 - 05:41:24 CDT)
- REMD on GPU cluster Michael Feig (Mon Apr 13 2015 - 17:09:05 CDT)
- Can't find documentation of known bug in NAMD 2.9 Klas Karis (Mon Apr 13 2015 - 12:02:25 CDT)
- TIP4P water for MD Abhishek TYAGI (Mon Apr 13 2015 - 07:44:51 CDT)
- Can NAMD simulation solve the problem of coordinate clash in a structural model? sunyeping (Sun Apr 12 2015 - 21:19:18 CDT)
- Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? sunyeping (Sun Apr 12 2015 - 21:18:30 CDT)
- Trouble using the extForces parameters Duster, Adam (Sat Apr 11 2015 - 04:11:42 CDT)
- Reg: topology file amidated and acetylated disulfide bridged Cystine Akshay Bhatnagar (Fri Apr 10 2015 - 05:05:42 CDT)
- Immediate Postdoctoral Position Opening Marawan Hussien (Thu Apr 09 2015 - 18:10:32 CDT)
- Algorithm used by NAMD Gurpreet Kaur Dhindsa (Thu Apr 02 2015 - 09:55:36 CDT)
- timestep querry Abhishek TYAGI (Wed Apr 01 2015 - 10:28:12 CDT)
- Daily cron stalls running NAMD outputs Vlastimil Zíma (Wed Apr 01 2015 - 03:04:26 CDT)
- problem about namdstats.tcl Hasan haska (Wed Apr 01 2015 - 01:34:32 CDT)
- Minimisation not converged Kevin C Chan (Wed Apr 01 2015 - 01:20:37 CDT)
- Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Tue Mar 31 2015 - 22:46:49 CDT)
- ABF with external electric field Bala subramanian (Tue Mar 31 2015 - 10:42:24 CDT)
- Dipole Moment Watcher, Ibuprofen JAVAD NOROOZI (Tue Mar 31 2015 - 01:01:46 CDT)
- Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Mon Mar 30 2015 - 00:21:35 CDT)
- Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Sun Mar 29 2015 - 21:16:03 CDT)
- pressure value Hasan haska (Sun Mar 29 2015 - 14:23:28 CDT)
- angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 09:17:41 CDT)
- bond angle and dihedral values oguz gurbulak (Thu Mar 26 2015 - 03:55:03 CDT)
- Fwd: FW: NAMD Brian Radak (Wed Mar 25 2015 - 11:35:27 CDT)
- Parallelization of External Program Forces btreece_at_andrew.cmu.edu (Tue Mar 24 2015 - 18:49:26 CDT)
- about hydrogen bond analysis Hasan haska (Tue Mar 24 2015 - 16:07:08 CDT)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015) Lela Vukovic (Tue Mar 24 2015 - 15:50:58 CDT)
- GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support Axel Kohlmeyer (Tue Mar 24 2015 - 14:17:40 CDT)
- NAMD nightly build compilation Vlad Cojocaru (Tue Mar 24 2015 - 12:07:03 CDT)
- Re: NAMD Subbarao Kanchi (Tue Mar 24 2015 - 01:48:39 CDT)
- Restraining angle between bond vector and coordinate vector Seth Axen (Mon Mar 23 2015 - 15:26:37 CDT)
- Immediate Postdoctoral Position Opening Marawan Hussien (Sun Mar 22 2015 - 16:08:16 CDT)
- number of close contacts and contact area Abhishek TYAGI (Sun Mar 22 2015 - 04:37:57 CDT)
- error while running namd on CRAY XC40 machine Santosh Kumar Chaudhary (Sun Mar 22 2015 - 02:40:31 CDT)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 16:47:50 CDT)
- DCD Error Abhishek TYAGI (Wed Mar 18 2015 - 06:23:58 CDT)
- Re: DCD Error manish kesherwani (Wed Mar 18 2015 - 08:10:18 CDT)
- Re: DCD Error btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 09:27:28 CDT)
- Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 09:29:42 CDT)
- Re: DCD Error Josh Vermaas (Wed Mar 18 2015 - 09:36:52 CDT)
- Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 09:51:17 CDT)
- Re: DCD Error btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 10:05:58 CDT)
- Re: DCD Error Josh Vermaas (Wed Mar 18 2015 - 10:06:43 CDT)
- Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 10:13:07 CDT)
- Re: DCD Error Atanu Maity (Wed Mar 18 2015 - 23:32:32 CDT)
- Re: DCD Error Abhishek TYAGI (Thu Mar 19 2015 - 03:59:56 CDT)
- Re: DCD Error Maxim Belkin (Wed Mar 18 2015 - 10:06:34 CDT)
- Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 09:29:42 CDT)
- Reg: solvating in a non-standard solvent Akshay Bhatnagar (Wed Mar 18 2015 - 01:29:20 CDT)
- Re: Reg: solvating in a non-standard solvent Branko (Wed Mar 18 2015 - 07:19:45 CDT)
- Re: Reg: solvating in a non-standard solvent Jeff Comer (Wed Mar 18 2015 - 09:44:12 CDT)
- Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Thu Mar 19 2015 - 01:40:55 CDT)
- Re: Reg: solvating in a non-standard solvent Jeff Comer (Thu Mar 19 2015 - 09:02:10 CDT)
- Re: Reg: solvating in a non-standard solvent Maxim Belkin (Thu Mar 19 2015 - 11:59:28 CDT)
- Re: Reg: solvating in a non-standard solvent Maxim Belkin (Thu Mar 19 2015 - 12:06:38 CDT)
- Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Thu Mar 19 2015 - 23:38:24 CDT)
- Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Wed Mar 25 2015 - 02:38:00 CDT)
- Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Thu Mar 19 2015 - 01:40:55 CDT)
- 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD clarkzhy (Tue Mar 17 2015 - 20:33:41 CDT)
- Restarting an abruptly interrupted simulation Sourav Ray (Tue Mar 17 2015 - 01:30:21 CDT)
- Truncated octahedron : Problems in PBC when reading a dcd file with NAMD Panel Nicolas (M.) (Mon Mar 16 2015 - 11:18:00 CDT)
- Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das (Mon Mar 16 2015 - 10:50:46 CDT)
- Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das (Mon Mar 16 2015 - 09:15:05 CDT)
- Re: Restarting NAMD simulation Sourav Ray (Thu Mar 12 2015 - 09:16:26 CDT)
- RE: Restarting NAMD simulation Norman Geist (Thu Mar 12 2015 - 09:13:14 CDT)
- Restarting NAMD simulation Sourav Ray (Thu Mar 12 2015 - 08:30:27 CDT)
- PACE Force Field and NAMD 2.10 Fotis Baltoumas (Thu Mar 12 2015 - 06:18:07 CDT)
- Colvar with variable axis Mitchell Gleed (Thu Mar 12 2015 - 06:01:56 CDT)
- Dihedral calculation with colvars Kevin C Chan (Wed Mar 11 2015 - 23:05:45 CDT)
- problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 14:59:46 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Mar 11 2015 - 18:29:36 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 22:49:51 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Thu Mar 12 2015 - 17:26:10 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Sun Mar 15 2015 - 10:45:14 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Sun Mar 15 2015 - 10:47:17 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Thu Mar 19 2015 - 17:24:29 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Thu Mar 19 2015 - 17:26:27 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Thu Mar 19 2015 - 17:44:25 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Thu Mar 19 2015 - 18:39:06 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Fri Mar 27 2015 - 11:48:02 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Sat Mar 28 2015 - 17:50:19 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Mon Mar 30 2015 - 13:23:24 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Apr 01 2015 - 15:05:30 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Thu Apr 02 2015 - 14:54:56 CDT)
- Re: problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 22:49:51 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Mar 11 2015 - 18:29:36 CDT)
- vdw parameter error | atom type <-> name problem Art (Wed Mar 11 2015 - 14:03:38 CDT)
- No steric clashes, still not minimizing Francesco Pietra (Wed Mar 11 2015 - 06:38:40 CDT)
- equilibrate the bulk water system Hasan haska (Tue Mar 10 2015 - 16:51:30 CDT)
- RE: equilibrate the bulk water system Norman Geist (Wed Mar 11 2015 - 02:03:46 CDT)
- Re: equilibrate the bulk water system Hasan haska (Fri Mar 13 2015 - 06:57:15 CDT)
- Re: equilibrate the bulk water system Maxim Belkin (Fri Mar 13 2015 - 11:28:35 CDT)
- Re: equilibrate the bulk water system Hasan haska (Sat Mar 14 2015 - 14:38:03 CDT)
- Re: equilibrate the bulk water system Axel Kohlmeyer (Sun Mar 15 2015 - 21:30:06 CDT)
- Re: equilibrate the bulk water system Abhishek Tyagi (Fri Mar 13 2015 - 09:49:20 CDT)
- Re: equilibrate the bulk water system Hasan haska (Fri Mar 13 2015 - 06:57:15 CDT)
- RE: equilibrate the bulk water system Norman Geist (Wed Mar 11 2015 - 02:03:46 CDT)
- Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:19:16 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 06:28:26 CDT)
- Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:52:53 CDT)
- Re: Dihedral definition in NAMD Josh Vermaas (Tue Mar 10 2015 - 09:14:27 CDT)
- Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 09:24:23 CDT)
- Re: Dihedral definition in NAMD Josh Vermaas (Tue Mar 10 2015 - 09:30:21 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 09:49:00 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 09:33:15 CDT)
- Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 13:13:00 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 18:46:42 CDT)
- Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 22:22:34 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Wed Mar 11 2015 - 03:13:27 CDT)
- Re: Dihedral definition in NAMD Kevin C Chan (Wed Mar 11 2015 - 05:03:54 CDT)
- Re: Dihedral definition in NAMD Josh Vermaas (Tue Mar 10 2015 - 13:32:12 CDT)
- Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:52:53 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 06:28:26 CDT)
- Alchemical FEP calculation involving glycine jostmey . (Mon Mar 09 2015 - 23:58:31 CDT)
- Topology and Parameter File Fransiska Kurniawan (Mon Mar 09 2015 - 01:52:36 CDT)
- about langevin dynamics Gisella Alfonsino (Sun Mar 08 2015 - 05:36:28 CDT)
- energy groups in NAMD Andre Ribeiro (Fri Mar 06 2015 - 14:22:34 CST)
- energy groups in NAMD Andre Ribeiro (Fri Mar 06 2015 - 14:23:14 CST)
- NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! Yarrow Madrona (Thu Mar 05 2015 - 10:58:11 CST)
- Announcement: ‘Hands On’ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015) Lela Vukovic (Wed Mar 04 2015 - 13:07:25 CST)
- BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly Norman Geist (Wed Mar 04 2015 - 01:47:42 CST)
- "Unknown command-line option +replicas" Mitul Saha (Mon Mar 02 2015 - 23:33:11 CST)
- WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Amin Dehkharghani (Sun Mar 01 2015 - 14:58:08 CST)
- How to let NAMD terminate automatically at a given time (Fri Feb 27 2015 - 20:02:18 CST)
- Re: How to let NAMD terminate automatically at a given time Dong Luo (Mon Mar 02 2015 - 09:27:22 CST)
- Re: How to let NAMD terminate automatically at a given time Jérôme Hénin (Mon Mar 02 2015 - 11:12:40 CST)
- RE: How to let NAMD terminate automatically at a given time hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 13:19:08 CST)
- Re: How to let NAMD terminate automatically at a given time Jeff Comer (Mon Mar 02 2015 - 13:58:14 CST)
- RE: How to let NAMD terminate automatically at a given time hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 14:17:16 CST)
- RE: How to let NAMD terminate automatically at a given time Norman Geist (Tue Mar 03 2015 - 02:35:36 CST)
- Re:Re: How to let NAMD terminate automatically at a given time Qing Lv (Mon Mar 02 2015 - 22:20:40 CST)
- Re: How to let NAMD terminate automatically at a given time Jérôme Hénin (Mon Mar 02 2015 - 11:12:40 CST)
- Re: How to let NAMD terminate automatically at a given time Dong Luo (Mon Mar 02 2015 - 09:27:22 CST)
- accelMD and GBIS? Brian Radak (Fri Feb 27 2015 - 18:15:13 CST)
- scaling non-bonded interactiion parameter for specific pairs MEHRAN MB (Fri Feb 27 2015 - 13:15:11 CST)
- configuration file question Hasan haska (Thu Feb 26 2015 - 16:49:55 CST)
- velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 09:41:04 CST)
- Re: vmd-l: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 10:24:36 CST)
- Re: velocity IO with psfgen? Ajasja Ljubetič (Thu Feb 26 2015 - 10:37:55 CST)
- Re: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
- Re: vmd-l: Re: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 11:03:15 CST)
- Re: vmd-l: Re: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 11:42:22 CST)
- Re: vmd-l: Re: velocity IO with psfgen? Maxim Belkin (Thu Feb 26 2015 - 12:14:24 CST)
- Re: vmd-l: Re: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 12:47:52 CST)
- Re: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
- Rotating Constraints Sourav Purohit (Tue Feb 24 2015 - 14:23:26 CST)
- Questions about lambda scheme in free energy perturbation Jian Dai (Tue Feb 24 2015 - 08:59:57 CST)
- Aggregation related analysis scripts Aditya Ranganathan (Tue Feb 24 2015 - 02:28:10 CST)
- Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 13:04:15 CST)
- My Plight Syed Kashif Zafar (Wed Feb 18 2015 - 18:28:19 CST)
- FATAL ERROR: Low global exclusion count! Yongcheng Zhou (Wed Feb 18 2015 - 18:29:33 CST)
- GPU Multinodes problem horacio poblete (Wed Feb 18 2015 - 15:59:07 CST)
- compile psfgen as shared object or Tcl package? Brian Radak (Wed Feb 18 2015 - 15:47:27 CST)
- Multicore-CUDA NAMD output hangs Mitchell Gleed (Wed Feb 18 2015 - 15:12:21 CST)
- NAMD Source, Molecule.c , Mass Critaria JAVAD NOROOZI (Wed Feb 18 2015 - 12:55:25 CST)
- Maximum limit for "run" parameter Mitul Saha (Tue Feb 17 2015 - 18:50:38 CST)
- multiple thermostats in adaptive tempering Igaev, Maxim (Wed Feb 18 2015 - 11:20:52 CST)
- Re: Incorrect atom count in binary file Mihaela Drenscko (Wed Feb 18 2015 - 07:34:15 CST)
- Incorrect atom count in binary file Mihaela Drenscko (Tue Feb 17 2015 - 18:59:43 CST)
- making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 09:42:59 CST)
- Putting multiple copies of peptide in a box Aditya Ranganathan (Tue Feb 17 2015 - 03:39:14 CST)
- Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10,2015) Lela Vukovic (Mon Feb 16 2015 - 14:44:55 CST)
- problem with equilibration of membrane-protein system Azadeh Alavi (Sat Feb 14 2015 - 05:35:59 CST)
- Compressibility of Berendesen Barostat (Simulations Near Critical Point) JAVAD NOROOZI (Fri Feb 13 2015 - 00:37:42 CST)
- PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Christian Jorgensen (Thu Feb 12 2015 - 10:16:00 CST)
- Grid forces visualisation Charan Thota (Wed Feb 11 2015 - 06:13:12 CST)
- GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Wed Feb 11 2015 - 04:18:11 CST)
- LangevinPistonPeriod (Simulation Near Critical Point) JAVAD NOROOZI (Tue Feb 10 2015 - 03:15:23 CST)
- New web server for setup of membrane simulation systems Chen, Po-chia (Sun Feb 08 2015 - 06:17:35 CST)
- Spikes in the Energy Plot Viswanath Pasumarthi (Mon Feb 09 2015 - 02:26:08 CST)
- namd-1: Simulation Terminating Early Akshata Rudrapatna (Sat Feb 07 2015 - 15:06:33 CST)
- Analysis plugins for Martini Coarse Grained protein simulations Aditya Ranganathan (Sat Feb 07 2015 - 03:55:33 CST)
- Targeted MD and the MARTINI Coarse-Grained Force Field Fotis Baltoumas (Fri Feb 06 2015 - 10:06:55 CST)
- preparing dsDNA Urszula Uciechowska (Fri Feb 06 2015 - 05:58:43 CST)
- Residue number changed to hexadecimal string K Miura (Thu Feb 05 2015 - 23:34:24 CST)
- on-the-fly parameter introspection Brian Radak (Thu Feb 05 2015 - 13:54:51 CST)
- Editing Patch Grid Dimensions Ryan Gordon (Thu Feb 05 2015 - 10:00:28 CST)
- (no subject) Ma'Mon Hatmal (Thu Feb 05 2015 - 06:32:09 CST)
- Could I run aMD in Drude force field? dream (Thu Feb 05 2015 - 02:14:04 CST)
- Extracting data Stephan Grein (Wed Feb 04 2015 - 05:55:37 CST)
- Alchemy Shift Coefficient at Low Density Regime (TI) JAVAD NOROOZI (Wed Feb 04 2015 - 02:58:15 CST)
- Phi vs GPU Francesco Pietra (Wed Feb 04 2015 - 01:52:43 CST)
- Fwd: all atom equilibrium of yeast PGK simulation with NAMD Qing Li (Tue Feb 03 2015 - 21:14:36 CST)
- namd simulation with TIP5P Shanshan Wu (Tue Feb 03 2015 - 18:36:34 CST)
- namd-1: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Tue Feb 03 2015 - 14:43:55 CST)
- LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Tue Feb 03 2015 - 14:34:42 CST)
- Calculation of the water inside of protein during trajectory James Starlight (Tue Feb 03 2015 - 09:51:07 CST)
- error running min Urszula Uciechowska (Tue Feb 03 2015 - 08:23:28 CST)
- Re: vmd-l: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Ajasja Ljubetič (Tue Feb 03 2015 - 07:06:43 CST)
- adjust water box size in RBCG Yongcheng Zhou (Sun Feb 01 2015 - 16:03:54 CST)
- Message about timing in *log file. Dawid das (Sun Feb 01 2015 - 05:05:39 CST)
- NAMD 2.10 with multiple-replica support Branko (Sat Jan 31 2015 - 14:06:06 CST)
- LCPO parameters P1-P4 yandong Huang (Sat Jan 31 2015 - 13:24:55 CST)
- LJcorrection and alchemy? Brian Radak (Fri Jan 30 2015 - 12:10:53 CST)
- Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 09:03:17 CST)
- AW: problem with water molecules angle in MD simulation Norman Geist (Thu Jan 29 2015 - 01:56:18 CST)
- AW: problem with water molecules angle in MD simulation Norman Geist (Wed Jan 28 2015 - 10:50:47 CST)
- Is it possible to rename atoms with psfgen? Brian Radak (Wed Jan 28 2015 - 09:54:16 CST)
- inconsistency in ABF results for helix unfolding MEHRAN MB (Tue Jan 27 2015 - 17:09:19 CST)
- System unstable after turning electric field on. Dawid das (Tue Jan 27 2015 - 11:26:50 CST)
- Re: problem with water molecules angle in MD simulation Shoresh (Tue Jan 27 2015 - 10:30:54 CST)
- AW: problem with water molecules angle in MD simulation Norman Geist (Tue Jan 27 2015 - 02:28:18 CST)
- AW: about angles in coordination complexes Norman Geist (Tue Jan 27 2015 - 02:23:29 CST)
- LCPO parameters P1-P4 yandong Huang (Mon Jan 26 2015 - 12:30:21 CST)
- Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 09:28:16 CST)
- Re: about angles in coordination complexes Jérôme Hénin (Mon Jan 26 2015 - 09:56:07 CST)
- Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:02:27 CST)
- Re: about angles in coordination complexes Jérôme Hénin (Mon Jan 26 2015 - 10:20:37 CST)
- Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:28:17 CST)
- Re: about angles in coordination complexes Jérôme Hénin (Mon Jan 26 2015 - 10:50:35 CST)
- Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:55:10 CST)
- Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 11:51:11 CST)
- Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:02:27 CST)
- Re: about angles in coordination complexes luca belmonte (Wed Feb 04 2015 - 04:37:28 CST)
- Re: about angles in coordination complexes Jérôme Hénin (Mon Jan 26 2015 - 09:56:07 CST)
- about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 08:39:17 CST)
- Re: problems compiling NAMD with mpicxx from mvapich2 Jose Borreguero (Mon Jan 26 2015 - 08:27:41 CST)
- problem with water molecules angle in MD simulation Shoresh Shafei (Sun Jan 25 2015 - 19:06:23 CST)
- PMEGridSize and parameters controlling electrostatic interactions. Dawid das (Sat Jan 24 2015 - 13:48:44 CST)
- problems compiling NAMD with mpicxx from mvapich2 Jose Borreguero (Sat Jan 24 2015 - 11:49:02 CST)
- Hamiltonian Replica Exchange MD Simulation in NAMD Fidan Sumbul (Fri Jan 23 2015 - 13:04:19 CST)
- NAMD "unable to find improper parameters" Asma El-Magboub (Thu Jan 22 2015 - 21:32:09 CST)
- about compiling NAMD using intel icc and impi XSC (Fri Jan 23 2015 - 04:00:29 CST)
- tclBCArgs, passing floating point lists btreece_at_andrew.cmu.edu (Thu Jan 22 2015 - 14:03:21 CST)
- Reverse osmosis simulation Z (Thu Jan 22 2015 - 05:09:24 CST)
- Local minima on minimiztion with colvars Francesco Pietra (Wed Jan 21 2015 - 12:45:14 CST)
- FEP Restart file g_at_ut#@m! (Wed Jan 21 2015 - 08:26:15 CST)
- NAMD Non-features JAVAD NOROOZI (Wed Jan 21 2015 - 01:54:50 CST)
- Re: problems running amber parm7 Francesco Pietra (Tue Jan 20 2015 - 01:25:17 CST)
- Periodic Box Dimension (WrapAll is on) JAVAD NOROOZI (Mon Jan 19 2015 - 23:55:19 CST)
- problems running amber parm7 Francesco Pietra (Mon Jan 19 2015 - 13:03:44 CST)
- Multiple Dihedral in CHARMM parameters JAVAD NOROOZI (Mon Jan 19 2015 - 01:19:37 CST)
- dual-boost aMD and the dV value in the output file Ozge Sensoy (Sun Jan 18 2015 - 14:00:47 CST)
- Steered NAMD using AMBER Forcefield [Config File] Zeinab Emami (Sun Jan 18 2015 - 10:07:51 CST)
- using NAMD with CHARMM36 ff Maria Bykhovskaia (Sat Jan 17 2015 - 19:26:29 CST)
- Restart heating Francesco Pietra (Fri Jan 16 2015 - 12:04:33 CST)
- NAMD 2.10 with MVAPICH2-GDR? David Chin (Thu Jan 15 2015 - 08:41:04 CST)
- colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 09:52:16 CST)
- Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 18:29:59 CST)
- colvars and drude don't play nice? JC Gumbart (Tue Jan 13 2015 - 18:08:42 CST)
- Re: colvars and drude don't play nice? Giacomo Fiorin (Tue Jan 13 2015 - 18:31:38 CST)
- Re: colvars and drude don't play nice? JC Gumbart (Wed Jan 14 2015 - 09:58:28 CST)
- Re: colvars and drude don't play nice? Giacomo Fiorin (Wed Jan 14 2015 - 10:07:23 CST)
- Re: colvars and drude don't play nice? Giacomo Fiorin (Fri Jan 16 2015 - 11:04:44 CST)
- Re: colvars and drude don't play nice? Jim Phillips (Fri Jan 16 2015 - 16:57:58 CST)
- Re: colvars and drude don't play nice? JC Gumbart (Sat Jan 17 2015 - 15:34:43 CST)
- Re: colvars and drude don't play nice? JC Gumbart (Wed Jan 14 2015 - 09:58:28 CST)
- Re: colvars and drude don't play nice? Giacomo Fiorin (Tue Jan 13 2015 - 18:31:38 CST)
- namd-I: How to assume the thickness of membrane when applying external Electric field ? Vy Phan (Tue Jan 13 2015 - 00:20:31 CST)
- NAMD slows at startup phase 1 smp problem Ryan Gordon (Mon Jan 12 2015 - 12:24:31 CST)
- Reg. restarting a Thermodynamic Integration Run Aditya Chattopadhyay (Mon Jan 12 2015 - 09:32:26 CST)
- Re: is there a method equivalent to conformational flooding in NAMD 2.10 Thomas Evangelidis (Mon Jan 12 2015 - 04:32:17 CST)
- Multiple Tcouple JAVAD NOROOZI (Mon Jan 12 2015 - 03:35:01 CST)
- is there a method equivalent to conformational flooding in NAMD 2.10 Thomas Evangelidis (Sun Jan 11 2015 - 07:43:36 CST)
- Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Christian Bope Domilongo (Fri Jan 09 2015 - 04:31:44 CST)
- Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Fri Jan 09 2015 - 03:19:04 CST)
- Re: Failure MD with par7/rst7 amber input Francesco Pietra (Fri Jan 09 2015 - 02:31:55 CST)
- Tempreture Profile along z axis JAVAD NOROOZI (Thu Jan 08 2015 - 03:23:12 CST)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Mihaela Drenscko (Wed Jan 07 2015 - 19:58:27 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Wed Jan 07 2015 - 14:00:02 CST)
- Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Jan 07 2015 - 12:30:35 CST)
- Using colvars for biasing potential in Umbrella Sampling begüm alaybeyoğlu (Wed Jan 07 2015 - 10:01:17 CST)
- Failure MD with par7/rst7 amber input Francesco Pietra (Wed Jan 07 2015 - 02:55:16 CST)
- Problem with Kinetic Energy of Atomselection JAVAD NOROOZI (Wed Jan 07 2015 - 00:53:38 CST)
- topology & force field parameters for Sorbitan monooleate (span 80) Madhusoodanan M.R (Tue Jan 06 2015 - 20:32:39 CST)
- Probelm with Lone Pairs on TIP4 model JAVAD NOROOZI (Tue Jan 06 2015 - 04:07:23 CST)
- Re: Asking help on results of our GPU benchmark Axel Kohlmeyer (Mon Jan 05 2015 - 10:36:24 CST)
- AW: Asking help on results of our GPU benchmark Norman Geist (Mon Jan 05 2015 - 00:37:40 CST)
- FEP, big variations in dG within a window Jonasson Gabriella (Mon Jan 05 2015 - 09:44:31 CST)
- Re: Temperature assignment REMD Yan Zhou (Mon Jan 05 2015 - 02:27:56 CST)
- AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 00:42:51 CST)
- Re: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 02:50:52 CST)
- AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 03:19:13 CST)
- Re: AW: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 04:39:58 CST)
- AW: AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 06:35:46 CST)
- Re: AW: AW: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 07:34:30 CST)
- AW: AW: AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 08:56:36 CST)
- AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 03:19:13 CST)
- Re: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 02:50:52 CST)
- AW: error parsing config file while executing Norman Geist (Mon Jan 05 2015 - 00:26:37 CST)
- regarding PME grid setting problem amit banerjee (Sun Jan 04 2015 - 18:31:44 CST)
- Temperature assignment REMD divya nayar (Sat Jan 03 2015 - 08:36:05 CST)
- Reg: simulating an amino acid in dichloromethane Akshay Bhatnagar (Fri Jan 02 2015 - 23:18:45 CST)
Last message date: Tue Dec 27 2016 - 20:48:03 CST
Archived on: Tue Dec 27 2016 - 23:22:48 CST
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