NAMD-L: By Thread
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About this archive
Starting: Sun Jan 01 2017 - 04:00:35 CST
Ending: Mon Dec 31 2018 - 09:42:31 CST
- unable to open restart.colvars Francesco Pietra (Mon Dec 31 2018 - 01:47:21 CST)
- QM-MM with MOPAC Francesco Pietra (Mon Dec 31 2018 - 01:32:04 CST)
- Coarse Grained simulation of silicon nitride nanopore - Reg Mani Kandan (Fri Dec 28 2018 - 13:35:58 CST)
- Error in NAMD Simulations -Drude HEMANTH H 18310019 (Mon Dec 24 2018 - 00:24:23 CST)
- What NAMD version to obtain Seibold, Steve Allan (Wed Dec 19 2018 - 14:35:12 CST)
- MOPAC Plugin Update McGuire, Kelly (Mon Dec 17 2018 - 14:01:13 CST)
- Question on restraints with MM-GBSA Francesco Pietra (Sun Dec 16 2018 - 04:47:36 CST)
- Running QM-MM MOPAC on a cluster Francesco Pietra (Fri Dec 14 2018 - 04:21:04 CST)
- Re: Running QM-MM MOPAC on a cluster Jim Phillips (Fri Dec 14 2018 - 09:29:51 CST)
- Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Sun Dec 16 2018 - 01:47:41 CST)
- Re: Running QM-MM MOPAC on a cluster Jim Phillips (Mon Dec 17 2018 - 09:12:25 CST)
- Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Mon Dec 17 2018 - 15:22:11 CST)
- Re: Running QM-MM MOPAC on a cluster Jim Phillips (Tue Dec 18 2018 - 16:03:22 CST)
- Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Fri Dec 21 2018 - 13:17:13 CST)
- Re: Running QM-MM MOPAC on a cluster Jim Phillips (Mon Dec 31 2018 - 09:42:27 CST)
- Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Sun Dec 16 2018 - 01:47:41 CST)
- Re: Running QM-MM MOPAC on a cluster Jim Phillips (Fri Dec 14 2018 - 09:29:51 CST)
- run MD simulation in NAMD using stages file strategy or all in one file ? L- (Thu Dec 13 2018 - 10:12:13 CST)
- Constant Force Pull McGuire, Kelly (Thu Dec 13 2018 - 03:44:18 CST)
- Wrapping multimeric protein issues Jacob Usadi (Wed Dec 12 2018 - 17:51:55 CST)
- User force field with FEP? Randy J. Zauhar (Tue Dec 11 2018 - 13:27:00 CST)
- C36 force field Ashkan Shekaari (Tue Dec 11 2018 - 07:34:38 CST)
- Regarding free energy Abhishek Kumar Singh (Sun Dec 09 2018 - 22:30:57 CST)
- problems running GPU-accelerated namd 李耀 (Sun Dec 09 2018 - 02:02:36 CST)
- Parallel Jobs McGuire, Kelly (Thu Dec 06 2018 - 14:36:45 CST)
- NAMD compiling problem Faramarz Joodaki (Thu Dec 06 2018 - 10:59:17 CST)
- tar.gz incorrect firmat? Francesco Pietra (Wed Dec 05 2018 - 14:51:50 CST)
- ERROR TOLERANCE L- (Wed Dec 05 2018 - 13:32:42 CST)
- Positive energy for protein Ashkan Shekaari (Mon Dec 03 2018 - 08:20:58 CST)
- Reg Membrane simulation Vidhya Sankar (Mon Dec 03 2018 - 07:43:58 CST)
- Positive energy values for protein Ashkan Shekaari (Sat Dec 01 2018 - 07:43:48 CST)
- Water Transport McGuire, Kelly (Thu Nov 29 2018 - 13:34:54 CST)
- NAMD QM/MM alchemical free energy change capabilities? Braden Kelly (Mon Nov 26 2018 - 22:07:33 CST)
- How to add a C code to NAMD properly? Faramarz Joodaki (Fri Nov 23 2018 - 12:58:39 CST)
- Re: How to add a C code to NAMD properly? yjcoshc (Sat Nov 24 2018 - 19:20:22 CST)
- Re: How to add a C code to NAMD properly? Jérôme Hénin (Mon Nov 26 2018 - 06:27:24 CST)
- Re: How to add a C code to NAMD properly? Faramarz Joodaki (Tue Nov 27 2018 - 16:10:46 CST)
- Re: How to add a C code to NAMD properly? yjcoshc (Tue Nov 27 2018 - 19:44:25 CST)
- Re: How to add a C code to NAMD properly? Faramarz Joodaki (Wed Dec 05 2018 - 18:39:07 CST)
- Re: How to add a C code to NAMD properly? yjcoshc (Wed Dec 05 2018 - 19:45:11 CST)
- Re: How to add a C code to NAMD properly? Faramarz Joodaki (Wed Dec 05 2018 - 19:51:57 CST)
- Re: How to add a C code to NAMD properly? yjcoshc_at_gmail.com (Sat Dec 15 2018 - 19:33:28 CST)
- Re: How to add a C code to NAMD properly? Faramarz Joodaki (Sun Dec 16 2018 - 11:50:41 CST)
- Re: How to add a C code to NAMD properly? Faramarz Joodaki (Sun Dec 16 2018 - 11:59:19 CST)
- Re: How to add a C code to NAMD properly? Giacomo Fiorin (Sun Dec 16 2018 - 22:36:26 CST)
- Re: How to add a C code to NAMD properly? Faramarz Joodaki (Tue Dec 18 2018 - 09:37:25 CST)
- Re: How to add a C code to NAMD properly? Giacomo Fiorin (Wed Dec 19 2018 - 13:45:21 CST)
- Re: How to add a C code to NAMD properly? Jérôme Hénin (Mon Nov 26 2018 - 06:27:24 CST)
- Re: How to add a C code to NAMD properly? yjcoshc (Sat Nov 24 2018 - 19:20:22 CST)
- Magnetic field Ashkan Shekaari (Thu Nov 22 2018 - 07:22:46 CST)
- [ REST2 ] Possible bug on NAMD example Diego Gomes (Thu Nov 22 2018 - 07:06:41 CST)
- NAMD 2.13 and RTX2080Ti Battocchio, Giovanni (Thu Nov 22 2018 - 06:52:57 CST)
- Problems about constraint (conskcol) in umbrella sampling conf file 李耀 (Wed Nov 21 2018 - 09:44:53 CST)
- [NAMD] Running REUS in many nodes The Cromicus Productions (Tue Nov 20 2018 - 16:12:01 CST)
- Is there a problem of ORCA running for NAMD MPI? Francesco Pietra (Tue Nov 20 2018 - 03:35:17 CST)
- NAMD/VMD installation for Windows 10 Joey Gehring (Mon Nov 19 2018 - 10:27:22 CST)
- Running QM-MM tutorial on a cluster Francesco Pietra (Sat Nov 17 2018 - 13:30:02 CST)
- ffTK torsion scan convergence using Gaussian. Dipak Balasaheb Sanap (Mon Nov 12 2018 - 18:08:12 CST)
- Re: ffTK torsion scan convergence using Gaussian. Gumbart, James C (Tue Nov 13 2018 - 19:56:23 CST)
- Unusual WT-Metadynamics gaussians heights Bruno Cuevas Zuviría (Mon Nov 12 2018 - 04:25:08 CST)
- Minimization Question McGuire, Kelly (Sun Nov 11 2018 - 19:46:19 CST)
- FEP Rattle Error Ebru Çetin (Sun Nov 11 2018 - 17:07:51 CST)
- CHARMM36 parameters for nucelobases Shivangi Nangia (Sat Nov 10 2018 - 07:03:34 CST)
- Concatenate Outputs McGuire, Kelly (Fri Nov 09 2018 - 14:12:21 CST)
- Setting alchElecLambdaStart 1.0 parameter for FEP calculations David Huggins (Fri Nov 09 2018 - 12:08:51 CST)
- Using center of mass to calculate the radial distribution function Yi Lun Lee (Fri Nov 09 2018 - 11:37:36 CST)
- Way to wget or curl download the precompiled NAMD? Darin Lory (Thu Nov 08 2018 - 15:13:22 CST)
- Building with GCC on Ubuntu 18 Jérôme Hénin (Thu Nov 08 2018 - 11:18:05 CST)
- Re: Building with GCC on Ubuntu 18 Julio Maia (Thu Nov 08 2018 - 11:26:36 CST)
- RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Thu Nov 08 2018 - 11:50:54 CST)
- Re: Building with GCC on Ubuntu 18 Jérôme Hénin (Fri Nov 09 2018 - 07:00:43 CST)
- RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Fri Nov 09 2018 - 12:42:37 CST)
- RE: Building with GCC on Ubuntu 18 Jim Phillips (Fri Nov 09 2018 - 16:17:41 CST)
- Re: Building with GCC on Ubuntu 18 Jérôme Hénin (Mon Nov 12 2018 - 07:45:37 CST)
- Re: Building with GCC on Ubuntu 18 Jim Phillips (Mon Nov 12 2018 - 09:08:30 CST)
- Re: Building with GCC on Ubuntu 18 Jérôme Hénin (Mon Nov 12 2018 - 09:14:01 CST)
- RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Mon Nov 12 2018 - 11:34:11 CST)
- Re: Building with GCC on Ubuntu 18 Jérôme Hénin (Tue Nov 13 2018 - 07:29:35 CST)
- RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Thu Nov 08 2018 - 11:50:54 CST)
- Re: Building with GCC on Ubuntu 18 Julio Maia (Thu Nov 08 2018 - 11:26:36 CST)
- creating topology for a unique structure soroush ziaei (Wed Nov 07 2018 - 11:05:08 CST)
- Langevin Dynamics Coefficient Value -Reg Mani Kandan (Tue Nov 06 2018 - 11:30:09 CST)
- Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Travis Hesketh (Mon Nov 05 2018 - 10:04:49 CST)
- Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Brian Radak (Mon Nov 05 2018 - 11:18:56 CST)
- QM/MM Question McGuire, Kelly (Sun Nov 04 2018 - 12:59:51 CST)
- Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 07:32:06 CST)
- Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 11:13:45 CST)
- Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 12:14:02 CST)
- Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 13:41:11 CST)
- Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 13:46:39 CST)
- Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 16:19:08 CST)
- Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 21:23:11 CST)
- Re: QM/MM Question Gerard Rowe (Tue Nov 06 2018 - 13:17:42 CST)
- Re: QM/MM Question McGuire, Kelly (Tue Nov 06 2018 - 13:40:14 CST)
- Re: QM/MM Question McGuire, Kelly (Tue Nov 06 2018 - 15:52:41 CST)
- Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 07:32:06 CST)
- Fix aminoacids - error Villalain Boullon, Jose (Sun Nov 04 2018 - 03:18:23 CST)
- creating topology for a unique structure soroush ziaei (Sun Nov 04 2018 - 02:02:03 CST)
- Gaussian Dihedral Scan Log files visualization. Dipak Balasaheb Sanap (Sat Nov 03 2018 - 21:47:47 CDT)
- qmSecProc Proper Use McGuire, Kelly (Fri Nov 02 2018 - 15:02:00 CDT)
- NVIDIA Quadro(R) GV100 card for NAMD studies sesha surya vara prasad reddy karri (Fri Nov 02 2018 - 05:58:41 CDT)
- ORCA GPUs McGuire, Kelly (Thu Nov 01 2018 - 20:48:47 CDT)
- detecting vanishing atoms in zero.fep soroush ziaei (Thu Nov 01 2018 - 18:03:12 CDT)
- detecting vanishing atoms in zero.fep soroush ziaei (Thu Nov 01 2018 - 15:39:07 CDT)
- Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Asghar Razavi (Thu Nov 01 2018 - 11:43:30 CDT)
- Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Nielsen, Steven (Thu Nov 01 2018 - 12:30:21 CDT)
- Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Peter Freddolino (Thu Nov 01 2018 - 15:45:16 CDT)
- Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Asghar Razavi (Fri Nov 02 2018 - 08:30:21 CDT)
- Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Brian Radak (Fri Nov 02 2018 - 09:28:21 CDT)
- Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Peter Freddolino (Thu Nov 01 2018 - 15:45:16 CDT)
- Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Nielsen, Steven (Thu Nov 01 2018 - 12:30:21 CDT)
- bpti example compiled source charmrun++ does not launch Hazard, E. Starr (Thu Nov 01 2018 - 09:31:05 CDT)
- Couldn't open DCD file Hazard, E. Starr (Wed Oct 31 2018 - 14:19:30 CDT)
- Membrane Simulation Alice Zheng (Tue Oct 30 2018 - 20:58:03 CDT)
- ORCA QMMM McGuire, Kelly (Mon Oct 29 2018 - 17:41:25 CDT)
- QM/MM Error McGuire, Kelly (Mon Oct 29 2018 - 00:01:25 CDT)
- QM/MM Question McGuire, Kelly (Sun Oct 28 2018 - 21:53:59 CDT)
- detecting vanishing atoms in zero.fep soroush ziaei (Sat Oct 27 2018 - 16:37:20 CDT)
- Alchdecouple for dihedral/improper terms David Huggins (Sat Oct 27 2018 - 10:21:26 CDT)
- parameter request for PRES bonding Francesco Pietra (Sat Oct 27 2018 - 02:27:05 CDT)
- Binding free energy tutorial jing liang (Fri Oct 26 2018 - 14:37:51 CDT)
- Re: Binding free energy tutorial David Hardy (Sat Oct 27 2018 - 03:15:30 CDT)
- Re: Binding free energy tutorial David Hardy (Sat Oct 27 2018 - 15:34:24 CDT)
- Re: Binding free energy tutorial Giacomo Fiorin (Sun Oct 28 2018 - 10:20:50 CDT)
- Re: Binding free energy tutorial David Hardy (Sun Oct 28 2018 - 11:47:37 CDT)
- Re: Binding free energy tutorial jing liang (Wed Oct 31 2018 - 04:31:13 CDT)
- Re: Binding free energy tutorial jing liang (Wed Nov 07 2018 - 08:17:44 CST)
- Re: Binding free energy tutorial Nassar, Omneya (Wed Nov 07 2018 - 08:56:56 CST)
- Re: Binding free energy tutorial Gumbart, James C (Wed Nov 07 2018 - 12:16:06 CST)
- Re: Binding free energy tutorial David Hardy (Sat Oct 27 2018 - 15:34:24 CDT)
- Re: Binding free energy tutorial David Hardy (Sat Oct 27 2018 - 03:15:30 CDT)
- FFtK Tutorial (Urey-Bradley angles error). Dipak Balasaheb Sanap (Fri Oct 26 2018 - 14:20:59 CDT)
- (no subject) Darin Lory (Fri Oct 26 2018 - 11:22:41 CDT)
- Equilibration of membrane water system (pressure in NVT) Rene Hamburger UNI KL (Fri Oct 26 2018 - 02:32:38 CDT)
- Positive VDW energies Nick Palmer (Thu Oct 25 2018 - 14:54:58 CDT)
- adaptive biasing force Artur Hermano (Wed Oct 24 2018 - 14:08:35 CDT)
- Standard density -reg Mani Kandan (Wed Oct 24 2018 - 02:07:44 CDT)
- Nano-bio interaction in NAMD Ashkan Shekaari (Tue Oct 23 2018 - 10:01:09 CDT)
- error in (runfepmin) soroush ziaei (Sun Oct 21 2018 - 18:02:24 CDT)
- Surface Tension calculation Yi Lun Lee (Fri Oct 19 2018 - 15:33:58 CDT)
- git rid of it Scott Brozell (Fri Oct 19 2018 - 14:21:57 CDT)
- constant temprature for vacuum condition in namd file soroush ziaei (Fri Oct 19 2018 - 14:19:53 CDT)
- vacuum condition in config file soroush ziaei (Fri Oct 19 2018 - 13:58:37 CDT)
- ABF Window Boundaries McGuire, Kelly (Fri Oct 19 2018 - 02:45:07 CDT)
- Fwd: the fep error in third part of config file Brian Radak (Wed Oct 17 2018 - 09:14:48 CDT)
- Colvars and distance restraint for umbrella sampling Udaya Dahal (Tue Oct 16 2018 - 19:08:07 CDT)
- Re: Colvars and distance restraint for umbrella sampling Giacomo Fiorin (Tue Oct 16 2018 - 19:31:15 CDT)
- Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Tue Oct 16 2018 - 19:41:21 CDT)
- Re: Colvars and distance restraint for umbrella sampling Gumbart, James C (Wed Oct 17 2018 - 10:27:01 CDT)
- Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Wed Oct 17 2018 - 10:41:00 CDT)
- Re: Colvars and distance restraint for umbrella sampling Gumbart, James C (Wed Oct 17 2018 - 10:49:11 CDT)
- Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Wed Oct 17 2018 - 10:58:13 CDT)
- Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Tue Oct 16 2018 - 19:41:21 CDT)
- Re: Colvars and distance restraint for umbrella sampling Giacomo Fiorin (Tue Oct 16 2018 - 19:31:15 CDT)
- Affinity Mahmood Naderan (Tue Oct 16 2018 - 15:20:52 CDT)
- Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area Rabeta Yeasmin (Mon Oct 15 2018 - 10:26:45 CDT)
- the fep error in third part of config file soroush ziaei (Mon Oct 15 2018 - 09:50:25 CDT)
- the instance type selection for NAMD simulation in Amason marketplace sunyeping (Mon Oct 15 2018 - 07:09:54 CDT)
- Setting up QM/MM calculations with QwikMD without the GUI Agisilaos Chantzis (Fri Oct 05 2018 - 11:20:54 CDT)
- E-field to Voltage - Reg Mani Kandan (Fri Oct 05 2018 - 09:58:19 CDT)
- Temperature Fluctuations in Drude Simulations - NAMD HEMANTH H 18310019 (Thu Oct 04 2018 - 23:39:14 CDT)
- g++ 5.3 fails on 2.12/2.13b1 with CUDA 8.0 Chris Borchert (Thu Oct 04 2018 - 15:59:10 CDT)
- How to simulate flexible water with TIP4P potential? Alfonso Gijón (Wed Oct 03 2018 - 08:15:12 CDT)
- Diffusion Coefficient calculation Kinkini Jayasundara (Fri Sep 28 2018 - 20:48:39 CDT)
- Mismatch in atom number between psf and dcd files Wintrode, Patrick (Fri Sep 28 2018 - 10:04:11 CDT)
- SWM4-NDP PSF File Julian Müller (Thu Sep 27 2018 - 02:48:10 CDT)
- ABF Question McGuire, Kelly (Wed Sep 26 2018 - 21:32:54 CDT)
- About CUDA version Mahmood Naderan (Tue Sep 25 2018 - 13:22:21 CDT)
- PBC error. Amber force field in NAMD M RCC (Tue Sep 25 2018 - 06:35:53 CDT)
- First "Hands-On" Workshop on Structural DNA Nanotechnology João Ribeiro (Mon Sep 24 2018 - 09:13:30 CDT)
- Critical isofrom selectivity in molecular dynamics M RCC (Mon Sep 24 2018 - 06:23:14 CDT)
- Constraint failure in Highly charged system - Reg Mani Kandan (Thu Sep 20 2018 - 23:33:16 CDT)
- Best water model 김민재 (Thu Sep 20 2018 - 07:54:34 CDT)
- calculating non bonded energy using namdenergy Monika Madhavi (Wed Sep 19 2018 - 22:19:16 CDT)
- Do firsttimestep, numsteps and run have maximum values? yjcoshc (Tue Sep 18 2018 - 20:42:05 CDT)
- Right NAMD version Fidan Sumbul (Tue Sep 18 2018 - 06:00:36 CDT)
- Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Mon Sep 17 2018 - 11:50:49 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Mon Sep 17 2018 - 15:58:31 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Tue Sep 18 2018 - 10:58:25 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Tue Sep 18 2018 - 12:26:59 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Tue Sep 18 2018 - 13:36:40 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Wed Sep 19 2018 - 13:00:29 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Wed Sep 19 2018 - 20:52:15 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Thu Sep 20 2018 - 09:58:39 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Thu Sep 20 2018 - 11:14:35 CDT)
- AW: Bad structure after converting the coarse grained last frame to all-atom Norman Geist (Fri Sep 21 2018 - 01:08:00 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Tue Sep 18 2018 - 10:58:25 CDT)
- Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Mon Sep 17 2018 - 15:58:31 CDT)
- Different cell vectors - Reg Mani Kandan (Mon Sep 17 2018 - 04:45:10 CDT)
- Using 4-site water model in NAMD Haohao Fu (Sun Sep 16 2018 - 20:05:23 CDT)
- regarding umbrella sampling simulation san kumar (Fri Sep 14 2018 - 23:11:54 CDT)
- Reg membrane hydration Vidhya Sankar (Thu Sep 13 2018 - 21:01:39 CDT)
- Ewald size-dependence correction in FEP simulation of an electric dipole Ali Mehdizadeh Rahimi (Wed Sep 12 2018 - 19:34:37 CDT)
- RE: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Wed Sep 12 2018 - 23:16:02 CDT)
- RE: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Thu Sep 13 2018 - 21:54:08 CDT)
- Re: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Fri Sep 14 2018 - 07:47:39 CDT)
- Re: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Fri Sep 14 2018 - 08:02:04 CDT)
- Re: Ewald size-dependence correction in FEP simulation of an electric dipole Brian Radak (Fri Sep 14 2018 - 09:37:16 CDT)
- RE: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Thu Sep 13 2018 - 21:54:08 CDT)
- Re: Ewald size-dependence correction in FEP simulation of an electric dipole Victor Kwan (Thu Sep 13 2018 - 10:57:31 CDT)
- RE: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Wed Sep 12 2018 - 23:16:02 CDT)
- Enhanced Sampling and Free-Energy Calculations Lectures João Ribeiro (Mon Sep 10 2018 - 12:02:42 CDT)
- Need help preventing hydration of the lipid-protein interface Vidhya Sankar (Mon Sep 10 2018 - 07:38:50 CDT)
- Need help preventing hydration of the lipid-protein using tcl script Vidhya Sankar (Mon Sep 10 2018 - 07:34:34 CDT)
- Rattle algorithm Constraint failure - Reg Mani Kandan (Fri Sep 07 2018 - 05:46:59 CDT)
- namd simulation input file setting from NPT to NVT Yi Lun Lee (Thu Sep 06 2018 - 15:31:10 CDT)
- Cutoff radius for electrostatic embedding in QM/MM calculations Agisilaos Chantzis (Wed Sep 05 2018 - 10:21:23 CDT)
- energy calculation with namdenergy Monika Madhavi (Wed Sep 05 2018 - 07:32:00 CDT)
- Unexpected Energy values - Reg Mani Kandan (Wed Sep 05 2018 - 07:07:29 CDT)
- parameter file for ACE and CT3 cap Dhiraj Srivastava (Sun Sep 02 2018 - 19:45:14 CDT)
- multi-node mpiexec issue Ryuzo Azuma (Fri Aug 31 2018 - 11:44:26 CDT)
- Weird PBC wrapping Michail Lazaratos (Thu Aug 30 2018 - 05:41:11 CDT)
- Error NPT simulation - Need Urgent Help - Reg Mani Kandan (Wed Aug 29 2018 - 11:35:02 CDT)
- Question: constant-pH to standard MD Yasser Bruno Ruiz Blanco (Fri Aug 24 2018 - 02:34:43 CDT)
- CGenFF 4.1 lone pairs Jeff Comer (Wed Aug 22 2018 - 13:56:30 CDT)
- Three bonds with water in vmd from NAMD DCD Seibold, Steve Allan (Tue Aug 21 2018 - 09:17:43 CDT)
- ERROR in multiple walker metadynamics simulation Miyu Tamura (Tue Aug 21 2018 - 01:30:09 CDT)
- MOPAC Point Charges Gerard Rowe (Mon Aug 20 2018 - 12:29:36 CDT)
- FEP atom velocity. Aashish Bhatt (Mon Aug 20 2018 - 01:10:35 CDT)
- Induced Electric filed and Electrostatics - Reg Mani Kandan (Sun Aug 19 2018 - 02:54:45 CDT)
- FATAL ERROR: Unable to access config file temp14.conf Charles Hoying (Thu Aug 16 2018 - 20:44:17 CDT)
- Converting a mixture system from NAMD to LAMMPS Sonibare, Kolawole (Thu Aug 16 2018 - 12:14:56 CDT)
- AW: AW: AW: Periodic cell has become too small for original patch grid Norman Geist (Wed Aug 15 2018 - 09:52:28 CDT)
- QM/MM MD and the qmParamPDB file Agisilaos Chantzis (Wed Aug 15 2018 - 07:48:40 CDT)
- Periodic cell has become too small for original patch grid Rohit Modee (Mon Aug 13 2018 - 03:26:13 CDT)
- Re: Periodic cell has become too small for original patch grid Giacomo Fiorin (Mon Aug 13 2018 - 07:00:35 CDT)
- AW: Periodic cell has become too small for original patch grid Norman Geist (Tue Aug 14 2018 - 01:28:06 CDT)
- Re: AW: Periodic cell has become too small for original patch grid Rohit Modee (Wed Aug 15 2018 - 04:34:52 CDT)
- AW: AW: Periodic cell has become too small for original patch grid Norman Geist (Wed Aug 15 2018 - 05:52:38 CDT)
- Re: AW: AW: Periodic cell has become too small for original patch grid Rohit Modee (Wed Aug 15 2018 - 06:06:12 CDT)
- AW: AW: AW: Periodic cell has become too small for original patch grid Norman Geist (Wed Aug 15 2018 - 09:52:13 CDT)
- Re: AW: Periodic cell has become too small for original patch grid Rohit Modee (Wed Aug 15 2018 - 04:34:52 CDT)
- Research Programmer Positions Available João Ribeiro (Fri Aug 10 2018 - 13:29:41 CDT)
- How to make water stay in the Z direction? Yi Lun Lee (Wed Aug 08 2018 - 11:26:11 CDT)
- Re: accelMDbdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 Omid Bavi (Tue Aug 07 2018 - 13:49:39 CDT)
- atom moving fast error in Coarse grained simulation: even reduced the time step Rabeta Yeasmin (Mon Aug 06 2018 - 14:30:40 CDT)
- question when apply external electric field Jiali Wang (Sat Aug 04 2018 - 16:43:04 CDT)
- convert a 3d system into a 2d system Yi Lun Lee (Fri Aug 03 2018 - 11:51:03 CDT)
- restarting Gaussian accelerated MD fails Vlad Cojocaru (Fri Aug 03 2018 - 07:00:30 CDT)
- Vibration Analysis Script Aashish Bhatt (Fri Aug 03 2018 - 05:16:24 CDT)
- Which one is more reliable to use in umbrella sampling- .traj data or vmd script data Rabeta Yeasmin (Thu Aug 02 2018 - 16:24:35 CDT)
- SegFault in QM/MM run Gerard Rowe (Wed Aug 01 2018 - 08:59:37 CDT)
- Isomerization between runs Michail Lazaratos (Wed Aug 01 2018 - 04:56:01 CDT)
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 João Ribeiro (Mon Jul 30 2018 - 16:15:45 CDT)
- 1-D ABF and Compressibility McGuire, Kelly (Mon Jul 30 2018 - 14:44:53 CDT)
- Problems with temperature control. Josep Ivan Balaguer Molins (Mon Jul 30 2018 - 05:21:09 CDT)
- Re: Problems with temperature control. Brian Radak (Mon Jul 30 2018 - 08:41:29 CDT)
- Re: Problems with temperature control. Josep Ivan Balaguer Molins (Mon Jul 30 2018 - 09:41:32 CDT)
- Re: Problems with temperature control. Brian Radak (Mon Jul 30 2018 - 13:31:20 CDT)
- Re: Problems with temperature control. Josep Ivan Balaguer Molins (Tue Jul 31 2018 - 01:24:58 CDT)
- Re: Problems with temperature control. Josep Ivan Balaguer Molins (Tue Jul 31 2018 - 06:37:49 CDT)
- Re: Problems with temperature control. Brian Radak (Tue Jul 31 2018 - 06:56:59 CDT)
- Re: Problems with temperature control. Josep Ivan Balaguer Molins (Tue Jul 31 2018 - 10:54:40 CDT)
- Re: Problems with temperature control. Brian Radak (Tue Jul 31 2018 - 12:57:43 CDT)
- RE: Problems with temperature control. Vermaas, Joshua (Tue Jul 31 2018 - 14:18:35 CDT)
- Re: Problems with temperature control. Brian Radak (Tue Jul 31 2018 - 14:57:09 CDT)
- Re: Problems with temperature control. Josep Ivan Balaguer Molins (Wed Aug 01 2018 - 12:34:30 CDT)
- Re: Problems with temperature control. Josep Ivan Balaguer Molins (Mon Jul 30 2018 - 09:41:32 CDT)
- Re: Problems with temperature control. Brian Radak (Mon Jul 30 2018 - 08:41:29 CDT)
- Reg autioionize plugin Vidhya Sankar (Sat Jul 28 2018 - 01:19:09 CDT)
- Multi-dimensional PMF McGuire, Kelly (Thu Jul 26 2018 - 16:40:28 CDT)
- Re: Multi-dimensional PMF Jérôme Hénin (Fri Jul 27 2018 - 02:45:20 CDT)
- Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 09:58:43 CDT)
- Re: Multi-dimensional PMF Jérôme Hénin (Fri Jul 27 2018 - 10:16:44 CDT)
- Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 10:38:58 CDT)
- RE: Multi-dimensional PMF Vermaas, Joshua (Fri Jul 27 2018 - 11:27:45 CDT)
- Re: Multi-dimensional PMF Jérôme Hénin (Fri Jul 27 2018 - 11:53:05 CDT)
- Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 12:04:34 CDT)
- Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 13:07:51 CDT)
- RE: Multi-dimensional PMF Vermaas, Joshua (Fri Jul 27 2018 - 14:43:26 CDT)
- Re: Multi-dimensional PMF Jeff Comer (Fri Jul 27 2018 - 18:39:37 CDT)
- Re: Multi-dimensional PMF Giacomo Fiorin (Fri Jul 27 2018 - 22:49:55 CDT)
- Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 23:25:11 CDT)
- Re: Multi-dimensional PMF JC Gumbart (Sat Jul 28 2018 - 09:48:08 CDT)
- Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 09:58:43 CDT)
- Re: Multi-dimensional PMF Jérôme Hénin (Fri Jul 27 2018 - 02:45:20 CDT)
- Sudden /\A drop in last FEP window Francesco Pietra (Thu Jul 26 2018 - 10:34:06 CDT)
- Re: Sudden /\A drop in last FEP window Jérôme Hénin (Thu Jul 26 2018 - 11:48:07 CDT)
- Re: Sudden /\A drop in last FEP window Francesco Pietra (Thu Jul 26 2018 - 12:54:12 CDT)
- Fwd: Sudden /\A drop in last FEP window Francesco Pietra (Fri Jul 27 2018 - 03:13:46 CDT)
- Fwd: Sudden /\A drop in last FEP window Francesco Pietra (Sat Jul 28 2018 - 05:30:07 CDT)
- Re: Sudden /\A drop in last FEP window Jérôme Hénin (Sat Jul 28 2018 - 08:41:19 CDT)
- Re: Sudden /\A drop in last FEP window Francesco Pietra (Mon Aug 06 2018 - 09:30:28 CDT)
- Fwd: Sudden /\A drop in last FEP window Francesco Pietra (Tue Aug 14 2018 - 23:44:06 CDT)
- Re: Sudden /\A drop in last FEP window Jérôme Hénin (Fri Aug 17 2018 - 04:39:12 CDT)
- Re: Sudden /\A drop in last FEP window Francesco Pietra (Thu Jul 26 2018 - 12:54:12 CDT)
- Re: Sudden /\A drop in last FEP window Jérôme Hénin (Thu Jul 26 2018 - 11:48:07 CDT)
- mail about autoionize plugin Vidhya Sankar (Thu Jul 26 2018 - 08:34:43 CDT)
- reg nan error in namd Vidhya Sankar (Tue Jul 24 2018 - 21:00:50 CDT)
- Rattle error with lateral pressure calculations Sadegh Faramarzi Ganjabad (Tue Jul 24 2018 - 17:24:17 CDT)
- Re: Rattle error with lateral pressure calculations Brian Radak (Sat Jul 28 2018 - 12:17:53 CDT)
- Multiple Colvars McGuire, Kelly (Tue Jul 24 2018 - 15:38:22 CDT)
- REMD restart tcl script meaning? Jacob Usadi (Tue Jul 24 2018 - 12:51:06 CDT)
- MAIL about namd velocity error Vidhya Sankar (Tue Jul 24 2018 - 09:08:08 CDT)
- velocity.pdb and velocity unit in NAMD Kowsar Khajeh (Tue Jul 24 2018 - 01:07:13 CDT)
- overlapping windows in ABF Olya Kravchenko (Mon Jul 23 2018 - 09:52:39 CDT)
- ABF Questions McGuire, Kelly (Fri Jul 20 2018 - 21:13:43 CDT)
- Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Nassar, Omneya (Fri Jul 20 2018 - 15:04:17 CDT)
- Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Jérôme Hénin (Sat Jul 21 2018 - 05:58:02 CDT)
- Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Nassar, Omneya (Sat Jul 21 2018 - 07:58:40 CDT)
- Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Jérôme Hénin (Tue Jul 24 2018 - 02:55:40 CDT)
- Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Jérôme Hénin (Sat Jul 21 2018 - 05:58:02 CDT)
- [NAMD] Define time-dependent grid force The Cromicus Productions (Fri Jul 20 2018 - 12:52:13 CDT)
- (no subject) Abhijit Gogoi (Fri Jul 20 2018 - 01:15:37 CDT)
- Is QM/MM compatible with Colvars? William Tao (Thu Jul 19 2018 - 16:16:35 CDT)
- Question about the fundamentals of MD and WHAM Junwoong Yoon (Thu Jul 19 2018 - 15:52:43 CDT)
- QM/MM with Orca: Memory allocation failed Gerard Rowe (Wed Jul 18 2018 - 17:18:33 CDT)
- CHARMM FF parameters for FE-S bond in CYP450 jeevan gc (Tue Jul 17 2018 - 16:39:50 CDT)
- NAMD Error Shriya Bansal (Tue Jul 17 2018 - 14:45:26 CDT)
- E-filed to individual channel in parallel system - Reg Mani Kandan (Tue Jul 17 2018 - 12:09:57 CDT)
- Converting GromacsForce File to NAMD using GromacsTopFile.C Ivan (Tue Jul 17 2018 - 06:25:58 CDT)
- Decreasing performance of cluster running FEP Francesco Pietra (Wed Jul 11 2018 - 00:29:51 CDT)
- RE: Decreasing performance of cluster running FEP Vermaas, Joshua (Wed Jul 11 2018 - 12:21:07 CDT)
- Re: Decreasing performance of cluster running FEP Francesco Pietra (Wed Jul 11 2018 - 16:31:55 CDT)
- RE: Decreasing performance of cluster running FEP Vermaas, Joshua (Wed Jul 11 2018 - 18:23:23 CDT)
- Re: Decreasing performance of cluster running FEP Francesco Pietra (Thu Jul 12 2018 - 01:58:45 CDT)
- Re: Decreasing performance of cluster running FEP Brian Radak (Thu Jul 12 2018 - 09:24:19 CDT)
- Re: Decreasing performance of cluster running FEP Brian Radak (Sat Jul 14 2018 - 09:24:47 CDT)
- Re: Decreasing performance of cluster running FEP Francesco Pietra (Sat Jul 14 2018 - 10:57:38 CDT)
- Re: Decreasing performance of cluster running FEP Francesco Pietra (Wed Jul 11 2018 - 16:31:55 CDT)
- RE: Decreasing performance of cluster running FEP Vermaas, Joshua (Wed Jul 11 2018 - 12:21:07 CDT)
- Consulting about buying new hardware (GPU) michael zhenin (Tue Jul 10 2018 - 03:44:31 CDT)
- Umbrella Sampling input parameters Junwoong Yoon (Tue Jul 10 2018 - 01:55:16 CDT)
- ABF Asymmetry McGuire, Kelly (Mon Jul 09 2018 - 16:48:51 CDT)
- Broken Structure after reverting coarse-grained system to all-atom system Rabeta Yeasmin (Mon Jul 09 2018 - 13:38:42 CDT)
- ABF, rigid bonds and constraints Ekaterina Sobakinskaja (Fri Jul 06 2018 - 05:23:10 CDT)
- ABF simulations with singularities? Junwoong Yoon (Thu Jul 05 2018 - 20:55:29 CDT)
- Distorted peptide bond with new residue Nick Palmer (Thu Jul 05 2018 - 16:18:28 CDT)
- Bond parameter error for the system which has been converted using residue-based coarse-grained method Rabeta Yeasmin (Wed Jul 04 2018 - 15:25:24 CDT)
- Equilibration in NPT simulation Mani Kandan (Wed Jul 04 2018 - 10:25:19 CDT)
- AW: NAMD SMP version warning - Reg Norman Geist (Wed Jul 04 2018 - 09:42:45 CDT)
- Total charge problem Abhishek Kumar Singh (Wed Jul 04 2018 - 07:50:36 CDT)
- Ph.D. candidate position in biomolecular modeling or bioinformatics Jan Brezovsky (Wed Jul 04 2018 - 05:33:36 CDT)
- AW: NAMD SMP version warning - Reg Norman Geist (Wed Jul 04 2018 - 05:18:45 CDT)
- NAMD SMP version warning - Reg Mani Kandan (Wed Jul 04 2018 - 04:57:40 CDT)
- Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 02:42:39 CDT)
- Re: Qwikmd ABF Question João Ribeiro (Wed Jul 04 2018 - 08:08:10 CDT)
- Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 11:21:21 CDT)
- Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 11:21:57 CDT)
- Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 18:44:26 CDT)
- Re: Qwikmd ABF Question João Ribeiro (Wed Jul 04 2018 - 19:25:30 CDT)
- Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 19:35:02 CDT)
- Re: Qwikmd ABF Question João Ribeiro (Thu Jul 05 2018 - 08:03:31 CDT)
- Re: Qwikmd ABF Question McGuire, Kelly (Thu Jul 05 2018 - 10:48:41 CDT)
- Re: Qwikmd ABF Question João Ribeiro (Thu Jul 05 2018 - 13:16:01 CDT)
- Re: Qwikmd ABF Question João Ribeiro (Mon Jul 09 2018 - 08:18:48 CDT)
- Re: Qwikmd ABF Question João Ribeiro (Wed Jul 04 2018 - 08:08:10 CDT)
- Random Velocities Question McGuire, Kelly (Tue Jul 03 2018 - 22:09:44 CDT)
- Included Topology (.itp) in gromacs to parameter file for NAMD Ivan (Tue Jul 03 2018 - 03:40:29 CDT)
- Problem in NAMD memory optimized version - Reg Mani Kandan (Mon Jul 02 2018 - 11:02:37 CDT)
- At high cutoff: "ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!" Victor Kwan (Sat Jun 30 2018 - 15:35:08 CDT)
- ABF Question McGuire, Kelly (Thu Jun 28 2018 - 23:59:03 CDT)
- QMMM FEP SM Bargeen A Turzo (Thu Jun 28 2018 - 14:38:31 CDT)
- QwikMD Question McGuire, Kelly (Thu Jun 28 2018 - 10:34:17 CDT)
- Phosphorylated Residues Oscar Bastidas (Tue Jun 26 2018 - 23:29:07 CDT)
- "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD Hazel, Anthony J (Tue Jun 26 2018 - 17:17:28 CDT)
- Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD João Ribeiro (Tue Jun 26 2018 - 17:41:48 CDT)
- Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD Hazel, Anthony J (Tue Jun 26 2018 - 17:48:08 CDT)
- Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD Hazel, Anthony J (Tue Jun 26 2018 - 17:48:31 CDT)
- Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD João Ribeiro (Tue Jun 26 2018 - 18:16:11 CDT)
- Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD João Ribeiro (Wed Jun 27 2018 - 09:47:41 CDT)
- Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD João Ribeiro (Tue Jun 26 2018 - 17:41:48 CDT)
- Hydronium parameters Kinkini Jayasundara (Tue Jun 26 2018 - 10:49:03 CDT)
- mail about usage of water tcl script in membrane Vidhya Sankar (Sat Jun 23 2018 - 08:09:26 CDT)
- Re: vmd-l: Re: Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 21:27:04 CDT)
- Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 15:42:20 CDT)
- Re: Strange Bond Behavior Question João Ribeiro (Fri Jun 22 2018 - 16:08:07 CDT)
- Better way to fix the atom -Reg Mani Kandan (Fri Jun 22 2018 - 10:51:57 CDT)
- "block" module for NAMD Tyler Wied (Fri Jun 22 2018 - 07:56:56 CDT)
- namd mpi Stefano Guglielmo (Fri Jun 22 2018 - 07:46:27 CDT)
- mail reg constraint force Vidhya Sankar (Fri Jun 22 2018 - 07:04:54 CDT)
- Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 12:01:18 CDT)
- Re: Colvars Restraint Question Bassam Haddad (Thu Jun 21 2018 - 12:33:58 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 13:43:18 CDT)
- Re: Colvars Restraint Question Brian Radak (Thu Jun 21 2018 - 14:01:23 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 14:53:17 CDT)
- Re: Colvars Restraint Question Brian Radak (Thu Jun 21 2018 - 15:01:39 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 15:04:41 CDT)
- RE: Colvars Restraint Question Vermaas, Joshua (Thu Jun 21 2018 - 15:22:10 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 15:46:49 CDT)
- RE: Colvars Restraint Question Vermaas, Joshua (Thu Jun 21 2018 - 16:02:54 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 16:45:39 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Sun Jun 24 2018 - 23:20:31 CDT)
- RE: Colvars Restraint Question Vermaas, Joshua (Mon Jun 25 2018 - 12:01:53 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Mon Jun 25 2018 - 12:15:44 CDT)
- RE: Colvars Restraint Question Vermaas, Joshua (Mon Jun 25 2018 - 12:18:16 CDT)
- Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 13:43:18 CDT)
- Re: Colvars Restraint Question Bassam Haddad (Thu Jun 21 2018 - 12:33:58 CDT)
- mail about constraints in namd configuration file Vidhya Sankar (Thu Jun 21 2018 - 07:52:17 CDT)
- problem with minimizer Laura Joana (Wed Jun 20 2018 - 07:53:41 CDT)
- electric field- forces in NAMD source code Kowsar Khajeh (Sat Jun 16 2018 - 02:25:29 CDT)
- PCA and vector Dhiraj Srivastava (Fri Jun 15 2018 - 13:59:07 CDT)
- How to run a TCL proc at every step in NAMD using callback command? yjcoshc (Thu Jun 14 2018 - 03:10:32 CDT)
- GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 21:54:19 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Wed Jun 13 2018 - 22:04:51 CDT)
- Re: GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 22:09:46 CDT)
- Re: GaMD in NAMD Alexander Adams (Wed Jun 13 2018 - 23:15:12 CDT)
- Re: GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 23:51:07 CDT)
- Re: GaMD in NAMD Francesco Pietra (Thu Jun 14 2018 - 01:05:52 CDT)
- Re: GaMD in NAMD Dhiraj Srivastava (Thu Jun 14 2018 - 07:40:52 CDT)
- Re: GaMD in NAMD Miao, Yinglong (Thu Jun 14 2018 - 08:46:45 CDT)
- Re: GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 22:09:46 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Wed Jun 13 2018 - 22:04:51 CDT)
- Error during simulation shyam sharma (Wed Jun 13 2018 - 06:27:46 CDT)
- non uniform attempts distribution in constant pH MD Yasser Bruno Ruiz Blanco (Wed Jun 13 2018 - 06:04:10 CDT)
- nonuniform sampling in ABF Artur Hermano (Tue Jun 12 2018 - 10:28:28 CDT)
- mail about non bonded parameters Vidhya Sankar (Mon Jun 11 2018 - 20:58:09 CDT)
- PMF calculation using CPU and GPU Souvik Sinha (Fri Jun 08 2018 - 08:36:27 CDT)
- psf from parmed Stefano Guglielmo (Fri Jun 08 2018 - 08:09:16 CDT)
- Mail about force field parameters Vidhya Sankar (Thu Jun 07 2018 - 21:25:38 CDT)
- Requesting abstracts for MRS Fall 2018 Symposium BM03: Multiscale Modeling of Soft Materials and Interfaces Sanket Deshmukh (Thu Jun 07 2018 - 09:22:42 CDT)
- (no subject) Laura Tiessler (Thu Jun 07 2018 - 06:24:00 CDT)
- BUG: ReplicaUniformPatchGrids and "output" command namd-2.13NB Norman Geist (Thu Jun 07 2018 - 01:56:47 CDT)
- AMBER NetCDF file for Simulation Aashish Bhatt (Wed Jun 06 2018 - 07:33:10 CDT)
- Sudden drop of /\A in ParseFEP.log near lamda 1.0 Francesco Pietra (Wed Jun 06 2018 - 00:58:11 CDT)
- enhanced sampling of flexible tail Dhiraj Srivastava (Tue Jun 05 2018 - 16:02:08 CDT)
- [NAMD] Apply an electric field only in a specific region The Cromicus Productions (Mon Jun 04 2018 - 01:39:28 CDT)
- namd2_ti.pl Error: Modification of non-creatable array value attempted Kooshul S. Jhaveri (Sun Jun 03 2018 - 11:34:09 CDT)
- Update particle position iteratively in between steps Nate Walkins (Sun Jun 03 2018 - 09:55:29 CDT)
- NAMD+PLUMED jing liang (Sat Jun 02 2018 - 13:34:26 CDT)
- mail about error in namd compilation Vidhya Sankar (Fri Jun 01 2018 - 03:08:09 CDT)
- temperature accelerated molecular dynamics Dhiraj Srivastava (Thu May 31 2018 - 23:59:35 CDT)
- MAIL REG NAMD PBS SCRIPT on mpi cluster Vidhya Sankar (Thu May 31 2018 - 23:15:09 CDT)
- Re: Issue using qwikMD with an uncommon cofactor Marcelo C. R. Melo (Thu May 31 2018 - 17:55:02 CDT)
- merging abf trajectories with different number of colvars Olya Kravchenko (Thu May 31 2018 - 11:13:50 CDT)
- Re: merging abf trajectories with different number of colvars Jérôme Hénin (Mon Jun 04 2018 - 07:22:34 CDT)
- Re: merging abf trajectories with different number of colvars Olya Kravchenko (Wed Jun 20 2018 - 13:18:11 CDT)
- Re: merging abf trajectories with different number of colvars Jérôme Hénin (Thu Jun 21 2018 - 05:21:17 CDT)
- Re: merging abf trajectories with different number of colvars Olya Kravchenko (Thu Jun 21 2018 - 09:19:17 CDT)
- Re: merging abf trajectories with different number of colvars Souvik Sinha (Thu Jun 21 2018 - 10:05:30 CDT)
- Re: merging abf trajectories with different number of colvars Olya Kravchenko (Thu Jun 21 2018 - 11:22:26 CDT)
- Re: merging abf trajectories with different number of colvars Olya Kravchenko (Wed Jun 20 2018 - 13:18:11 CDT)
- Re: merging abf trajectories with different number of colvars Jérôme Hénin (Mon Jun 04 2018 - 07:22:34 CDT)
- Problem in generating psf Srijita Paul (Thu May 31 2018 - 01:25:39 CDT)
- Microtubule Simulation Alex Saad-Falcon (Wed May 30 2018 - 17:13:40 CDT)
- "non-numeric floating-point value" error while using distanceXY Olya Kravchenko (Wed May 30 2018 - 09:06:00 CDT)
- Mail from vidhyasankar Vidhya Sankar (Tue May 29 2018 - 22:10:49 CDT)
- Re: vmd-l: Large number of harmonic distance restraints Axel Kohlmeyer (Tue May 29 2018 - 11:26:36 CDT)
- Solutescaling not working with Amber files Norman Geist (Tue May 29 2018 - 06:06:57 CDT)
- Info on solutescaling Norman Geist (Tue May 29 2018 - 02:13:27 CDT)
- Difference between REMD replica temperature and actual temperature jozs2019_at_uni.sydney.edu.au (Mon May 28 2018 - 21:03:05 CDT)
- FEP performance Francesco Pietra (Mon May 28 2018 - 10:05:01 CDT)
- mail reg Namd compilation Vidhya Sankar (Mon May 28 2018 - 03:06:06 CDT)
- Periodic cell basis too small for GridForce Carla Gmez Santiago (Sun May 27 2018 - 09:29:30 CDT)
- Which parameters to use in the MD simulation of defected carbon nanotube/graphene? jashnvareh 1395 (Sun May 27 2018 - 03:10:25 CDT)
- xMDFF: model file is not given Antonio Vila Sanjurjo (Fri May 25 2018 - 07:00:32 CDT)
- Spectre/Meltdown patch performance hits Bryan Roessler (Thu May 24 2018 - 09:34:00 CDT)
- run different simulation of the same system by using different initial velocities Serena Vittorio (Thu May 24 2018 - 07:35:39 CDT)
- Segmentation fault Sonibare, Kolawole (Wed May 23 2018 - 13:41:03 CDT)
- PBC and restraints Carla Gmez Santiago (Wed May 23 2018 - 11:05:06 CDT)
- restrain lateral movement during ABF Olya Kravchenko (Wed May 16 2018 - 16:34:48 CDT)
- Are there plans on thermostat groups? Norman Geist (Wed May 16 2018 - 09:56:01 CDT)
- accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 yjcoshc (Tue May 15 2018 - 20:59:09 CDT)
- How to create multiple molecules using psfgen Sonibare, Kolawole (Tue May 15 2018 - 17:32:32 CDT)
- NAMD hangs at "Load balancer assumes all CPUs are same." when runs on an infiniband cluster. yjcoshc (Mon May 14 2018 - 22:08:46 CDT)
- Hard wall on Z direction for ions Fateme Ghadirian (Mon May 14 2018 - 09:06:31 CDT)
- reverting atoms introduced by name into standard PDB ones Oleksiy Kovtun (Mon May 14 2018 - 04:45:43 CDT)
- Problem generating pdb psf of ATP Srijita Paul (Mon May 14 2018 - 02:33:43 CDT)
- dummyAtom in distance colvar in ABF calculations Olya Kravchenko (Sat May 12 2018 - 16:44:16 CDT)
- Creating an infinite graphene sheet jashnvareh 1395 (Sat May 12 2018 - 10:34:09 CDT)
- Re: Creating an infinite graphene sheet Giacomo Fiorin (Sat May 12 2018 - 13:19:11 CDT)
- RE: Creating an infinite graphene sheet Vermaas, Joshua (Sat May 12 2018 - 16:27:42 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 02:11:07 CDT)
- Re: Creating an infinite graphene sheet Giacomo Fiorin (Sun May 13 2018 - 10:08:46 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 10:34:11 CDT)
- Re: Creating an infinite graphene sheet Giacomo Fiorin (Sun May 13 2018 - 10:53:39 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 11:23:54 CDT)
- Re: Creating an infinite graphene sheet Aksimentiev, Aleksei (Sun May 13 2018 - 12:38:52 CDT)
- RE: Creating an infinite graphene sheet Vermaas, Joshua (Sun May 13 2018 - 13:58:05 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Wed May 16 2018 - 00:54:03 CDT)
- RE: Creating an infinite graphene sheet Vermaas, Joshua (Wed May 16 2018 - 08:30:50 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Sat May 19 2018 - 20:23:17 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 02:13:13 CDT)
- Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 02:27:42 CDT)
- RE: Creating an infinite graphene sheet Vermaas, Joshua (Sat May 12 2018 - 16:27:42 CDT)
- Re: Creating an infinite graphene sheet Giacomo Fiorin (Sat May 12 2018 - 13:19:11 CDT)
- FEP slowdown during execution Francesco Pietra (Sat May 12 2018 - 01:10:39 CDT)
- unit dipole moment vector Suresh Ghimire (Fri May 11 2018 - 02:58:09 CDT)
- Get NAMD version from the tcl script interface yjcoshc (Wed May 09 2018 - 03:36:18 CDT)
- Re: Get NAMD version from the tcl script interface Giacomo Fiorin (Wed May 09 2018 - 06:50:57 CDT)
- Re: Get NAMD version from the tcl script interface Brian Radak (Wed May 09 2018 - 09:36:44 CDT)
- Re: Get NAMD version from the tcl script interface Ajasja Ljubetič (Wed May 09 2018 - 10:06:48 CDT)
- Re: Get NAMD version from the tcl script interface Brian Radak (Wed May 09 2018 - 10:38:36 CDT)
- Re: Get NAMD version from the tcl script interface Ajasja Ljubetič (Wed May 09 2018 - 10:43:11 CDT)
- Re: Get NAMD version from the tcl script interface yjcoshc (Wed May 09 2018 - 19:51:23 CDT)
- Re: Get NAMD version from the tcl script interface Brian Radak (Wed May 09 2018 - 09:36:44 CDT)
- Re: Get NAMD version from the tcl script interface Giacomo Fiorin (Wed May 09 2018 - 06:50:57 CDT)
- distance filter during data analysis Dhiraj Srivastava (Tue May 08 2018 - 23:43:39 CDT)
- Angle of lone pair in TIP4P 2005 simulation Geo Reuter (Tue May 08 2018 - 19:08:34 CDT)
- Missing cphrst file Yasser Bruno Ruiz Blanco (Mon May 07 2018 - 07:59:15 CDT)
- Aromatic rings don't maintain the planarity during the heating Serena Vittorio (Fri May 04 2018 - 11:14:30 CDT)
- Continuing metadynamics run Rabeta Yeasmin (Fri May 04 2018 - 10:25:08 CDT)
- How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? LIAO Mingling (Fri May 04 2018 - 07:07:13 CDT)
- SM Bargeen A Turzo wants to share the file Min_error with you SM Bargeen A Turzo (Wed May 02 2018 - 21:43:51 CDT)
- (no subject) SM Bargeen A Turzo (Wed May 02 2018 - 21:43:45 CDT)
- FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Wed May 02 2018 - 14:51:14 CDT)
- Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Fri May 04 2018 - 00:39:24 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section JC Gumbart (Fri May 04 2018 - 10:43:47 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Fri May 04 2018 - 14:47:42 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Giacomo Fiorin (Fri May 04 2018 - 17:04:28 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Sat May 05 2018 - 01:43:17 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section JC Gumbart (Sat May 05 2018 - 07:20:13 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Chris Chipot (Sat May 05 2018 - 09:28:27 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Mon May 07 2018 - 08:03:34 CDT)
- Re: Fwd: FEP protein-ligand tutorial 2017 unclear section JC Gumbart (Fri May 04 2018 - 10:43:47 CDT)
- Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Fri May 04 2018 - 00:39:24 CDT)
- Martini CG parameter errors for lipids thiagorrg UFC (Wed May 02 2018 - 12:00:05 CDT)
- Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD Jacob Usadi (Wed May 02 2018 - 00:14:40 CDT)
- Equilibrated TIP4P_2005 Waterbox Geo Reuter (Tue May 01 2018 - 15:09:53 CDT)
- FEP & node/core number Francesco Pietra (Mon Apr 30 2018 - 10:36:26 CDT)
- Re: FEP & node/core number Brian Radak (Tue May 01 2018 - 11:58:04 CDT)
- Re: FEP & node/core number Francesco Pietra (Wed May 02 2018 - 00:53:44 CDT)
- Fwd: FEP & node/core number Francesco Pietra (Mon May 07 2018 - 08:19:22 CDT)
- Re: FEP & node/core number Brian Radak (Mon May 07 2018 - 08:38:37 CDT)
- Re: FEP & node/core number Jérôme Hénin (Mon May 07 2018 - 08:39:21 CDT)
- Fwd: FEP & node/core number Francesco Pietra (Mon May 07 2018 - 09:34:14 CDT)
- Re: FEP & node/core number Francesco Pietra (Wed May 02 2018 - 00:53:44 CDT)
- Re: FEP & node/core number Brian Radak (Tue May 01 2018 - 11:58:04 CDT)
- Colvars alternative recommendations Zachary Ulissi (Mon Apr 30 2018 - 08:57:27 CDT)
- Energy Minimization failure for mutants SM Bargeen A Turzo (Sun Apr 29 2018 - 22:36:54 CDT)
- Negative step number Bartlomiej Tywoniuk (Sat Apr 28 2018 - 14:03:54 CDT)
- water box tilts during equilibration Olya Kravchenko (Fri Apr 27 2018 - 17:51:39 CDT)
- FEP with intermediary segments Francesco Pietra (Thu Apr 26 2018 - 10:20:21 CDT)
- Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 00:37:18 CDT)
- Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 08:01:28 CDT)
- Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 10:51:45 CDT)
- Re: Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 11:04:10 CDT)
- Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 15:00:22 CDT)
- Re: Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 15:46:56 CDT)
- Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Sat May 05 2018 - 01:21:23 CDT)
- Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 08:01:28 CDT)
- Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 00:37:18 CDT)
- (no subject) shyam sharma (Thu Apr 26 2018 - 07:02:17 CDT)
- Re: Jérôme Hénin (Thu Apr 26 2018 - 07:20:11 CDT)
- Re: Giacomo Fiorin (Thu Apr 26 2018 - 08:35:29 CDT)
- Re: Axel Kohlmeyer (Thu Apr 26 2018 - 08:50:28 CDT)
- Re: Jérôme Hénin (Thu Apr 26 2018 - 08:56:08 CDT)
- Re: Brian Radak (Thu Apr 26 2018 - 09:05:49 CDT)
- Re: Giacomo Fiorin (Thu Apr 26 2018 - 09:12:42 CDT)
- Re: Axel Kohlmeyer (Thu Apr 26 2018 - 10:04:58 CDT)
- Re: Axel Kohlmeyer (Thu Apr 26 2018 - 10:19:18 CDT)
- Re: Giacomo Fiorin (Thu Apr 26 2018 - 08:35:29 CDT)
- Re: Jérôme Hénin (Thu Apr 26 2018 - 07:20:11 CDT)
- Enabling charmrun in NAMD simulation Denish Poudyal (Wed Apr 25 2018 - 01:00:35 CDT)
- Setting up amorphous SiO2 slab Carlo Guardiani (Tue Apr 24 2018 - 12:52:20 CDT)
- NAMD Developer Workshop at Urbana IL, June 11-12, 2018 João Ribeiro (Tue Apr 24 2018 - 08:57:57 CDT)
- CZAR Estimator: grad file philippe Bourly (Tue Apr 24 2018 - 03:38:49 CDT)
- SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 00:21:43 CDT)
- Re: SMD with colvar not working Jérôme Hénin (Tue Apr 24 2018 - 04:27:49 CDT)
- Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 10:45:24 CDT)
- Re: SMD with colvar not working Jérôme Hénin (Tue Apr 24 2018 - 10:56:46 CDT)
- Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 11:02:29 CDT)
- Re: SMD with colvar not working Jérôme Hénin (Tue Apr 24 2018 - 11:04:24 CDT)
- Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 11:12:17 CDT)
- Re: SMD with colvar not working Jérôme Hénin (Tue Apr 24 2018 - 12:50:47 CDT)
- Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 10:45:24 CDT)
- Re: SMD with colvar not working Jérôme Hénin (Tue Apr 24 2018 - 04:27:49 CDT)
- PSFGEN 1.6.4 autogenerate PATCH keyword not available Thomas C. Bishop (Mon Apr 23 2018 - 19:57:47 CDT)
- Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 07:34:01 CDT)
- RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 10:59:35 CDT)
- Re: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 11:23:47 CDT)
- RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 12:08:20 CDT)
- RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Lennart Nilsson (Tue Apr 24 2018 - 12:45:26 CDT)
- RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 10:59:35 CDT)
- Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 07:34:01 CDT)
- Question about "useConstantArea" in puresure control model 张锦途 (Sat Apr 21 2018 - 11:00:31 CDT)
- FEP slowdown Francesco Pietra (Sat Apr 21 2018 - 10:34:58 CDT)
- long simulation and error "integer value too large" Dhiraj Srivastava (Fri Apr 20 2018 - 23:24:23 CDT)
- torsion scan Stefano Guglielmo (Thu Apr 19 2018 - 18:30:00 CDT)
- variation of pressure Suresh Ghimire (Thu Apr 19 2018 - 05:31:57 CDT)
- colvar with moving frame of reference Dhiraj Srivastava (Mon Apr 16 2018 - 13:29:53 CDT)
- Reverting coarse-grain system to all-atom system Rabeta Yeasmin (Sun Apr 15 2018 - 18:49:21 CDT)
- Re: Reverting coarse-grain system to all-atom system Peter Freddolino (Sun Apr 15 2018 - 19:57:33 CDT)
- re-centering the molecule while restarting the run Dhiraj Srivastava (Fri Apr 13 2018 - 13:27:30 CDT)
- Bug with FEP? Francesco Pietra (Thu Apr 12 2018 - 15:28:31 CDT)
- Re: Bug with FEP? Francesco Pietra (Fri Apr 13 2018 - 02:49:14 CDT)
- Re: Re: Bug with FEP? Brian Radak (Fri Apr 13 2018 - 10:03:17 CDT)
- Re: Re: Bug with FEP? Francesco Pietra (Sun Apr 15 2018 - 02:48:10 CDT)
- Re: vmd-l: Re: Re: Bug with FEP? Brian Radak (Mon Apr 16 2018 - 11:31:45 CDT)
- Re: vmd-l: Re: Re: Bug with FEP? Francesco Pietra (Tue Apr 17 2018 - 00:05:38 CDT)
- Re: vmd-l: Re: Re: Bug with FEP? Brian Radak (Tue Apr 17 2018 - 09:42:46 CDT)
- Re: Re: Bug with FEP? Brian Radak (Fri Apr 13 2018 - 10:03:17 CDT)
- Re: Bug with FEP? Francesco Pietra (Fri Apr 13 2018 - 02:49:14 CDT)
- How does NAMD calculate AccumulatedWork when using RMSD colvar? Asghar Razavi (Thu Apr 12 2018 - 12:29:19 CDT)
- scriptedColvarForces doesn't work in recent NAMD builds Jeff Comer (Wed Apr 11 2018 - 11:04:53 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Jérôme Hénin (Wed Apr 11 2018 - 11:26:58 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Jérôme Hénin (Wed Apr 11 2018 - 12:12:26 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Giacomo Fiorin (Wed Apr 11 2018 - 15:09:13 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Jeff Comer (Thu Apr 12 2018 - 08:14:26 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Giacomo Fiorin (Thu Apr 12 2018 - 11:55:59 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Jérôme Hénin (Wed Apr 11 2018 - 12:12:26 CDT)
- Re: scriptedColvarForces doesn't work in recent NAMD builds Jérôme Hénin (Wed Apr 11 2018 - 11:26:58 CDT)
- Regarding Topology and Parameterization SM Bargeen A Turzo (Tue Apr 10 2018 - 18:51:35 CDT)
- Re: Bad global bond count! (48842 vs 48843) Ashutosh Shandilya (Tue Apr 10 2018 - 11:41:32 CDT)
- Proper use of psfgen "mutate"? Brian Radak (Tue Apr 10 2018 - 08:58:47 CDT)
- Re: TCBG Workshop lecture videos😝😚😚 董超 (Sun Apr 08 2018 - 14:21:02 CDT)
- ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Sun Apr 08 2018 - 08:46:35 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Chris Chipot (Sun Apr 08 2018 - 08:58:34 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Brian Radak (Tue Apr 10 2018 - 07:56:40 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Wed Aug 01 2018 - 05:40:22 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Brian Radak (Wed Aug 01 2018 - 06:53:18 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Wed Aug 01 2018 - 09:10:54 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Sat Aug 04 2018 - 08:21:10 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Brian Radak (Tue Apr 10 2018 - 07:56:40 CDT)
- Re: ParseFEP error with FEP in segments at different lambda schedule Chris Chipot (Sun Apr 08 2018 - 08:58:34 CDT)
- TCBG Workshop lecture videos João Ribeiro (Sat Apr 07 2018 - 10:45:12 CDT)
- calculation of helical axis in NAMD Dhiraj Srivastava (Sat Apr 07 2018 - 01:01:20 CDT)
- Re: Selective accelerated MD in NAMD Alexander Adams (Fri Apr 06 2018 - 15:36:59 CDT)
- Selective accelerated MD in NAMD Alexander Adams (Fri Apr 06 2018 - 14:08:43 CDT)
- CMIAbort Error Harish Srinivasan (Fri Apr 06 2018 - 05:38:39 CDT)
- colvars: make an extended CV periodic yjcoshc (Thu Apr 05 2018 - 22:42:01 CDT)
- Query for coarse grain system Abhishek TYAGI (Thu Apr 05 2018 - 09:53:36 CDT)
- Re: Query for coarse grain system Giacomo Fiorin (Thu Apr 05 2018 - 10:17:47 CDT)
- Re: Query for coarse grain system Abhishek TYAGI (Thu Apr 05 2018 - 10:23:18 CDT)
- Re: Query for coarse grain system Giacomo Fiorin (Thu Apr 05 2018 - 10:27:16 CDT)
- Re: Query for coarse grain system Abhishek TYAGI (Mon Apr 09 2018 - 08:42:35 CDT)
- Re: Query for coarse grain system Giacomo Fiorin (Mon Apr 09 2018 - 09:02:23 CDT)
- Re: Query for coarse grain system Axel Kohlmeyer (Mon Apr 09 2018 - 09:22:11 CDT)
- Re: Query for coarse grain system Abhishek TYAGI (Mon Apr 09 2018 - 12:17:06 CDT)
- Re: Query for coarse grain system Abhishek TYAGI (Wed Apr 11 2018 - 00:39:49 CDT)
- Re: Query for coarse grain system Abhishek TYAGI (Thu Apr 05 2018 - 10:23:18 CDT)
- Re: Query for coarse grain system Giacomo Fiorin (Thu Apr 05 2018 - 10:17:47 CDT)
- NAMD-CUDA GPU workload Yu Zhou (Mon Apr 02 2018 - 10:11:51 CDT)
- Using restraint on the dye using radius of gyration value in namd Life Sciences Inc (Mon Apr 02 2018 - 09:26:47 CDT)
- effect of acceptors Suresh Ghimire (Sun Apr 01 2018 - 10:44:37 CDT)
- Atom velocity error in coarse grained simulation using MARTINI Rakesh K (Sat Mar 31 2018 - 10:16:39 CDT)
- Fatty Acid Topology Nisler, Collin R. (Fri Mar 30 2018 - 21:25:30 CDT)
- Steered MD simulation with pull and rotation Dhiraj Srivastava (Wed Mar 28 2018 - 14:23:08 CDT)
- Meaning of warning in output log file Denish Poudyal (Wed Mar 28 2018 - 02:57:23 CDT)
- Using PBC tools for a cubic and a rectangular box Monika Madhavi (Tue Mar 27 2018 - 05:34:10 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Brian Radak (Tue Mar 27 2018 - 08:09:43 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Giacomo Fiorin (Tue Mar 27 2018 - 08:35:54 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Brian Radak (Tue Mar 27 2018 - 09:03:55 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Giacomo Fiorin (Tue Mar 27 2018 - 09:18:17 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Monika Madhavi (Wed Mar 28 2018 - 23:07:41 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Giacomo Fiorin (Tue Mar 27 2018 - 08:35:54 CDT)
- Re: Using PBC tools for a cubic and a rectangular box Brian Radak (Tue Mar 27 2018 - 08:09:43 CDT)
- metadynamics problem Rabeta Yeasmin (Mon Mar 26 2018 - 11:39:28 CDT)
- Restrict drift of Graphene sheet in X-Y plane using Colvars ANIRBAN MANDAL (Mon Mar 26 2018 - 05:04:55 CDT)
- Regarding free energy calculation varun dewaker (Mon Mar 26 2018 - 02:39:54 CDT)
- NAMD Simulation in a laptop Denish Poudyal (Sun Mar 25 2018 - 20:56:44 CDT)
- ParseFEP for restating FEP Francesco Pietra (Fri Mar 23 2018 - 02:05:41 CDT)
- [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin The Cromicus Productions (Thu Mar 22 2018 - 18:17:30 CDT)
- patch ID error deep deep (Wed Mar 21 2018 - 15:18:04 CDT)
- colvars: Questions about the metadynamics hillWIdth option. yjcoshc (Wed Mar 21 2018 - 02:39:09 CDT)
- Selecting waters from dynamics trajectory Randy J. Zauhar (Tue Mar 20 2018 - 16:47:38 CDT)
- ffTK Without Using Gaussian Alex Saad-Falcon (Tue Mar 20 2018 - 10:49:48 CDT)
- VMD/NMAD on AWS Strenic Computations (Sat Mar 17 2018 - 18:50:17 CDT)
- "'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018 João Ribeiro (Fri Mar 16 2018 - 15:47:15 CDT)
- (no subject) Srijita Paul (Fri Mar 16 2018 - 14:14:22 CDT)
- Lowe-Andersen Thermostat Speed Nick Guros (Fri Mar 16 2018 - 13:59:43 CDT)
- (no subject) Srijita Paul (Fri Mar 16 2018 - 06:40:03 CDT)
- (no subject) Srijita Paul (Fri Mar 16 2018 - 05:54:30 CDT)
- (no subject) Srijita Paul (Thu Mar 15 2018 - 06:44:21 CDT)
- statistical error in ABF calculations Artur Hermano (Wed Mar 14 2018 - 10:27:15 CDT)
- mscs.pdb Mahmood Naderan (Tue Mar 13 2018 - 11:03:33 CDT)
- Low global CUDA exclusion count! (9592 vs 9618) ANIRBAN MANDAL (Tue Mar 13 2018 - 04:39:31 CDT)
- Running on GPU Mahmood Naderan (Mon Mar 12 2018 - 14:22:31 CDT)
- AutoPSF Error Alex Saad-Falcon (Mon Mar 12 2018 - 10:40:47 CDT)
- colvars: How to implement a collective variable of vector type? yjcoshc (Sat Mar 10 2018 - 03:27:54 CST)
- Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Sun Mar 11 2018 - 07:05:09 CDT)
- Re: colvars: How to implement a collective variable of vector type? Jérôme Hénin (Sun Mar 11 2018 - 16:54:15 CDT)
- Re: colvars: How to implement a collective variable of vector type? yjcoshc (Mon Mar 12 2018 - 05:01:52 CDT)
- Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Mon Mar 12 2018 - 07:13:52 CDT)
- Re: colvars: How to implement a collective variable of vector type? yjcoshc (Tue Mar 13 2018 - 03:12:51 CDT)
- Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Tue Mar 13 2018 - 09:07:18 CDT)
- Re: colvars: How to implement a collective variable of vector type? yjcoshc (Wed Mar 14 2018 - 04:13:19 CDT)
- Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Wed Mar 14 2018 - 08:26:48 CDT)
- Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Sun Mar 11 2018 - 07:05:09 CDT)
- (no subject) shyam sharma (Fri Mar 09 2018 - 02:02:09 CST)
- Python based tool for analysis of DCD trajectories Harish Srinivasan (Thu Mar 08 2018 - 23:46:32 CST)
- Hydrogen Mass Repartitioning in NAMD JC Gumbart (Wed Mar 07 2018 - 17:31:32 CST)
- Thermodynamic integration output analysis Giorgio Amendola (Wed Mar 07 2018 - 05:57:08 CST)
- Functionality of wrapWater and wrapAll commands for periodic simulations Harish Srinivasan (Wed Mar 07 2018 - 05:34:08 CST)
- Segmentation fault for the tutorial Mahmood Naderan (Tue Mar 06 2018 - 13:06:11 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Tue Mar 06 2018 - 13:58:56 CST)
- Re: Segmentation fault for the tutorial Vermaas, Joshua (Tue Mar 06 2018 - 14:27:43 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 01:33:55 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 09:48:08 CST)
- Re: Segmentation fault for the tutorial David Hardy (Wed Mar 07 2018 - 10:51:44 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 11:38:44 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 12:02:02 CST)
- Re: Segmentation fault for the tutorial Vermaas, Joshua (Wed Mar 07 2018 - 12:30:36 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 14:24:31 CST)
- Re: Segmentation fault for the tutorial Vermaas, Joshua (Tue Mar 06 2018 - 14:27:43 CST)
- Re: Segmentation fault for the tutorial Mahmood Naderan (Tue Mar 06 2018 - 13:58:56 CST)
- Simulating a Binding Event Alex Saad-Falcon (Tue Mar 06 2018 - 11:53:54 CST)
- AW: periodic cell has become too small for original patch grid Norman Geist (Tue Mar 06 2018 - 01:50:42 CST)
- Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Mon Mar 05 2018 - 11:10:28 CST)
- Re: How to set up a window distance of 2 angstroms in Umbrella sampling Lutimba Stuart (Mon Mar 05 2018 - 03:40:10 CST)
- Fwd: parseFEP domain error Francesco Pietra (Sat Mar 03 2018 - 11:44:06 CST)
- Build for CUDA support Mahmood Naderan (Sat Mar 03 2018 - 08:22:47 CST)
- UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656) Ashutosh Shandilya (Fri Mar 02 2018 - 13:55:43 CST)
- periodic cell has become too small for original patch grid Ashutosh Shandilya (Fri Mar 02 2018 - 13:55:10 CST)
- Residue Charges Alex Saad-Falcon (Fri Mar 02 2018 - 08:35:30 CST)
- FEP minimum requirements Francesco Pietra (Thu Mar 01 2018 - 03:05:22 CST)
- Handling of nonbonded lists in PSF - please clarify Randy J. Zauhar (Sun Feb 25 2018 - 14:42:10 CST)
- parameter Suresh Ghimire (Sat Feb 24 2018 - 07:40:24 CST)
- How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Fri Feb 23 2018 - 18:09:19 CST)
- Re: How to interpret Thermodynamic Integration output Brian Radak (Sun Feb 25 2018 - 12:45:10 CST)
- Re: How to interpret Thermodynamic Integration output Vermaas, Joshua (Sun Feb 25 2018 - 17:23:39 CST)
- Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Tue Feb 27 2018 - 12:26:17 CST)
- Re: How to interpret Thermodynamic Integration output Brian Radak (Tue Feb 27 2018 - 13:00:48 CST)
- Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Thu Mar 22 2018 - 14:13:03 CDT)
- Re: How to interpret Thermodynamic Integration output Brian Radak (Fri Mar 23 2018 - 10:30:26 CDT)
- Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Wed Apr 18 2018 - 14:57:56 CDT)
- Re: How to interpret Thermodynamic Integration output Brian Radak (Thu Apr 19 2018 - 09:15:32 CDT)
- Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Mon Apr 23 2018 - 11:01:02 CDT)
- Re: How to interpret Thermodynamic Integration output Vermaas, Joshua (Sun Feb 25 2018 - 17:23:39 CST)
- Re: How to interpret Thermodynamic Integration output Brian Radak (Sun Feb 25 2018 - 12:45:10 CST)
- Coarse-grained umbrella sampling for POPS-protein system Rabeta Yeasmin (Fri Feb 23 2018 - 17:53:53 CST)
- Re: Error in the Continuation TMD simulation Run. Lutimba Stuart (Wed Feb 21 2018 - 13:49:36 CST)
- Simple PME Question Alex Saad-Falcon (Mon Feb 19 2018 - 10:04:54 CST)
- PME Tolerance Lesli Oiling Mark (Mon Feb 19 2018 - 10:03:48 CST)
- Re: Alchemify? Jérôme Hénin (Mon Feb 19 2018 - 09:32:33 CST)
- FAD topology and parameters Marco kadowaki (Mon Feb 19 2018 - 09:23:53 CST)
- ParseFEP error Sadegh Faramarzi Ganjabad (Sat Feb 17 2018 - 23:39:52 CST)
- Ligand atoms moving too fast with FEP Francesco Pietra (Thu Feb 15 2018 - 02:00:39 CST)
- Re: Ligand atoms moving too fast with FEP Brian Radak (Thu Feb 15 2018 - 08:27:42 CST)
- Re: Ligand atoms moving too fast with FEP Francesco Pietra (Thu Feb 15 2018 - 09:47:51 CST)
- Re: Ligand atoms moving too fast with FEP Brian Radak (Fri Feb 16 2018 - 07:47:18 CST)
- Re: Ligand atoms moving too fast with FEP Francesco Pietra (Fri Feb 16 2018 - 09:31:08 CST)
- Fwd: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 01:58:37 CST)
- Fwd: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 02:08:17 CST)
- Fwd: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 09:23:05 CST)
- Re: Ligand atoms moving too fast with FEP Brian Radak (Tue Feb 20 2018 - 09:24:04 CST)
- Re: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 10:10:50 CST)
- Re: Ligand atoms moving too fast with FEP Brian Radak (Tue Feb 20 2018 - 10:21:48 CST)
- Re: Ligand atoms moving too fast with FEP Francesco Pietra (Thu Feb 15 2018 - 09:47:51 CST)
- Re: Ligand atoms moving too fast with FEP Brian Radak (Thu Feb 15 2018 - 08:27:42 CST)
- namd2 GPU error Miraj Naik (Tue Feb 13 2018 - 22:43:10 CST)
- (no subject) Srijita Paul (Tue Feb 13 2018 - 05:06:51 CST)
- Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Sun Feb 11 2018 - 23:08:42 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Giacomo Fiorin (Mon Feb 12 2018 - 08:38:15 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system SHAHEE ISLAM (Mon Feb 12 2018 - 09:05:04 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Giacomo Fiorin (Mon Feb 12 2018 - 09:20:04 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Mon Feb 12 2018 - 09:27:03 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Tue Feb 13 2018 - 05:53:23 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Fotis Baltoumas (Tue Feb 13 2018 - 06:13:14 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Tue Feb 13 2018 - 06:56:10 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system SHAHEE ISLAM (Mon Feb 12 2018 - 09:05:04 CST)
- Re: Re: simulation becomes unstable in residue base coarse grained system Giacomo Fiorin (Mon Feb 12 2018 - 08:38:15 CST)
- Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Sun Feb 11 2018 - 15:59:31 CST)
- Question on making 'reversible' solvated simulation Randy J. Zauhar (Sat Feb 10 2018 - 12:15:37 CST)
- Re: Question on making 'reversible' solvated simulation Jérôme Hénin (Sun Feb 11 2018 - 04:56:22 CST)
- Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 11 2018 - 12:52:18 CST)
- Re: Question on making 'reversible' solvated simulation Brian Radak (Mon Feb 12 2018 - 10:00:18 CST)
- Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sat Feb 17 2018 - 11:20:48 CST)
- Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 18 2018 - 16:54:20 CST)
- Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 18 2018 - 17:01:27 CST)
- Re: Question on making 'reversible' solvated simulation Brian Radak (Mon Feb 19 2018 - 11:00:20 CST)
- Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Mon Feb 19 2018 - 12:42:36 CST)
- Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 11 2018 - 12:52:18 CST)
- Re: Question on making 'reversible' solvated simulation Jérôme Hénin (Sun Feb 11 2018 - 04:56:22 CST)
- Dielectric Constant in the gas phase Ahmad Kiani (Fri Feb 09 2018 - 11:47:08 CST)
- Lipid bilayer deformed during coarse grain simulation Rabeta Yeasmin (Fri Feb 09 2018 - 10:58:19 CST)
- Pair interaction energies: TCL error -reg Jeyaram R A (Thu Feb 08 2018 - 01:32:44 CST)
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 João Ribeiro (Wed Feb 07 2018 - 10:46:51 CST)
- NAMD Developer Workshop at Urbana IL, June 11-12, 2018 João Ribeiro (Wed Feb 07 2018 - 10:46:41 CST)
- "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 João Ribeiro (Wed Feb 07 2018 - 10:44:57 CST)
- FEP/REMD (ERROR: 'alchLambda' is a required configuration option) rakesh kumar (Wed Feb 07 2018 - 03:25:17 CST)
- NAMD run on Intel hyperthreaded cores Souvik Sinha (Tue Feb 06 2018 - 02:41:49 CST)
- Jobs and Evens in CHARMM-GUI Jumin Lee (Mon Feb 05 2018 - 16:00:01 CST)
- QwikMD SMD force calculation Aysima Hacisuleyman (Mon Feb 05 2018 - 04:00:02 CST)
- Holding molecules on one side of membrane Omid Bavi (Sun Feb 04 2018 - 07:14:26 CST)
- NAMD 2.12 Volta Compatibility Richard Overstreet (Sat Feb 03 2018 - 13:24:45 CST)
- Double-defined segid, resid for more than 9999 id's Chun Heung Wong (Fri Feb 02 2018 - 10:17:30 CST)
- all-atom to coarse-grained system Rabeta Yeasmin (Thu Feb 01 2018 - 15:29:45 CST)
- trouble with colvars module Artur Hermano (Thu Feb 01 2018 - 12:48:02 CST)
- [NAMD] Units of Efieldfreq The Cromicus Productions (Wed Jan 31 2018 - 23:23:16 CST)
- colvars selecting frames Stefano Guglielmo (Tue Jan 30 2018 - 19:37:54 CST)
- Re: colvars selecting frames Jérôme Hénin (Wed Jan 31 2018 - 03:22:22 CST)
- Re: colvars selecting frames Stefano Guglielmo (Thu Feb 01 2018 - 06:06:41 CST)
- Re: colvars selecting frames Jérôme Hénin (Thu Feb 01 2018 - 06:32:00 CST)
- Re: colvars selecting frames Giacomo Fiorin (Thu Feb 01 2018 - 10:03:14 CST)
- Re: colvars selecting frames Florian Blanc (Thu Feb 01 2018 - 10:21:18 CST)
- Re: colvars selecting frames Jérôme Hénin (Thu Feb 01 2018 - 10:42:17 CST)
- Re: colvars selecting frames Stefano Guglielmo (Tue Feb 20 2018 - 14:54:20 CST)
- Re: colvars selecting frames Stefano Guglielmo (Thu Feb 01 2018 - 06:06:41 CST)
- Re: colvars selecting frames Jérôme Hénin (Wed Jan 31 2018 - 03:22:22 CST)
- Simulation of imprinting process in NAMD Abhaysinh Gaikwad (Tue Jan 30 2018 - 10:52:50 CST)
- Error Regarding minimization Aashish Bhatt (Tue Jan 30 2018 - 09:36:37 CST)
- Calculate energy of a residue using NAMD energy Monika Madhavi (Mon Jan 29 2018 - 21:22:19 CST)
- Re: Calculate energy of a residue using NAMD energy Brian Radak (Tue Jan 30 2018 - 09:18:44 CST)
- Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Tue Jan 30 2018 - 20:51:50 CST)
- Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Wed Jan 31 2018 - 17:25:13 CST)
- Re: Calculate energy of a residue using NAMD energy Onur Serçinoğlu (Thu Feb 01 2018 - 06:06:08 CST)
- Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Thu Feb 01 2018 - 18:08:15 CST)
- Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Thu Feb 01 2018 - 21:59:53 CST)
- Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Thu Feb 01 2018 - 22:51:37 CST)
- Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Thu Feb 01 2018 - 22:59:57 CST)
- Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Fri Feb 02 2018 - 01:05:47 CST)
- Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Mon Feb 05 2018 - 00:42:43 CST)
- Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Wed Jan 31 2018 - 17:25:13 CST)
- Stress calculation Abhaysinh Gaikwad (Mon Jan 29 2018 - 10:04:34 CST)
- Question on restraint behavior when part of system decouples Randy J. Zauhar (Mon Jan 29 2018 - 09:19:28 CST)
- Re: Question on restraint behavior when part of system decouples Jérôme Hénin (Mon Jan 29 2018 - 09:53:51 CST)
- Calculation of Diffusion coefficient Souvik Sinha (Mon Jan 29 2018 - 08:01:13 CST)
- Fwd: pressure in interfacial tension Kowsar Khajeh (Sun Jan 28 2018 - 21:18:39 CST)
- minimization Suresh Ghimire (Sat Jan 27 2018 - 01:29:00 CST)
- Replica exchange simulation with GPU Accelaration Souvik Sinha (Thu Jan 25 2018 - 03:02:15 CST)
- Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Thu Jan 25 2018 - 08:22:24 CST)
- Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Thu Jan 25 2018 - 12:59:26 CST)
- Re: Replica exchange simulation with GPU Accelaration Renfro, Michael (Thu Jan 25 2018 - 13:40:28 CST)
- Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Fri Jan 26 2018 - 09:12:28 CST)
- Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 12:24:27 CST)
- Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Fri Jan 26 2018 - 12:32:55 CST)
- Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 13:02:56 CST)
- Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Fri Jan 26 2018 - 13:18:17 CST)
- Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 13:35:12 CST)
- Re: Replica exchange simulation with GPU Accelaration Jeff Comer (Fri Jan 26 2018 - 15:46:57 CST)
- Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 23:20:14 CST)
- Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Thu Jan 25 2018 - 12:59:26 CST)
- Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Thu Jan 25 2018 - 08:22:24 CST)
- nonequilibrium SMD with fixed atoms Ekaterina Sobakinskaja (Wed Jan 24 2018 - 09:27:28 CST)
- Missing Parameters For H3O+ Ahmad Kiani (Tue Jan 23 2018 - 12:13:00 CST)
- Vectors and indexing in VMD Chun Heung Wong (Tue Jan 23 2018 - 06:16:00 CST)
- Trouble with NAMD Win64-CUDA 2.12 on my new PC Yu Zhou (Mon Jan 22 2018 - 11:24:26 CST)
- Tilting angle of lipid calculation Rabeta Yeasmin (Thu Jan 18 2018 - 18:29:44 CST)
- Ways to find water molecules passing through the water channel in lipid bilayer Rabeta Yeasmin (Thu Jan 18 2018 - 18:19:29 CST)
- Hamiltonian Replica Exchange MD in NAMD Youngwoo Woo (Thu Jan 18 2018 - 16:01:28 CST)
- acceptor Suresh Ghimire (Wed Jan 17 2018 - 00:02:10 CST)
- accepter Suresh Ghimire (Tue Jan 16 2018 - 23:51:20 CST)
- UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) Ahmad Kiani (Tue Jan 16 2018 - 11:13:20 CST)
- Stress calculation Abhaysinh Gaikwad (Tue Jan 16 2018 - 09:03:15 CST)
- (no subject) Suresh Ghimire (Sun Jan 14 2018 - 07:31:05 CST)
- Different resid in pdb fie but showing same molecule in VMD Rabeta Yeasmin (Fri Jan 12 2018 - 17:42:14 CST)
- SMD: Combined Constant Velocity and Constant Force method Keshab Thapa (Thu Jan 11 2018 - 15:51:18 CST)
- reinitatoms Laura Joana (Thu Jan 11 2018 - 08:26:28 CST)
- Pressure ? High values ; Pressavg Gpressavg ? value of first step of restart very different from the last of the previous MD Charline FAGNEN (Tue Jan 09 2018 - 10:09:16 CST)
- Setting up GPU workstation advice Lewis Martin (Sun Jan 07 2018 - 20:28:49 CST)
- (no subject) Suresh Ghimire (Sun Jan 07 2018 - 04:09:05 CST)
- (no subject) Suresh Ghimire (Sat Jan 06 2018 - 09:46:20 CST)
- having problem with disulfide bond Shahee Islam (Thu Jan 04 2018 - 05:48:38 CST)
- metadynamics reaction coordinate Rabeta Yeasmin (Wed Jan 03 2018 - 11:42:57 CST)
- (no subject) Suresh Ghimire (Mon Jan 01 2018 - 09:14:36 CST)
- question about point substitution A→U parinaz bashirbanaem (Sat Dec 30 2017 - 12:47:43 CST)
- (no subject) Suresh Ghimire (Fri Dec 29 2017 - 19:57:56 CST)
- Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 02:10:07 CST)
- Re: Having problem with restarting colvar distance, Jérôme Hénin (Fri Dec 29 2017 - 04:34:56 CST)
- Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 14:46:29 CST)
- Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Wed Jan 03 2018 - 10:35:52 CST)
- Re: Having problem with restarting colvar distance, Jérôme Hénin (Wed Jan 03 2018 - 10:38:26 CST)
- Re: Having problem with restarting colvar distance, Giacomo Fiorin (Wed Jan 03 2018 - 11:02:00 CST)
- Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Wed Jan 03 2018 - 13:44:19 CST)
- Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 14:46:29 CST)
- Re: Having problem with restarting colvar distance, Jérôme Hénin (Fri Dec 29 2017 - 04:34:56 CST)
- Gradual cooling of the system Monika Madhavi (Sun Dec 24 2017 - 22:27:27 CST)
- [NAMD] Question about patches The Cromicus Productions (Sun Dec 24 2017 - 03:49:07 CST)
- Re: [NAMD] Question about patches JC Gumbart (Sun Dec 24 2017 - 15:16:10 CST)
- RE: [NAMD] Question about patches Lennart Nilsson (Mon Dec 25 2017 - 09:17:51 CST)
- Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:29:06 CST)
- Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:53:36 CST)
- Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 18:04:43 CST)
- RE: [NAMD] Question about patches Lennart Nilsson (Tue Dec 26 2017 - 04:43:30 CST)
- Re: [NAMD] Question about patches JC Gumbart (Tue Dec 26 2017 - 09:26:12 CST)
- Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:29:06 CST)
- (no subject) Suresh Ghimire (Fri Dec 22 2017 - 09:54:23 CST)
- facing problem while downloading NAMD Jyoti Sharma (Fri Dec 22 2017 - 03:20:26 CST)
- gbsa Stefano Guglielmo (Tue Dec 19 2017 - 19:55:21 CST)
- reconstructing pmf Stefano Guglielmo (Mon Dec 18 2017 - 18:24:15 CST)
- Re: reconstructing pmf Vermaas, Joshua (Mon Dec 18 2017 - 18:35:31 CST)
- Re: reconstructing pmf Giacomo Fiorin (Mon Dec 18 2017 - 19:40:03 CST)
- Re: reconstructing pmf Stefano Guglielmo (Tue Dec 19 2017 - 02:48:53 CST)
- Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 08:08:03 CST)
- Re: reconstructing pmf Jeff Comer (Tue Dec 19 2017 - 09:20:57 CST)
- Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 10:27:09 CST)
- Re: reconstructing pmf Jeff Comer (Tue Dec 19 2017 - 12:52:21 CST)
- Re: reconstructing pmf Stefano Guglielmo (Tue Dec 19 2017 - 18:17:35 CST)
- Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 18:24:46 CST)
- Re: reconstructing pmf Stefano Guglielmo (Wed Dec 20 2017 - 01:55:15 CST)
- Re: reconstructing pmf Giacomo Fiorin (Mon Dec 18 2017 - 19:40:03 CST)
- Re: reconstructing pmf Vermaas, Joshua (Mon Dec 18 2017 - 18:35:31 CST)
- tcl used for binary compilation Francesco Pietra (Mon Dec 18 2017 - 14:26:30 CST)
- colvars: Error: keyword "translatereference" is not supported, or not recognized in this context. Victor Kwan (Sun Dec 17 2017 - 22:35:33 CST)
- Unable to run CUDA NAMD but able to run non-CUDA version on Windows Chun Heung Wong (Sat Dec 16 2017 - 06:50:06 CST)
- FATAL ERROR: Bad global improper count! Nehad Elsalamouny (Fri Dec 15 2017 - 23:53:33 CST)
- Define a colvar from other colvars Ben Adams (Thu Dec 14 2017 - 13:50:29 CST)
- Script for Terachem QMMM Chris Butch (Thu Dec 14 2017 - 03:29:17 CST)
- Periodic molecules in NAMD Bogdan MAREKHA (Wed Dec 13 2017 - 05:13:54 CST)
- Re: namd-l digest V1 #2316 Yaxin An (Fri Dec 08 2017 - 09:06:19 CST)
- atom selection error Shahee Islam (Fri Dec 08 2017 - 02:33:19 CST)
- Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 07:59:51 CST)
- Re: atom selection error Shahee Islam (Fri Dec 08 2017 - 08:22:51 CST)
- Re: atom selection error Brian Radak (Fri Dec 08 2017 - 10:41:57 CST)
- Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 11:54:00 CST)
- Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:04:47 CST)
- Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 00:24:47 CST)
- Re: atom selection error Brian Radak (Mon Dec 11 2017 - 11:14:36 CST)
- Re: atom selection error Vermaas, Joshua (Mon Dec 11 2017 - 11:28:09 CST)
- Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:33:38 CST)
- Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 00:38:19 CST)
- Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:52:18 CST)
- Re: atom selection error Atanu Maity (Mon Dec 11 2017 - 08:30:55 CST)
- Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 14:26:26 CST)
- Re: atom selection error Shahee Islam (Tue Dec 12 2017 - 01:31:22 CST)
- Re: atom selection error Shahee Islam (Fri Dec 08 2017 - 08:22:51 CST)
- Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 07:59:51 CST)
- metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Thu Dec 07 2017 - 17:49:22 CST)
- Re: metadynamics run in NAMD or using plumed in NAMD yjcoshc (Thu Dec 07 2017 - 19:22:06 CST)
- Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 02:06:22 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 07:08:36 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 12:14:11 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 12:19:43 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 12:39:49 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 07:08:36 CST)
- Free energy did not converge by using ABF Yaxin An (Thu Dec 07 2017 - 17:22:31 CST)
- nvt vs nve file NEHİR NALINCI (Mon Dec 04 2017 - 12:11:27 CST)
- Colvar Error Souvik Sinha (Mon Dec 04 2017 - 07:33:12 CST)
- colvars/rmsd: Error: definition for atom group "atoms" not found. Victor Kwan (Sun Dec 03 2017 - 05:12:06 CST)
- (no subject) Shahee Islam (Fri Dec 01 2017 - 02:28:17 CST)
- [NAMD] Patch 5MC2 The Cromicus Productions (Wed Nov 29 2017 - 17:45:16 CST)
- Targeted MD, "Biased atoms" and "Fitted atoms", RMSD 黄姝姮 (Wed Nov 29 2017 - 07:27:15 CST)
- Electric field simulation: eFieldNormalized Carlo Guardiani (Tue Nov 28 2017 - 13:53:57 CST)
- nan for Drude's LP in distance-like colvars Bogdan MAREKHA (Fri Nov 24 2017 - 10:44:01 CST)
- SMP instructions for multi-node calculation on POWER 8 + P100 Adrien Cerdan (Wed Nov 22 2017 - 10:09:51 CST)
- RATTLE error with lipid bilayer system Ahmad Kiani Karanji (Tue Nov 21 2017 - 13:08:46 CST)
- Re: NAMD energy run in VMD Peter Freddolino (Tue Nov 21 2017 - 13:02:07 CST)
- NAMD energy run in VMD Srijita Paul (Tue Nov 21 2017 - 09:43:08 CST)
- Improper section for parameterization Theodora Teddy (Tue Nov 21 2017 - 07:20:59 CST)
- REMD using NAMD 2.13 Aliasghar Alizadeh-Mojarad (Fri Nov 17 2017 - 18:02:46 CST)
- Bias-exchange metadynamics Azadeh Alavizargar (Fri Nov 17 2017 - 05:07:56 CST)
- NPT simulations with PLUMED in NAMD Eric Lang (Wed Nov 15 2017 - 07:58:27 CST)
- missing parameters. NEHİR NALINCI (Wed Nov 15 2017 - 06:53:06 CST)
- Change pressure during simulation Monika Madhavi (Wed Nov 15 2017 - 01:07:39 CST)
- NAMD QM/MM Constanza Galaz Araya (Tue Nov 14 2017 - 10:08:45 CST)
- SMD: constant velocity output analysis (Develop force and displacement plot) Keshab Thapa (Mon Nov 13 2017 - 17:20:38 CST)
- Using Gromacs topology in NAMD Amali Guruge (Sun Nov 12 2017 - 22:19:43 CST)
- About the performance of RAMD Francesco Pietra (Fri Nov 10 2017 - 10:55:42 CST)
- Downloads are .tar files but have .tar.gz extension Toon Verstraelen (Thu Nov 09 2017 - 05:07:26 CST)
- NAMD job termination Amali Guruge (Wed Nov 08 2017 - 21:01:25 CST)
- RMSD colvar not working in NAMD2.12 Linux version Abhaysinh Gaikwad (Tue Nov 07 2017 - 21:46:28 CST)
- Psf file generation with Gromacs Parameters Amali Guruge (Mon Nov 06 2017 - 19:53:58 CST)
- problem in writing the coor files Fidan Sumbul (Mon Nov 06 2017 - 11:11:28 CST)
- Running multiple-replicas metadynamics Prapasiri Pongprayoon (Fri Nov 03 2017 - 18:30:11 CDT)
- Some water molecules are missing in psf Amali Guruge (Thu Nov 02 2017 - 17:33:06 CDT)
- RMSD of backbone changes rapidly at the beginning of production run Monika Madhavi (Thu Nov 02 2017 - 04:52:11 CDT)
- Re: RMSD of backbone changes rapidly at the beginning of production run Peter Freddolino (Thu Nov 02 2017 - 09:02:13 CDT)
- Re: RMSD of backbone changes rapidly at the beginning of production run Fidan Sumbul (Fri Nov 03 2017 - 06:27:42 CDT)
- Which NAMD-Build for my local HPC? Bassam Haddad (Tue Oct 31 2017 - 13:34:12 CDT)
- [NAMD] Too many collective variables? The Cromicus Productions (Thu Oct 26 2017 - 15:11:19 CDT)
- Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Wed Oct 25 2017 - 15:26:57 CDT)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Victor Ovchinnikov (Wed Oct 25 2017 - 15:59:42 CDT)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Vermaas, Joshua (Wed Oct 25 2017 - 16:01:57 CDT)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Thu Oct 26 2017 - 12:34:06 CDT)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Giacomo Fiorin (Thu Oct 26 2017 - 13:56:26 CDT)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Thu Nov 09 2017 - 11:00:09 CST)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Giacomo Fiorin (Thu Nov 09 2017 - 16:12:41 CST)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Thu Oct 26 2017 - 12:34:06 CDT)
- Amber force filed input failure on GPU Bata Zsófia (Wed Oct 25 2017 - 10:40:06 CDT)
- Stack Traceback problem in colvar restrain PRITI ROY (Wed Oct 25 2017 - 07:46:57 CDT)
- Re: namd-l digest V1 #2289 Zahra Mohammadi (Wed Oct 25 2017 - 02:58:36 CDT)
- FATAL ERROR: cuda_check_progress polled 1000000 times over ... Zahra Mohammadi (Tue Oct 24 2017 - 06:12:55 CDT)
- Simulation crashes on GPU Mohan maruthi sena (Tue Oct 24 2017 - 05:25:10 CDT)
- Restarting FEP calculations Sadegh Faramarzi Ganjabad (Mon Oct 23 2017 - 15:10:55 CDT)
- flat and smooth energy? Brian Radak (Mon Oct 23 2017 - 14:07:13 CDT)
- Water atoms' explosion out of solvate box in my RBCG simulation on NAMD ThatMind TV (Mon Oct 23 2017 - 05:57:39 CDT)
- Enhanced sampling methods for oligomers Jacob Usadi (Fri Oct 20 2017 - 15:33:34 CDT)
- building system with or without water for metadynamics Rabeta Yeasmin (Tue Oct 17 2017 - 16:52:38 CDT)
- colvars: Did the orthogonality requirements of colvars change in ABF? yjcoshc (Mon Oct 16 2017 - 20:20:29 CDT)
- sortreplicas on Stampede 2 Chitrak Gupta (Mon Oct 16 2017 - 14:34:15 CDT)
- Fwd: About wall clock time Rik Chakraborty (Mon Oct 16 2017 - 01:20:40 CDT)
- Running 2.12 Dr. Eddie (Fri Oct 13 2017 - 19:56:46 CDT)
- REST2 simulations: Corecting shifted dcd files! Bhati, Agastya (Wed Oct 11 2017 - 14:36:14 CDT)
- Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:12:44 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 14:32:54 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:50:46 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 20:20:24 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Thu Oct 12 2017 - 06:50:40 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Thu Oct 12 2017 - 08:21:09 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Thu Oct 12 2017 - 09:00:27 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:50:46 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 14:32:54 CDT)
- Optimizing namd run Dr. Eddie (Wed Oct 11 2017 - 13:04:29 CDT)
- Re: FATAL ERROR: Duplicate bond when going from nvt to npt Marlon Sidore (Mon Oct 09 2017 - 04:04:17 CDT)
- Movement of chloride ions during MD Luba Simhaev (Sun Oct 08 2017 - 06:21:53 CDT)
- Sample umbrella sampling input file Rabeta Yeasmin (Fri Oct 06 2017 - 17:14:02 CDT)
- NAMD on Stampede 2 Chitrak Gupta (Thu Oct 05 2017 - 18:23:05 CDT)
- Fwd: Klaus Schulten Memorial Symposium, registration and accommodation David Hardy (Thu Oct 05 2017 - 15:29:08 CDT)
- convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Thu Oct 05 2017 - 13:36:07 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Thu Oct 05 2017 - 15:30:28 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:04:39 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Fri Oct 06 2017 - 14:11:27 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:19:56 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Fri Oct 06 2017 - 14:28:56 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:04:39 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Thu Oct 05 2017 - 15:30:28 CDT)
- Constrain on DNA when using ABF for protein-DNA system Mehdi Bagherpour (Thu Oct 05 2017 - 13:25:33 CDT)
- NAMDEnergy with xtc file Sneha M (Thu Oct 05 2017 - 05:11:37 CDT)
- excluding ions based on mass Olya Kravchenko (Wed Oct 04 2017 - 14:38:44 CDT)
- ion moving laterally during Umbrella Sampling? Olya Kravchenko (Tue Oct 03 2017 - 12:45:09 CDT)
- colvars: keepFreeEnergyFiles doesn't work in latest colvars version yjcoshc (Fri Sep 29 2017 - 21:38:13 CDT)
- performance of NAMD on KNL jing liang (Fri Sep 29 2017 - 15:10:04 CDT)
- [NAMD] Running NAMD in Stampede2 The Cromicus Productions (Fri Sep 29 2017 - 14:59:34 CDT)
- Building namd 2.12 from source an ARM64 architecture istamkos_at_auth.gr (Wed Sep 27 2017 - 17:06:00 CDT)
- Re: Building namd 2.12 from source an ARM64 architecture Vermaas, Joshua (Wed Sep 27 2017 - 18:09:31 CDT)
- Re: Building namd 2.12 from source an ARM64 architecture Fotis Baltoumas (Wed Sep 27 2017 - 18:15:36 CDT)
- Re: Building namd 2.12 from source an ARM64 architecture istamkos_at_auth.gr (Fri Sep 29 2017 - 17:38:21 CDT)
- margin and pressure in CUDA version JC Gumbart (Wed Sep 27 2017 - 11:48:52 CDT)
- minimum CUDA compute capability required for NAMD2.12 Albers, Thomas (Sat Sep 23 2017 - 16:03:24 CDT)
- How to sample pressure from NAMD log file. Daipayan Sarkar (Thu Sep 21 2017 - 22:16:54 CDT)
- displacement of protein Estefanía Hugo (Thu Sep 21 2017 - 09:08:19 CDT)
- Build NAMD with CUDA for unix workstation (centos 7) Daipayan Sarkar (Wed Sep 20 2017 - 01:54:25 CDT)
- FAD parameter and topology files amit kumar (Tue Sep 19 2017 - 23:12:39 CDT)
- What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 01:37:21 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Brian Radak (Tue Sep 19 2017 - 08:30:20 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 11:33:46 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Brian Radak (Tue Sep 19 2017 - 11:39:05 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Giacomo Fiorin (Tue Sep 19 2017 - 12:23:46 CDT)
- RE: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Lennart Nilsson (Tue Sep 19 2017 - 12:29:33 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 12:39:34 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Jérôme Hénin (Tue Sep 19 2017 - 13:03:04 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 11:33:46 CDT)
- Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Brian Radak (Tue Sep 19 2017 - 08:30:20 CDT)
- performance is more poor for namd 2.12 Yi Huizhan (Wed Sep 13 2017 - 22:25:13 CDT)
- QM/MM With Mopac Error Nisler, Collin R. (Wed Sep 13 2017 - 15:27:19 CDT)
- Ion type in NAMD Implicit solvent model for ionizing the system Susmita Ghosh (Wed Sep 13 2017 - 00:31:50 CDT)
- [NAMD] Simulations in guanidinium chloride The Cromicus Productions (Tue Sep 12 2017 - 15:57:13 CDT)
- QM/MM Parallel Computing With Orca Nisler, Collin R. (Tue Sep 12 2017 - 09:12:59 CDT)
- [NAMD] File Missing in Nanopore Tutorial The Cromicus Productions (Mon Sep 11 2017 - 22:38:23 CDT)
- pairInteraction and PME? Michael LeVine (Mon Sep 11 2017 - 19:20:59 CDT)
- Molecule-based Electrostatics Cutoff? David Huggins (Mon Sep 11 2017 - 16:58:59 CDT)
- extracting avarage pdb from dcd file Srijita Paul (Mon Sep 11 2017 - 00:48:06 CDT)
- minimization error Natasha Gupta (Fri Sep 08 2017 - 19:48:14 CDT)
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- Free MD simulation (Production run) Roshan Shrestha (Fri Sep 08 2017 - 02:32:50 CDT)
- -nan values and fatal error Natasha Gupta (Thu Sep 07 2017 - 11:24:29 CDT)
- No minimized system after running minimization in NAMD Roshan Shrestha (Thu Sep 07 2017 - 09:17:02 CDT)
- Concatenating log files Roshan Shrestha (Wed Sep 06 2017 - 11:07:51 CDT)
- applying constant force on water molecules in a particular direction Sanjib Paul (Wed Sep 06 2017 - 06:14:16 CDT)
- Too many iterations in routine jacobi during FEP Francesco Pietra (Wed Sep 06 2017 - 01:36:16 CDT)
- How to set the configuration file for a NVE simulation Monika Madhavi (Mon Sep 04 2017 - 19:02:29 CDT)
- RFC: shell scripts and support functions for NAMD on Slurm (including GPU and Infiniband) Renfro, Michael (Mon Sep 04 2017 - 13:57:54 CDT)
- Dihedral colvar PRITI ROY (Mon Sep 04 2017 - 06:08:00 CDT)
- Re: Dihedral colvar Jérôme Hénin (Mon Sep 04 2017 - 07:40:26 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 08:44:31 CDT)
- Re: Dihedral colvar Jérôme Hénin (Fri Sep 08 2017 - 08:53:28 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 13:55:01 CDT)
- Re: Dihedral colvar Vermaas, Joshua (Fri Sep 08 2017 - 14:06:25 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 14:33:45 CDT)
- Re: Dihedral colvar Giacomo Fiorin (Fri Sep 08 2017 - 14:54:44 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 08:44:31 CDT)
- Re: Dihedral colvar Jérôme Hénin (Mon Sep 04 2017 - 07:40:26 CDT)
- QM atoms outside the PBC boundary in QM/MM calculation Haohao Fu (Sat Sep 02 2017 - 21:55:26 CDT)
- FATAL ERROR: Singular matrix in routine ludcmp Natasha Gupta (Fri Sep 01 2017 - 18:41:24 CDT)
- Constraining and imparting motion to a geometry Abhaysinh Gaikwad (Fri Sep 01 2017 - 14:47:21 CDT)
- AW: NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Fri Sep 01 2017 - 03:23:28 CDT)
- Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 18:23:43 CDT)
- Re: Regular vs US sampling runs. Vermaas, Joshua (Thu Aug 31 2017 - 18:56:17 CDT)
- Re: Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 20:13:38 CDT)
- Re: Regular vs US sampling runs. Giacomo Fiorin (Thu Aug 31 2017 - 21:34:56 CDT)
- Re: Regular vs US sampling runs. jeevan gc (Fri Sep 01 2017 - 11:32:27 CDT)
- Re: Regular vs US sampling runs. Vermaas, Joshua (Fri Sep 01 2017 - 11:53:11 CDT)
- Re: Regular vs US sampling runs. jeevan gc (Fri Sep 01 2017 - 16:32:20 CDT)
- Re: Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 20:13:38 CDT)
- Re: Regular vs US sampling runs. Vermaas, Joshua (Thu Aug 31 2017 - 18:56:17 CDT)
- problem with minimization and calculation of force on a fixed atom Ben Adams (Thu Aug 31 2017 - 17:03:21 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Thu Aug 31 2017 - 17:36:54 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 10:36:21 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Fri Sep 01 2017 - 10:48:49 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 11:01:49 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Fri Sep 01 2017 - 11:02:52 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Fri Sep 01 2017 - 11:23:23 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 10:36:21 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Thu Aug 31 2017 - 17:36:54 CDT)
- Proper combination of langevinHydrogen with rigidbonds Benjamin Rousseau (Thu Aug 31 2017 - 10:31:31 CDT)
- error - atom type not in psf Natasha Gupta (Thu Aug 31 2017 - 05:56:15 CDT)
- Radial pair distribution function for internal water analysis James Starlight (Thu Aug 31 2017 - 05:49:39 CDT)
- extracting force on a single atom Ben Adams (Wed Aug 30 2017 - 19:18:49 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 05:37:13 CDT)
- Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 08:38:05 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 08:46:28 CDT)
- Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 10:03:04 CDT)
- Re: extracting force on a single atom Florian Blanc (Thu Aug 31 2017 - 10:07:59 CDT)
- Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 10:11:19 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 10:25:18 CDT)
- Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 08:38:05 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 05:37:13 CDT)
- Re: vmd-l: 780Ti and NAMD2 David Hardy (Wed Aug 30 2017 - 10:21:40 CDT)
- Re: NAMD-2.12 CUDA2 and PMECUDA problems Nicholas M. Glykos (Tue Aug 29 2017 - 12:54:40 CDT)
- Production run after equilibration Roshan Shrestha (Tue Aug 29 2017 - 05:38:00 CDT)
- calculate cumulative dG Nehad Elsalamouny (Tue Aug 29 2017 - 00:18:16 CDT)
- NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Mon Aug 28 2017 - 05:54:58 CDT)
- Movie in VMD Daipayan Sarkar (Sat Aug 26 2017 - 22:56:24 CDT)
- raising temperature after equiliobration t.shivam_at_iitg.ernet.in (Sat Aug 26 2017 - 02:20:20 CDT)
- NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! 王茜茜 (Fri Aug 25 2017 - 22:47:16 CDT)
- NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! 王茜茜 (Fri Aug 25 2017 - 22:33:43 CDT)
- Steered Molecular Dynamics Abhaysinh Gaikwad (Thu Aug 24 2017 - 13:28:49 CDT)
- Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer Arthur Vale (Wed Aug 23 2017 - 18:58:59 CDT)
- make psf error for ligand Natasha Gupta (Wed Aug 23 2017 - 16:46:55 CDT)
- error - parameter file for fluorine on a benzene ring Natasha Gupta (Wed Aug 23 2017 - 15:07:08 CDT)
- Issues about Keep_water_out.tcl acript Vidhya Sankar (Fri Aug 18 2017 - 10:25:55 CDT)
- NAMD with multiple molecules Benz, Max (Thu Aug 17 2017 - 10:09:17 CDT)
- Reg membrane assembly Vidhya Sankar (Thu Aug 17 2017 - 00:37:42 CDT)
- restarting and continuing - difference t.shivam_at_iitg.ernet.in (Mon Aug 14 2017 - 09:05:03 CDT)
- reg diffusion of water molecules Vidhya Sankar (Sat Aug 12 2017 - 23:51:25 CDT)
- Creating psf file for ligand Roshan Shrestha (Sat Aug 12 2017 - 09:34:29 CDT)
- How to get the right density of a methane system Monika Madhavi (Fri Aug 11 2017 - 21:56:51 CDT)
- How to get 3D figure of solvent accessible surface area from APBS output Rabeta Yeasmin (Fri Aug 11 2017 - 17:18:54 CDT)
- simulation crashing in 2nd stage equilibration t.shivam_at_iitg.ernet.in (Fri Aug 11 2017 - 06:32:32 CDT)
- replica_bias and colvars JC Gumbart (Thu Aug 10 2017 - 12:07:45 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 12:51:26 CDT)
- Re: replica_bias and colvars Vermaas, Joshua (Thu Aug 10 2017 - 12:58:27 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 15:25:35 CDT)
- Re: replica_bias and colvars JC Gumbart (Thu Aug 10 2017 - 16:17:21 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 21:10:21 CDT)
- Re: replica_bias and colvars JC Gumbart (Sat Aug 12 2017 - 06:49:35 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Sat Aug 12 2017 - 13:29:48 CDT)
- Re: replica_bias and colvars Vermaas, Joshua (Thu Aug 10 2017 - 12:58:27 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 12:51:26 CDT)
- difference between .vel and .vel.restart t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 04:39:49 CDT)
- value of langevinTemp in case of binvelocities t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 02:05:43 CDT)
- finding atoms in protein-lipid system having electrostatic interaction Rabeta Yeasmin (Wed Aug 09 2017 - 13:32:35 CDT)
- Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 13:03:49 CDT)
- Re: Software for molecular electrostatic calculations Giacomo Fiorin (Wed Aug 09 2017 - 14:16:54 CDT)
- Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 16:44:01 CDT)
- Re: Software for molecular electrostatic calculations Giacomo Fiorin (Thu Aug 10 2017 - 08:15:28 CDT)
- Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Thu Aug 10 2017 - 10:31:58 CDT)
- Re: Software for molecular electrostatic calculations David Hardy (Thu Aug 17 2017 - 13:28:19 CDT)
- Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 16:44:01 CDT)
- Re: Software for molecular electrostatic calculations Giacomo Fiorin (Wed Aug 09 2017 - 14:16:54 CDT)
- Coarse Grain of a Calcium Binding Protein Nisler, Collin R. (Wed Aug 09 2017 - 10:31:24 CDT)
- NAMD for Stampede2 Maria Bykhovskaia (Wed Aug 09 2017 - 10:26:57 CDT)
- Functional role of the internal water channel within the receptor James Starlight (Tue Aug 08 2017 - 07:42:07 CDT)
- Are KNL a good choice for classical MD? Francesco Pietra (Fri Aug 04 2017 - 15:51:48 CDT)
- TMD without alignment John Green (Fri Aug 04 2017 - 13:27:31 CDT)
- Problem in running wham Rabeta Yeasmin (Fri Aug 04 2017 - 10:41:06 CDT)
- Syntax for replicaRecv Florian Blanc (Fri Aug 04 2017 - 10:17:27 CDT)
- difference between constraining,restraining and fixing the atoms t.shivam_at_iitg.ernet.in (Fri Aug 04 2017 - 01:25:23 CDT)
- ABF for dihedrals Albers, Thomas (Thu Aug 03 2017 - 12:48:24 CDT)
- Namd 2.12 error with Nvidia M2090 cards Michelle Kuttel (Thu Aug 03 2017 - 03:30:21 CDT)
- two stage equilibration in single configuration file t.shivam_at_iitg.ernet.in (Thu Aug 03 2017 - 01:03:46 CDT)
- Setting up softcore parameters for FEP John Green (Wed Aug 02 2017 - 16:18:32 CDT)
- ABF vs Umbrella Sampling entrance barrier heights discrepancy Olya Kravchenko (Wed Aug 02 2017 - 13:39:16 CDT)
- Free energy (eABF): negative RMSD and harmonic restraints. philippe Bourly (Wed Aug 02 2017 - 11:45:56 CDT)
- Configuration of new HPC Cluster for NAMD and GROMACS Vogel, Alexander (Mon Jul 31 2017 - 05:36:30 CDT)
- How to calculate free energy to unbias colvars restraint? Victoria Lim (Fri Jul 28 2017 - 18:56:44 CDT)
- PACE CG Model Alexander Adams (Fri Jul 28 2017 - 12:53:24 CDT)
- Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:00:04 CDT)
- Re: Running NAMD on Intel OmniPath Mauro Lapelosa (Thu Jul 27 2017 - 13:06:24 CDT)
- Re: Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:47:54 CDT)
- Re: Running NAMD on Intel OmniPath David Hardy (Thu Jul 27 2017 - 14:18:47 CDT)
- Re: Running NAMD on Intel OmniPath Giacomo Fiorin (Thu Jul 27 2017 - 14:33:38 CDT)
- Re: Running NAMD on Intel OmniPath David Hardy (Thu Jul 27 2017 - 16:36:47 CDT)
- Re: Running NAMD on Intel OmniPath Giacomo Fiorin (Thu Jul 27 2017 - 17:53:52 CDT)
- Re: Running NAMD on Intel OmniPath David Hardy (Fri Jul 28 2017 - 10:29:37 CDT)
- Re: Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:47:54 CDT)
- Re: Running NAMD on Intel OmniPath Mauro Lapelosa (Thu Jul 27 2017 - 13:06:24 CDT)
- Does FEP really run on Knights Landing? Francesco Pietra (Thu Jul 27 2017 - 11:44:13 CDT)
- polymer Nehir NALINCI (Thu Jul 27 2017 - 03:02:49 CDT)
- Problems running FEP on Lenovo NextScale KNL Francesco Pietra (Wed Jul 26 2017 - 09:23:19 CDT)
- making glucose chains using charmm36 Mohammad Hassan Khatami (Mon Jul 24 2017 - 13:29:18 CDT)
- I don't have any eabf output file. philippe Bourly (Fri Jul 21 2017 - 13:46:39 CDT)
- Re: I don't have any eabf output file. yjcoshc_at_gmail.com (Tue Jul 25 2017 - 05:06:44 CDT)
- Re: I don't have any eabf output file. philippe Bourly (Tue Jul 25 2017 - 05:20:51 CDT)
- Re: Re: I don't have any eabf output file. Haohao (Tue Jul 25 2017 - 06:14:48 CDT)
- Re: Re: I don't have any eabf output file. Haohao (Tue Jul 25 2017 - 06:20:33 CDT)
- Re: Re: I don't have any eabf output file. philippe Bourly (Tue Jul 25 2017 - 07:23:34 CDT)
- Re: Re: I don't have any eabf output file. fhh2626_at_gmail.com (Wed Jul 26 2017 - 01:47:09 CDT)
- Re: I don't have any eabf output file. philippe Bourly (Tue Jul 25 2017 - 05:20:51 CDT)
- Re: I don't have any eabf output file. yjcoshc_at_gmail.com (Tue Jul 25 2017 - 05:06:44 CDT)
- Too many iterations in routine jacobi. Francesco Pietra (Fri Jul 21 2017 - 12:06:45 CDT)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 CTL3 (ATOMS 8773 8776) Arthur Vale (Thu Jul 20 2017 - 20:08:28 CDT)
- "Periodic cell has become too small for original patch grid!" with membrane system on GPU James Starlight (Thu Jul 20 2017 - 06:03:29 CDT)
- Compiling NAMD on stampede 2. Chitrak Gupta (Wed Jul 19 2017 - 17:47:07 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Wed Jul 19 2017 - 20:14:30 CDT)
- Re: Compiling NAMD on stampede 2. Chitrak Gupta (Thu Jul 20 2017 - 11:09:29 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Thu Jul 20 2017 - 11:20:29 CDT)
- Re: Compiling NAMD on stampede 2. Chitrak Gupta (Thu Jul 20 2017 - 11:29:37 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Thu Jul 20 2017 - 11:45:18 CDT)
- Re: Compiling NAMD on stampede 2. Chitrak Gupta (Fri Jul 21 2017 - 12:20:38 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Fri Jul 21 2017 - 12:47:07 CDT)
- Re: Compiling NAMD on stampede 2. Chitrak Gupta (Thu Jul 20 2017 - 11:09:29 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Wed Jul 19 2017 - 20:14:30 CDT)
- eABF - Fullsamples and windows merging philippe Bourly (Wed Jul 19 2017 - 08:41:56 CDT)
- NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault Wilson,Michael (Tue Jul 18 2017 - 13:57:16 CDT)
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL João Ribeiro (Mon Jul 17 2017 - 14:45:43 CDT)
- Error in thermodynamic integration for calculating ligand absolute binding free energy Marawan Hussien (Mon Jul 17 2017 - 11:45:22 CDT)
- Simulation of the mechanical stress in NAMD James Starlight (Mon Jul 17 2017 - 02:55:30 CDT)
- ABF: umbrella_int.awk Francesco Pietra (Thu Jul 13 2017 - 10:32:40 CDT)
- Re: ABF: umbrella_int.awk Jérôme Hénin (Thu Jul 13 2017 - 13:14:33 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Fri Jul 14 2017 - 03:39:48 CDT)
- Re: ABF: umbrella_int.awk Giacomo Fiorin (Fri Jul 14 2017 - 08:20:15 CDT)
- Re: ABF: umbrella_int.awk Giacomo Fiorin (Fri Jul 14 2017 - 08:21:10 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Sat Jul 15 2017 - 03:36:33 CDT)
- Re: ABF: umbrella_int.awk yjcoshc_at_gmail.com (Sat Jul 15 2017 - 07:02:33 CDT)
- Re: ABF: umbrella_int.awk Giacomo Fiorin (Sat Jul 15 2017 - 07:04:13 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Sat Jul 15 2017 - 08:45:00 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Fri Jul 14 2017 - 03:39:48 CDT)
- Re: ABF: umbrella_int.awk Jérôme Hénin (Thu Jul 13 2017 - 13:14:33 CDT)
- Protein trapped on an edge of the simulation cell using C36 force field istamkos_at_auth.gr (Tue Jul 11 2017 - 03:15:51 CDT)
- Maintaining PBC on Collective Variables Malay Ranjan Biswal (Mon Jul 10 2017 - 08:17:30 CDT)
- GAAMP Stefano Guglielmo (Mon Jul 10 2017 - 06:55:21 CDT)
- Collective variable remains at zero during Umbrella Sampling Hemanth Vemuri (Sun Jul 09 2017 - 23:59:18 CDT)
- Cross-term (CMAP) Faramarz Joodaki (Fri Jul 07 2017 - 18:04:48 CDT)
- Water permeation through aquaporin-Z Isaac Twelves (Fri Jul 07 2017 - 13:04:37 CDT)
- ABF FEP with multichain receptor Francesco Pietra (Fri Jul 07 2017 - 10:21:52 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Sat Jul 08 2017 - 05:46:31 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Sat Jul 08 2017 - 11:08:41 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Sat Jul 08 2017 - 15:07:36 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Sun Jul 09 2017 - 00:44:14 CDT)
- Fwd: ABF FEP with multichain receptor Francesco Pietra (Mon Jul 10 2017 - 05:25:30 CDT)
- Fwd: ABF FEP with multichain receptor Francesco Pietra (Tue Jul 11 2017 - 01:20:12 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Tue Jul 11 2017 - 08:12:51 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Tue Jul 11 2017 - 11:28:48 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Tue Jul 11 2017 - 11:52:23 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Sat Jul 08 2017 - 11:08:41 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Sat Jul 08 2017 - 05:46:31 CDT)
- Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield yousef nademi (Thu Jul 06 2017 - 20:49:48 CDT)
- Creating psf file DNA Roshan Shrestha (Thu Jul 06 2017 - 11:47:54 CDT)
- How to set setting periodic boundary condition Vidhya Sankar (Thu Jul 06 2017 - 07:43:56 CDT)
- Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Wed Jul 05 2017 - 02:09:14 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs Joshua . (Wed Jul 05 2017 - 09:39:40 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Wed Jul 05 2017 - 11:02:14 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Mon Jul 17 2017 - 09:09:20 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Tue Jul 18 2017 - 17:05:00 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Fri Aug 04 2017 - 06:44:37 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Fri Aug 25 2017 - 14:31:31 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs JC Gumbart (Fri Aug 25 2017 - 17:09:49 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Fri Aug 25 2017 - 21:34:38 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs JC Gumbart (Sat Aug 26 2017 - 08:11:13 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Wed Jul 05 2017 - 11:02:14 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs Joshua . (Wed Jul 05 2017 - 09:39:40 CDT)
- Protein trapped on an edge of the simulation cell using C36 force field istamkos_at_auth.gr (Tue Jul 04 2017 - 01:25:13 CDT)
- Re: Calculating electrostatic force from NAMD trajectory sunyeping (Mon Jul 03 2017 - 21:42:56 CDT)
- Calculating electrostatic force from NAMD trajectory Ben Lowe (Mon Jul 03 2017 - 21:35:50 CDT)
- Enhanced sampling of domain motion and gsafold dhirajks_at_gmail.com (Mon Jul 03 2017 - 19:18:38 CDT)
- NAMD on UCSD Comet Alexander Adams (Mon Jul 03 2017 - 13:26:48 CDT)
- write first point into (vel)dcd file Laura Joana (Mon Jul 03 2017 - 07:11:37 CDT)
- enhanced sampling of domain motion, GSAfold Dhiraj Srivastava (Sat Jul 01 2017 - 23:49:00 CDT)
- Simulating SDS molecules Siddharth Girdhar (Fri Jun 30 2017 - 09:11:08 CDT)
- veldcdfile command Laura Joana (Wed Jun 28 2017 - 09:59:45 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
- Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 13:09:28 CDT)
- Re: veldcdfile command Giacomo Fiorin (Wed Jun 28 2017 - 13:36:43 CDT)
- Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 14:25:35 CDT)
- Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 14:26:17 CDT)
- Re: veldcdfile command Jérôme Hénin (Thu Jun 29 2017 - 05:12:26 CDT)
- Re: veldcdfile command Jérôme Hénin (Thu Jun 29 2017 - 07:11:45 CDT)
- Re: veldcdfile command Laura Joana (Fri Jun 30 2017 - 07:38:02 CDT)
- Re: veldcdfile command Laura Joana (Mon Jul 03 2017 - 06:13:06 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 CDT)
- About the robustness of ABF and FEB protein-ligand Francesco Pietra (Wed Jun 28 2017 - 09:40:15 CDT)
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL João Ribeiro (Tue Jun 27 2017 - 13:46:57 CDT)
- Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Sun Jun 25 2017 - 05:56:01 CDT)
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 05:28:49 CDT)
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 11:24:59 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Mon Jun 26 2017 - 11:32:58 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Tue Jun 27 2017 - 02:46:38 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Wed Jun 28 2017 - 11:35:19 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Thu Jun 29 2017 - 08:47:59 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Wed Jul 05 2017 - 11:03:05 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Wed Jul 05 2017 - 11:30:59 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Thu Jul 06 2017 - 01:15:50 CDT)
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 11:24:59 CDT)
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 05:28:49 CDT)
- topology file for the residue CSO Hyun (Fri Jun 23 2017 - 11:43:38 CDT)
- measuring Euler angles and polar angles Francesco Pietra (Thu Jun 22 2017 - 12:01:39 CDT)
- Re: measuring Euler angles and polar angles Giacomo Fiorin (Thu Jun 22 2017 - 12:18:00 CDT)
- Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 09:55:31 CDT)
- Re: measuring Euler angles and polar angles Giacomo Fiorin (Fri Jun 23 2017 - 10:00:36 CDT)
- Re: measuring Euler angles and polar angles Jérôme Hénin (Fri Jun 23 2017 - 10:04:46 CDT)
- Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 12:06:18 CDT)
- Fwd: measuring Euler angles and polar angles Francesco Pietra (Sat Jun 24 2017 - 01:22:17 CDT)
- Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 09:55:31 CDT)
- Re: measuring Euler angles and polar angles Giacomo Fiorin (Thu Jun 22 2017 - 12:18:00 CDT)
- Harmonic force Keyword "centers" significance Rabeta Yeasmin (Wed Jun 21 2017 - 17:40:43 CDT)
- Re: run namd cuda with srun. Fırat Yılmaz (Wed Jun 21 2017 - 03:36:09 CDT)
- run namd cuda with srun. Fırat Yılmaz (Tue Jun 20 2017 - 16:03:29 CDT)
- Organic Solvent & Water Simulation Oscar Bastidas (Tue Jun 20 2017 - 15:15:05 CDT)
- Reg seeting of periodic boundary condition Vidhya Sankar (Tue Jun 20 2017 - 11:56:59 CDT)
- REG Protein inserion in to membrane bi layear Vidhya Sankar (Tue Jun 20 2017 - 05:05:39 CDT)
- Defining custom Colvars to measure pmf with Umbrella Sampling Hemanth Vemuri (Tue Jun 20 2017 - 00:25:29 CDT)
- Re: Defining custom Colvars to measure pmf with Umbrella Sampling Giacomo Fiorin (Tue Jun 20 2017 - 21:49:26 CDT)
- Re: Defining custom Colvars to measure pmf with Umbrella Sampling Radak, Brian K (Wed Jun 21 2017 - 11:16:49 CDT)
- Simulating Protein Entering membrane Arthur Oliveira Vale (Sun Jun 18 2017 - 20:14:32 CDT)
- GaMD in NAMD Chitrak Gupta (Sat Jun 17 2017 - 15:16:18 CDT)
- Re: GaMD in NAMD Francesco Pietra (Sun Jun 18 2017 - 01:04:59 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 09:20:11 CDT)
- Re: GaMD in NAMD jeevan gc (Sun Jun 18 2017 - 10:49:40 CDT)
- Re: GaMD in NAMD David Hardy (Sun Jun 18 2017 - 11:02:19 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 14:57:20 CDT)
- Re: GaMD in NAMD Francesco Pietra (Mon Jun 19 2017 - 00:36:19 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Mon Jun 19 2017 - 08:43:37 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 09:20:11 CDT)
- Re: GaMD in NAMD Francesco Pietra (Sun Jun 18 2017 - 01:04:59 CDT)
- Setting up the range for movement of protein in umbrella sampling Rabeta Yeasmin (Fri Jun 16 2017 - 16:21:55 CDT)
- missing binary operator before token "(" Fırat Yılmaz (Thu Jun 15 2017 - 02:30:12 CDT)
- Reg seeting of periodic boundary condition Vidhya Sankar (Wed Jun 14 2017 - 21:59:27 CDT)
- Gyration in colvars doesn't work with eABF. yjcoshc (Wed Jun 14 2017 - 06:49:51 CDT)
- principal axes in colvars Stefano Guglielmo (Wed Jun 14 2017 - 06:28:44 CDT)
- How to pull protein-Monomer from DNA using ABF without any force on DNA? Mehdi Bagherpour (Tue Jun 13 2017 - 12:30:29 CDT)
- Questions on implementing new collective variable in colvars. yjcoshc (Mon Jun 12 2017 - 22:14:35 CDT)
- Re: Questions on implementing new collective variable in colvars. Axel Kohlmeyer (Mon Jun 12 2017 - 22:38:48 CDT)
- Re: Questions on implementing new collective variable in colvars. yjcoshc (Mon Jun 12 2017 - 22:48:26 CDT)
- Re: Questions on implementing new collective variable in colvars. Jérôme Hénin (Tue Jun 13 2017 - 10:32:23 CDT)
- Re: Questions on implementing new collective variable in colvars. yjcoshc (Tue Jun 13 2017 - 20:36:32 CDT)
- Re: Questions on implementing new collective variable in colvars. Jérôme Hénin (Wed Jun 14 2017 - 07:26:16 CDT)
- Re: Questions on implementing new collective variable in colvars. yjcoshc (Mon Jun 12 2017 - 22:48:26 CDT)
- Re: Questions on implementing new collective variable in colvars. Axel Kohlmeyer (Mon Jun 12 2017 - 22:38:48 CDT)
- FEP with ExtraBonds Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Mon Jun 12 2017 - 15:30:59 CDT)
- Converting x,y,z coordinates to dcd file Kashish Punjani (Sun Jun 11 2017 - 12:44:18 CDT)
- Re: namd-l digest V1 #2196 Rabeta Yeasmin (Fri Jun 09 2017 - 15:40:37 CDT)
- coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Yaxin An (Fri Jun 09 2017 - 09:39:28 CDT)
- Two parameter file in NAMD configuration file divyabharathi korlepara (Fri Jun 09 2017 - 02:58:16 CDT)
- NAMD DCD file format Dmitri Priimak (Fri Jun 09 2017 - 01:47:36 CDT)
- Colvars wall boundaries for CoordNum Wasut Pornpatcharapong (Thu Jun 08 2017 - 19:27:50 CDT)
- Umbrella Sampling colvar file parameters Rabeta Yeasmin (Thu Jun 08 2017 - 12:20:16 CDT)
- Restraining the mass centre coordinate during Umbrella Sampling Rabeta Yeasmin (Wed Jun 07 2017 - 10:46:57 CDT)
- Restring the coordinate during Umbrella Sampling Rabeta Yeasmin (Tue Jun 06 2017 - 16:13:08 CDT)
- about GaMD reweighting Francesco Pietra (Tue Jun 06 2017 - 10:58:40 CDT)
- Keeping potassium ions out of an area during equilibration Charles Hoying (Mon Jun 05 2017 - 22:57:40 CDT)
- Center of mass drift M. Wong (Fri Jun 02 2017 - 04:10:50 CDT)
- DNA capping Nicholus Bhattacharjee (Thu Jun 01 2017 - 04:11:48 CDT)
- Problem with running on multiple nodes Karteek Bejagam (Wed May 31 2017 - 11:33:48 CDT)
- Fatal error in the simulation of a water box M. Wong (Wed May 31 2017 - 04:04:38 CDT)
- Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:17:12 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Richard Overstreet (Tue May 30 2017 - 16:41:33 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:48:09 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Thu Jun 01 2017 - 13:05:09 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue Jun 06 2017 - 14:07:24 CDT)
- Re: Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Wed May 31 2017 - 13:37:09 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Brian Radak (Wed May 31 2017 - 18:24:19 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Richard Overstreet (Tue May 30 2017 - 16:41:33 CDT)
- NAMD crashes when Multilevel Summation Method (MSM) is on Shadrina Maria (Tue May 30 2017 - 10:12:46 CDT)
- performance of NAMD SMP MPI version jing liang (Thu May 25 2017 - 13:38:10 CDT)
- Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 10:49:32 CDT)
- Re: Error regarding missing angles between perturbed groups for fep calculation Jeff Comer (Thu May 25 2017 - 16:16:18 CDT)
- RE: Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 16:24:08 CDT)
- Re: Error regarding missing angles between perturbed groups for fep calculation Vermaas, Joshua (Thu May 25 2017 - 17:29:59 CDT)
- RE: Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri May 26 2017 - 17:03:36 CDT)
- Re: Error regarding missing angles between perturbed groups for fep calculation Vermaas, Joshua (Fri May 26 2017 - 17:09:53 CDT)
- RE: Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 16:24:08 CDT)
- Re: Error regarding missing angles between perturbed groups for fep calculation Jeff Comer (Thu May 25 2017 - 16:16:18 CDT)
- Equilibrium Energies Theodora Teddy (Tue May 23 2017 - 11:10:19 CDT)
- psfgen readpsf error with no more explanation Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 15:58:37 CDT)
- Writing pdb file for a particular frame Rabeta Yeasmin (Tue May 16 2017 - 18:18:33 CDT)
- Howto gaussian accelerated MD Francesco Pietra (Tue May 16 2017 - 09:34:11 CDT)
- colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Mon May 15 2017 - 04:18:28 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 08:20:31 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Jérôme Hénin (Tue May 16 2017 - 09:08:46 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 09:36:38 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Giacomo Fiorin (Tue May 16 2017 - 09:39:59 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 10:50:10 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Giacomo Fiorin (Tue May 16 2017 - 12:18:18 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Jérôme Hénin (Tue May 16 2017 - 09:08:46 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 08:20:31 CDT)
- [NAMD] Outputting PMF at half the time using Metadynamics The Cromicus Productions (Sun May 14 2017 - 14:04:32 CDT)
- restraining selected atom's z coordinates Rabeta Yeasmin (Sat May 13 2017 - 19:17:26 CDT)
- [NAMD] Problem with colvar "tilt" The Cromicus Productions (Fri May 12 2017 - 08:34:33 CDT)
- Pulling protein through membrane without changing the position of membrane Rabeta Yeasmin (Thu May 11 2017 - 11:51:44 CDT)
- CHARMRUN ERROR Zeki Zeybek (Thu May 11 2017 - 02:39:43 CDT)
- MPIRUN SLURM SCRIPT Zeki Zeybek (Tue May 09 2017 - 05:08:22 CDT)
- energy difference between HSE and HSD Hao Dong (Mon May 08 2017 - 23:48:48 CDT)
- pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Mon May 08 2017 - 14:59:06 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Mon May 08 2017 - 17:01:05 CDT)
- RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Tue May 09 2017 - 10:41:52 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 10 2017 - 19:36:16 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Thu May 11 2017 - 10:27:25 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Thu May 11 2017 - 11:52:48 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 02:00:11 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Hannes Loeffler (Wed May 17 2017 - 03:37:52 CDT)
- RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Wed May 17 2017 - 09:54:39 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Tue May 23 2017 - 01:04:17 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Tue May 23 2017 - 09:32:14 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 24 2017 - 10:48:29 CDT)
- RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Wed May 24 2017 - 11:35:50 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 24 2017 - 13:16:46 CDT)
- RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Wed May 24 2017 - 13:29:59 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Mon May 29 2017 - 15:45:10 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Tue May 30 2017 - 09:23:34 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 13:12:23 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Mon May 08 2017 - 17:01:05 CDT)
- Question about new NAMD QM/MM code Eric Smoll (Sun May 07 2017 - 22:08:08 CDT)
- [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 13:14:34 CDT)
- RE: [NAMD] How to build and simulate a periodic DNA in NAMD Nielsen, Steven (Sat May 06 2017 - 13:49:13 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 19:02:57 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 23:30:26 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sun May 07 2017 - 00:03:43 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Fri Jun 09 2017 - 12:31:08 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD Vermaas, Joshua (Fri Jun 09 2017 - 12:42:49 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Tue Jun 13 2017 - 05:42:00 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD Vermaas, Joshua (Tue Jun 13 2017 - 12:09:32 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sun Jun 18 2017 - 17:47:39 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 19:02:57 CDT)
- RE: [NAMD] How to build and simulate a periodic DNA in NAMD Nielsen, Steven (Sat May 06 2017 - 13:49:13 CDT)
- Bond-jitter/Total-energy-spikes during energy minimization in vacuum Eric Smoll (Mon May 01 2017 - 02:58:10 CDT)
- Free energy calculation under external bias, (e)ABF/US/etc Jim (Fri Apr 28 2017 - 20:25:57 CDT)
- compilation of NAMD 2.12 fails Vlad Cojocaru (Thu Apr 27 2017 - 10:02:19 CDT)
- Re: compilation of NAMD 2.12 fails Vermaas, Joshua (Thu Apr 27 2017 - 11:37:08 CDT)
- Re: compilation of NAMD 2.12 fails David Hardy (Thu Apr 27 2017 - 12:36:35 CDT)
- Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 09:14:58 CDT)
- Re: compilation of NAMD 2.12 fails David Hardy (Fri Apr 28 2017 - 10:15:04 CDT)
- Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 10:23:24 CDT)
- Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 10:24:18 CDT)
- Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 10:36:12 CDT)
- Re: compilation of NAMD 2.12 fails David Hardy (Fri Apr 28 2017 - 10:41:18 CDT)
- Re: compilation of NAMD 2.12 fails David Hardy (Thu Apr 27 2017 - 12:36:35 CDT)
- Re: compilation of NAMD 2.12 fails Vermaas, Joshua (Thu Apr 27 2017 - 11:37:08 CDT)
- Custum made residue addition Zeki Zeybek (Thu Apr 27 2017 - 08:08:17 CDT)
- Equilibration using NPT and Production run using NVE ensemble Akshay Bhatnagar (Thu Apr 27 2017 - 07:47:29 CDT)
- Kinetic energy outputs matthew reeves (Thu Apr 27 2017 - 06:29:38 CDT)
- Fwd: colvars to restrain peptide close to lipid Chitrak Gupta (Wed Apr 26 2017 - 17:22:37 CDT)
- verbs-smp on a single node Jeff Comer (Wed Apr 26 2017 - 15:13:40 CDT)
- colvars to restrain peptide close to lipid Chitrak Gupta (Wed Apr 26 2017 - 15:01:23 CDT)
- Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? sunyeping (Wed Apr 26 2017 - 12:51:17 CDT)
- Shear flow simulation setup James Starlight (Wed Apr 26 2017 - 08:51:54 CDT)
- Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too Angelo Rossi (Wed Apr 26 2017 - 08:06:03 CDT)
- namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 05:20:28 CDT)
- Re: namd 2.12 and plumed 2.3 Bassam Haddad (Wed Apr 26 2017 - 10:48:55 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 11:23:54 CDT)
- Re: namd 2.12 and plumed 2.3 Vermaas, Joshua (Wed Apr 26 2017 - 11:43:41 CDT)
- Re: namd 2.12 and plumed 2.3 Giacomo Fiorin (Wed Apr 26 2017 - 12:01:51 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 08:12:22 CDT)
- Re: namd 2.12 and plumed 2.3 Giacomo Fiorin (Tue May 02 2017 - 08:38:06 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 09:00:14 CDT)
- Re: namd 2.12 and plumed 2.3 Giacomo Fiorin (Tue May 02 2017 - 09:45:17 CDT)
- Re: namd 2.12 and plumed 2.3 Vermaas, Joshua (Tue May 02 2017 - 10:22:01 CDT)
- Re: namd 2.12 and plumed 2.3 yjcoshc_at_gmail.com (Tue May 02 2017 - 11:02:33 CDT)
- Re: namd 2.12 and plumed 2.3 vlad.cojocaru_at_mpi-muenster.mpg.de (Tue May 02 2017 - 11:50:02 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 10:33:34 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 11:23:54 CDT)
- Re: namd 2.12 and plumed 2.3 Bassam Haddad (Wed Apr 26 2017 - 10:48:55 CDT)
- Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 01:40:21 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 06:17:03 CDT)
- Re: Querries on eABF Jérôme Hénin (Thu Apr 27 2017 - 16:00:31 CDT)
- Re: Querries on eABF Souvik Sinha (Thu May 25 2017 - 05:02:32 CDT)
- Re: Querries on eABF Jeff Comer (Thu May 25 2017 - 16:06:33 CDT)
- Re: Querries on eABF Souvik Sinha (Fri May 26 2017 - 00:45:37 CDT)
- Re: Querries on eABF Jérôme Hénin (Fri May 26 2017 - 10:30:46 CDT)
- Re: Querries on eABF Souvik Sinha (Fri May 26 2017 - 10:53:04 CDT)
- Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 02:51:31 CDT)
- Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 07:37:19 CDT)
- Re: Querries on eABF Jérôme Hénin (Tue May 30 2017 - 07:54:55 CDT)
- Re: Querries on eABF Giacomo Fiorin (Tue May 30 2017 - 08:12:30 CDT)
- Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 11:01:09 CDT)
- Re: Querries on eABF yjcoshc_at_gmail.com (Tue May 30 2017 - 20:18:40 CDT)
- Re: Querries on eABF Jérôme Hénin (Tue May 30 2017 - 23:10:42 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Jul 12 2017 - 07:15:51 CDT)
- Re: Querries on eABF Jérôme Hénin (Wed Jul 12 2017 - 07:24:14 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Jul 12 2017 - 07:34:46 CDT)
- Re: Querries on eABF Souvik Sinha (Sat Jul 15 2017 - 07:39:34 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 06:17:03 CDT)
- Re: More FEP using separated topologies David Huggins (Tue Apr 25 2017 - 14:10:06 CDT)
- NAMD developer workshop - Chicago, May 22-23, 2017 João Ribeiro (Tue Apr 25 2017 - 07:45:59 CDT)
- Continuing SMD from restart files Kevin Chun Chan (Mon Apr 24 2017 - 08:32:18 CDT)
- generating topology file Nehir NALINCI (Mon Apr 24 2017 - 07:25:06 CDT)
- Klaus Schulten Memorial Issue (http://pubs.acs.org/toc/jpcbfk/121/15) Chris Chipot (Thu Apr 20 2017 - 12:10:34 CDT)
- NAMD 2.12 using CUDA 8.0 Wright, David (Thu Apr 20 2017 - 08:40:28 CDT)
- RE: Hybrid QM/MM in NAMD 2.12 with Gaussian Stober, Spencer T (Wed Apr 19 2017 - 10:44:18 CDT)
- Continuing SMD from restart files Kevin C Chan (Wed Apr 19 2017 - 08:20:03 CDT)
- Type of solvent water molecules Oscar Bastidas (Tue Apr 18 2017 - 16:05:06 CDT)
- What to cite for CHARMM22 Oscar Bastidas (Tue Apr 18 2017 - 12:37:04 CDT)
- NAMD developer workshop - Chicago, May 22-23, 2017 João Ribeiro (Tue Apr 18 2017 - 07:45:04 CDT)
- Hybrid QM/MM in NAMD 2.12 with Gaussian Stober, Spencer T (Tue Apr 18 2017 - 10:24:03 CDT)
- Segmentation fault during water MD nikolaev_at_spbau.ru (Tue Apr 18 2017 - 09:37:10 CDT)
- how to have large coordinate values in the "coordinates PDB" file Nielsen, Steven (Mon Apr 17 2017 - 13:33:37 CDT)
- TCBG Live Computational Biophysics Workshop Lectures João Ribeiro (Mon Apr 17 2017 - 09:13:24 CDT)
- How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations sunyeping (Mon Apr 17 2017 - 05:54:46 CDT)
- performance on ~1.5 million atoms system Steven Neumann (Mon Apr 17 2017 - 00:42:12 CDT)
- Slurm Script for Multi Node Run Zeki Zeybek (Sun Apr 16 2017 - 11:42:41 CDT)
- generating topology file Nehir NALINCI (Sat Apr 15 2017 - 03:09:07 CDT)
- Energy values matthew reeves (Fri Apr 14 2017 - 16:49:54 CDT)
- Best NAMD distribution for COEUS cluster? Bassam Haddad (Thu Apr 13 2017 - 15:27:10 CDT)
- Neutralize a box for FEP David Huggins (Wed Apr 12 2017 - 10:30:20 CDT)
- Incorporate aluminum oxide monolayer The Cromicus Productions (Tue Apr 11 2017 - 14:50:37 CDT)
- lipid centering Mihaela Drenscko (Tue Apr 11 2017 - 13:08:24 CDT)
- TCBG Live Computational Biophysics Workshop Lectures João Ribeiro (Mon Apr 10 2017 - 08:24:13 CDT)
- Standard Output: Benchmark vs Timing Jim (Fri Apr 07 2017 - 17:31:55 CDT)
- charmm parameters for buffer molecules Martin, Erik W (Fri Apr 07 2017 - 15:10:46 CDT)
- Post-doc position at ALCF - HPC post-doc in Computational Materials Wei Jiang (Fri Apr 07 2017 - 10:18:55 CDT)
- Error : components of colvar "alpha" does not support system force calculation Souvik Sinha (Fri Apr 07 2017 - 03:47:11 CDT)
- wrong pdb struvture generated while using patch hem_chandra_at_iitg.ernet.in (Fri Apr 07 2017 - 02:06:11 CDT)
- psfgen giving wrong structure in the autopdb file Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
- FATAL ERROR running apoa1 with NAMD 2.12 Tim.Ho_at_csiro.au (Wed Apr 05 2017 - 01:53:26 CDT)
- patch hem_chandra_at_iitg.ernet.in (Fri Mar 31 2017 - 04:03:15 CDT)
- Fatal Error in NAMD Faramarz Joodaki (Thu Mar 30 2017 - 12:14:51 CDT)
- patch hem_chandra_at_iitg.ernet.in (Mon Mar 27 2017 - 23:28:53 CDT)
- Solvent box fluctuations Götz, Alexander (Mon Mar 27 2017 - 11:56:09 CDT)
- Problem in NAMD QMMM Kshatresh Dutta Dubey (Sat Mar 25 2017 - 13:37:25 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelerators Norman Geist (Fri Mar 24 2017 - 08:25:52 CDT)
- (no subject) Marco Antonio Ramirez Martinez (Thu Mar 23 2017 - 13:23:33 CDT)
- Scaling behaviour of NAMD on hosts with GPU accelrators Kraus, Sebastian (Thu Mar 23 2017 - 11:18:14 CDT)
- Re: Scaling behaviour of NAMD on hosts with GPU accelrators Jeff Comer (Thu Mar 23 2017 - 12:24:23 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:27:46 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:35:00 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:47:39 CDT)
- Re: AW: Scaling behaviour of NAMD on hosts with GPU accelrators Maxime Boissonneault (Fri Mar 24 2017 - 06:42:04 CDT)
- Re: Scaling behaviour of NAMD on hosts with GPU accelrators Boonstra, S. (Fri Mar 24 2017 - 06:41:19 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:35:00 CDT)
- Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 12:55:12 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? Vermaas, Joshua (Wed Mar 22 2017 - 13:09:02 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 13:56:15 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? David Hardy (Wed Mar 22 2017 - 14:09:17 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? David Hardy (Wed Mar 22 2017 - 14:17:09 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 16:59:19 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 13:56:15 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? Vermaas, Joshua (Wed Mar 22 2017 - 13:09:02 CDT)
- Hands-On Workshop on Computational Biophysics: May 30 - June 2 in Pittsburgh, PA João Ribeiro KS (Wed Mar 22 2017 - 10:15:40 CDT)
- Constraining bonds that aren't hydrogens - splitPatch usefulness ? Marlon Sidore (Wed Mar 22 2017 - 07:08:50 CDT)
- (no subject) Debaditya Mukherjee (Tue Mar 21 2017 - 23:38:56 CDT)
- Workshop on MD simulation software design Giacomo Fiorin (Tue Mar 21 2017 - 13:42:55 CDT)
- Re: FATAL ERROR: Duplicate bond PRITI ROY (Tue Mar 21 2017 - 08:25:08 CDT)
- is NVE ensemble for production run justified? Akshay Bhatnagar (Tue Mar 21 2017 - 00:13:19 CDT)
- Defining colvars based on a region Bob Faith (Mon Mar 20 2017 - 19:48:00 CDT)
- Problem with namd2 execution on Windows GPU version md_at_novamechanics.com (Fri Mar 17 2017 - 15:57:26 CDT)
- problem to generate LPS PSF file using PSFGEN 송연호 (Thu Mar 16 2017 - 23:19:36 CDT)
- Implicit solvent no non-bonded pairing Eric Pederson (Thu Mar 16 2017 - 19:41:51 CDT)
- Charm++ supports RoCE ? Hyun (Thu Mar 16 2017 - 18:06:01 CDT)
- generating nodelist and error Hyun (Thu Mar 16 2017 - 10:10:19 CDT)
- Some questions about the orthogonality of colvars in ABF. yjcoshc (Wed Mar 15 2017 - 07:11:46 CDT)
- Re: A problem in ABF simulation Jérôme Hénin (Mon Mar 13 2017 - 17:04:00 CDT)
- gbis for acetonitrile hem_chandra_at_iitg.ernet.in (Sat Mar 11 2017 - 00:40:15 CST)
- (no subject) Debaditya Mukherjee (Fri Mar 10 2017 - 23:40:50 CST)
- Specify number of water molecules:simulation set up in VMD Rabeta Yeasmin (Fri Mar 10 2017 - 13:21:31 CST)
- NAMD-2.12 handful of issues with CUDA Norman Geist (Fri Mar 10 2017 - 03:16:13 CST)
- specify H-bond in CGMD Deng, Jinxia (Nancy) (Thu Mar 09 2017 - 08:42:14 CST)
- Cascade MDFF Luba Simhaev (Thu Mar 09 2017 - 02:34:08 CST)
- (no subject) Debaditya Mukherjee (Wed Mar 08 2017 - 22:52:17 CST)
- TMD: initial and targeted structure does not have same number of atoms Rabeta Yeasmin (Tue Mar 07 2017 - 09:42:58 CST)
- Choice of bromide ion LJ parameters Harish Srinivasan (Tue Mar 07 2017 - 07:03:16 CST)
- problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 04:27:28 CST)
- RE: problems mutating HID to TYR for free energy calculations Radak, Brian K (Tue Mar 07 2017 - 09:49:38 CST)
- Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 CST)
- Re: problems mutating HID to TYR for free energy calculations Brian Radak (Tue Mar 07 2017 - 17:02:27 CST)
- Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 17:39:37 CST)
- Re: Re: problems mutating HID to TYR for free energy calculations Vermaas, Joshua (Wed Mar 08 2017 - 09:45:49 CST)
- Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 CST)
- RE: problems mutating HID to TYR for free energy calculations Radak, Brian K (Tue Mar 07 2017 - 09:49:38 CST)
- Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 13:56:30 CST)
- Re: Question about applying external force Jérôme Hénin (Mon Mar 06 2017 - 14:23:24 CST)
- Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:32:36 CST)
- Re: Question about applying external force Giacomo Fiorin (Mon Mar 06 2017 - 15:40:38 CST)
- Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:59:25 CST)
- Re: Question about applying external force Giacomo Fiorin (Mon Mar 06 2017 - 16:23:57 CST)
- Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 18:27:20 CST)
- Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:32:36 CST)
- Re: Question about applying external force Jérôme Hénin (Mon Mar 06 2017 - 14:23:24 CST)
- analyze NAMD trajectory in Curves+ Oleksii Zdorevskyi (Mon Mar 06 2017 - 11:46:03 CST)
- Carma/grcarma v.1.7 released. Nicholas M Glykos (Mon Mar 06 2017 - 10:31:26 CST)
- REMD on HPC HOUSTON Douglas (Mon Mar 06 2017 - 08:15:25 CST)
- Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th João Ribeiro KS (Sat Mar 04 2017 - 15:56:47 CST)
- cuda errors when running NAMD sunyeping (Fri Mar 03 2017 - 18:51:34 CST)
- AW: vmd-l: Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 CST)
- Selecting atoms in NAMD .conf file and time-varying electric field Ben Lowe (Wed Mar 01 2017 - 15:42:55 CST)
- Multiple Electric Field simulation Athreya, Nagendra Bala Murali (Wed Mar 01 2017 - 15:13:37 CST)
- error during minimization Lara rajam (Mon Feb 27 2017 - 13:07:44 CST)
- CPU/GPU energy difference Boonstra, S. (Mon Feb 27 2017 - 05:08:28 CST)
- Lipid bilayer and ligand interactions Saleh AlKhalifa (Sun Feb 26 2017 - 08:47:58 CST)
- FFTK Determination of Dihedrals to be Scanned Zeki Zeybek (Sun Feb 26 2017 - 08:20:30 CST)
- NAMD developer workshop at Chicago IL, May 22-23, 2017 João Ribeiro KS (Fri Feb 24 2017 - 19:23:08 CST)
- colvars not scaling well in NAMD 2.10 Chitrak Gupta (Thu Feb 23 2017 - 17:25:14 CST)
- torsional restrain Lara rajam (Thu Feb 23 2017 - 10:14:21 CST)
- colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Wed Feb 22 2017 - 18:17:44 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Ajasja Ljubetič (Thu Feb 23 2017 - 01:36:03 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 03:10:20 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 10:38:39 CST)
- RE: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 14:35:22 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 14:44:00 CST)
- RE: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 14:58:54 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 21:50:08 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Fri Feb 24 2017 - 10:33:28 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Mon Feb 27 2017 - 17:36:53 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Wed Mar 01 2017 - 02:04:00 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 03:10:20 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Ajasja Ljubetič (Thu Feb 23 2017 - 01:36:03 CST)
- MDFF simulations in membrane environment Luba Simhaev (Wed Feb 22 2017 - 06:15:09 CST)
- restraints and constraints in NAMD Lara rajam (Tue Feb 21 2017 - 17:42:40 CST)
- Questions on creating constraints in NAMD Randy J. Zauhar (Tue Feb 21 2017 - 09:03:21 CST)
- How to define spheres of different sizes and their spatial constrains using NAMD? Sahoo, Dushyant (Tue Feb 21 2017 - 02:40:33 CST)
- Regarding Error on HB2 Obayed Ullah (Mon Feb 20 2017 - 18:48:56 CST)
- Charm++ Fatal Error Question Oscar Bastidas (Mon Feb 20 2017 - 11:36:53 CST)
- pairInteraction commands matthew reeves (Sun Feb 19 2017 - 16:39:27 CST)
- Define spheres using NAMD Dushyant Sahoo (Sun Feb 19 2017 - 12:17:37 CST)
- mail reg membrane tutorial Vidhya Sankar (Sat Feb 18 2017 - 23:34:54 CST)
- Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL João Ribeiro KS (Fri Feb 17 2017 - 16:57:13 CST)
- protein stability in a membrane and SMD Martin, Erik W (Fri Feb 17 2017 - 17:14:31 CST)
- REST2 patch for NAMD 2.12 Chitrak Gupta (Fri Feb 17 2017 - 14:49:07 CST)
- Metadynamics state file Carlo Guardiani (Fri Feb 17 2017 - 06:53:31 CST)
- Npt lipid simulation with electrostatics 2 Life Sciences Inc (Thu Feb 16 2017 - 16:46:32 CST)
- question about Steered Molecular Dynamics Oleksii Zdorevskyi (Wed Feb 15 2017 - 08:38:22 CST)
- Fixing COM of one atom in selection and letting the other move Life Sciences Inc (Tue Feb 14 2017 - 12:15:00 CST)
- [NAMD] Obtain dynamical matrix away from equilibrium The Cromicus Productions (Thu Feb 09 2017 - 12:02:35 CST)
- PSFgen failed to guess coordinate due to bad angle CD CG HG2 Sarath Josh M.K (Thu Feb 09 2017 - 03:19:39 CST)
- regarding constant velocity steered molecular dynamics mrinal patel (Wed Feb 08 2017 - 04:07:24 CST)
- AW: question about GPU Norman Geist (Wed Feb 08 2017 - 02:24:53 CST)
- Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12 Bryan Roessler (Tue Feb 07 2017 - 19:55:59 CST)
- PDB file creation matthew reeves (Tue Feb 07 2017 - 17:52:08 CST)
- FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE The Cromicus Productions (Tue Feb 07 2017 - 17:43:40 CST)
- NAMD Acceleration using P100 (GP-GPU) accelerator Atanu Maity (Tue Feb 07 2017 - 03:25:52 CST)
- AW: question about GPU Norman Geist (Tue Feb 07 2017 - 03:15:30 CST)
- question about GPU parinaz bashirbanaem (Mon Feb 06 2017 - 09:00:53 CST)
- Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x Greipel.Joachim_at_mh-hannover.de (Mon Feb 06 2017 - 08:54:08 CST)
- ++idlepoll Zeki Zeybek (Mon Feb 06 2017 - 01:21:19 CST)
- strange diffs in energy output of NAMD 2.9 vs. 2.11 Erik Nordgren (Fri Feb 03 2017 - 14:05:23 CST)
- High pressure calculations faride badalkhani (Fri Feb 03 2017 - 10:10:39 CST)
- Re: High pressure calculations Vermaas, Joshua (Fri Feb 03 2017 - 11:15:04 CST)
- Re: High pressure calculations faride badalkhani (Fri Feb 03 2017 - 13:23:34 CST)
- AW: High pressure calculations Norman Geist (Sat Feb 04 2017 - 05:33:49 CST)
- Re: AW: High pressure calculations Andrey KALINICHEV (Sat Feb 04 2017 - 05:54:36 CST)
- Re: AW: High pressure calculations Francesco Pietra (Sat Feb 04 2017 - 06:00:53 CST)
- Re: AW: High pressure calculations faride badalkhani (Sat Feb 04 2017 - 06:11:52 CST)
- Re: High pressure calculations faride badalkhani (Fri Feb 03 2017 - 13:23:34 CST)
- Re: High pressure calculations Vermaas, Joshua (Fri Feb 03 2017 - 11:15:04 CST)
- Positions for Ph.D. candidates in biomolecular modeling Jan Brezovsky (Thu Feb 02 2017 - 05:30:48 CST)
- namd2.exe has stopped working, NAMD Energy Darya Fadavi (Wed Feb 01 2017 - 12:31:15 CST)
- about colvar module in NAMD Jessen Lucas (Wed Feb 01 2017 - 11:47:41 CST)
- How to calculate the number of solvent molecules for simulations in a specified pressure faride badalkhani (Wed Feb 01 2017 - 04:33:55 CST)
- Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Tue Jan 31 2017 - 00:52:22 CST)
- AW: AW: AW: not a number in NAMD log file Norman Geist (Mon Jan 30 2017 - 01:44:14 CST)
- Protein Penetrating Water Box Oscar Bastidas (Sun Jan 29 2017 - 03:15:25 CST)
- [NAMD] Using as collective variable the minimum of a set of distances The Cromicus Productions (Sat Jan 28 2017 - 17:07:52 CST)
- On-the-fly eABF: Problem with the tcl script. Emmanuel MOUTOUSSAMY (Thu Jan 26 2017 - 06:06:52 CST)
- basis set for QM-MM dft Francesco Pietra (Wed Jan 25 2017 - 09:15:43 CST)
- how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 14:39:12 CST)
- Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 14:50:41 CST)
- Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 15:14:55 CST)
- Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 15:20:38 CST)
- Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 15:44:32 CST)
- Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 16:09:13 CST)
- Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 16:11:17 CST)
- Re: how do I restart umbrella sampling calculations? Vermaas, Joshua (Tue Jan 24 2017 - 16:26:39 CST)
- Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Wed Jan 25 2017 - 09:19:10 CST)
- Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 15:14:55 CST)
- Re: how do I restart umbrella sampling calculations? Vermaas, Joshua (Tue Jan 24 2017 - 14:57:36 CST)
- Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 14:50:41 CST)
- [NAMD] Using ABF to study separation of two molecules The Cromicus Productions (Mon Jan 23 2017 - 01:00:48 CST)
- Slurm Run on supercomputer Marisol Oswald (Sun Jan 22 2017 - 18:21:01 CST)
- minimizing each structure of a DCD file saeed amini (Sun Jan 22 2017 - 07:21:23 CST)
- ABF with alpha colvar? Douglas Houston (Sat Jan 21 2017 - 11:30:49 CST)
- introduction to research on free energies asaffarhi_at_post.tau.ac.il (Fri Jan 20 2017 - 09:34:05 CST)
- Energy Gradient Plotting Zeki Zeybek (Wed Jan 18 2017 - 02:19:03 CST)
- Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 10:16:08 CST)
- dihedral colvar Stefano Guglielmo (Tue Jan 17 2017 - 19:11:09 CST)
- not a number in NAMD log file Mohaddeseh Habibzadeh (Tue Jan 17 2017 - 00:31:55 CST)
- NAMD performance monitor Nikhil Maroli (Tue Jan 17 2017 - 06:42:41 CST)
- QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Mon Jan 16 2017 - 01:55:38 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Mon Jan 16 2017 - 16:17:19 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Tue Jan 17 2017 - 12:10:52 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Tue Jan 17 2017 - 15:58:58 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Thu Jan 19 2017 - 11:56:20 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Fri Jan 20 2017 - 08:33:18 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Tue Jan 17 2017 - 12:10:52 CST)
- Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Mon Jan 16 2017 - 16:17:19 CST)
- Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 10:19:03 CST)
- How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations Jessen Lucas (Thu Jan 12 2017 - 20:09:30 CST)
- Calculating gradient of the potential (force field) on each atom. Wasut Pornpatcharapong (Thu Jan 12 2017 - 17:37:55 CST)
- Colvar distance xy to restrain ions Azadeh Alavizargar (Thu Jan 12 2017 - 02:42:25 CST)
- Re: 2.12, cufft problems on a GTX 1070 ? [SOLVED] Nicholas M. Glykos (Wed Jan 11 2017 - 12:51:54 CST)
- fatal error in running namd/2.12 sunyeping (Wed Jan 11 2017 - 07:46:01 CST)
- Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Tue Jan 10 2017 - 05:09:01 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 06:15:02 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ B.W.J. Irwin (Tue Jan 10 2017 - 09:09:52 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 09:59:35 CST)
- RE: Solvation free energy difference of alchemical transformation of K+ into Na+ Radak, Brian K (Tue Jan 10 2017 - 12:27:07 CST)
- RE: Solvation free energy difference of alchemical transformation of K+ into Na+ Radak, Brian K (Tue Jan 10 2017 - 14:28:57 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Wed Jan 11 2017 - 00:39:11 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Brian Radak (Wed Jan 11 2017 - 10:20:21 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ B.W.J. Irwin (Tue Jan 10 2017 - 09:09:52 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 06:15:02 CST)
- Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Tue Jan 10 2017 - 01:56:35 CST)
- Re: Charm++ fatal error with QM-MM MOPAC Marcelo C. R. Melo (Tue Jan 10 2017 - 08:11:02 CST)
- The reason for the formation of bubbles in heating stage Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 08:16:51 CST)
- not a number error Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 01:53:08 CST)
- Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Mon Jan 09 2017 - 00:09:32 CST)
- How to restart metadynamics in namd Wang, X. Y. (Sun Jan 08 2017 - 22:29:41 CST)
- Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Sun Jan 08 2017 - 22:12:34 CST)
- readable output of gbis.coor hem_chandra_at_iitg.ernet.in (Sat Jan 07 2017 - 00:43:19 CST)
- very small cell 小澤友 (Fri Jan 06 2017 - 20:29:34 CST)
- multiple replicas metadynamics Mihaela Drenscko (Fri Jan 06 2017 - 20:24:46 CST)
- Re: multiple replicas metadynamics Giacomo Fiorin (Sun Jan 08 2017 - 17:37:21 CST)
- Re: multiple replicas metadynamics Mihaela Drenscko (Mon Jan 09 2017 - 16:02:45 CST)
- Regarding: Free energy of alchemical transformation of K + and Na + Amit Kumar (Fri Jan 06 2017 - 05:09:35 CST)
- Constraining bonds that don't include hydrogens Marlon Sidore (Thu Jan 05 2017 - 08:11:06 CST)
- dcd to pdb conversion Srijita Paul (Wed Jan 04 2017 - 06:18:21 CST)
- How to perform REMD of a system a membrane-protein system? Panagiota Kyriakou (Tue Jan 03 2017 - 18:38:54 CST)
- (no subject) Raul Araya (Tue Jan 03 2017 - 14:22:09 CST)
- Running IMD with TMD (domain restraints) Steven Cohen (Mon Jan 02 2017 - 10:43:09 CST)
- Metadynamics simulation Azadeh Alavi (Tue Jan 03 2017 - 09:00:43 CST)
- QM-MM flooding potential Francesco Pietra (Tue Jan 03 2017 - 01:40:20 CST)
- The use of NPT or NVT ensemble to observe dynamical parameters Harish Srinivasan (Mon Jan 02 2017 - 02:27:50 CST)
- (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals Francesco Pietra (Mon Jan 02 2017 - 01:38:54 CST)
- 2.12, cufft problems on a GTX 1070 ? Nicholas M Glykos (Sun Jan 01 2017 - 03:56:32 CST)
Last message date: Mon Dec 31 2018 - 09:42:31 CST
Archived on: Mon Dec 31 2018 - 23:21:37 CST
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