NAMD-L: By Thread
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About this archive
Starting: Mon Jan 02 2006 - 18:54:15 CST
Ending: Thu Dec 27 2007 - 12:55:11 CST
- charmm charge style carlos alberto gueto tettay (Thu Dec 27 2007 - 12:55:00 CST)
- Dihedral energy not getting generated ( is zero ) prateeksha s (Wed Dec 26 2007 - 01:58:15 CST)
- Problems of mpi with namd 2.6 cong chen (Mon Dec 24 2007 - 00:53:25 CST)
- Compiling NAMD on PPC G4 w/Apple's Leopard Joshua Adelman (Sun Dec 23 2007 - 10:31:57 CST)
- (no subject) jfgaff_at_ncsu.edu (Sat Dec 22 2007 - 08:30:16 CST)
- Re: enery evaluation inside Tcl-Forces? harish vashisth (Fri Dec 21 2007 - 16:16:23 CST)
- ligand parameters... I know the next step carlos alberto gueto tettay (Fri Dec 21 2007 - 11:36:53 CST)
- ligands parameters carlos alberto gueto tettay (Fri Dec 21 2007 - 08:42:15 CST)
- Segmentation violation when running without an internet connection jadelman_at_berkeley.edu (Thu Dec 20 2007 - 12:20:51 CST)
- enery evaluation inside Tcl-Forces? harish vashisth (Thu Dec 20 2007 - 10:14:48 CST)
- Re: Creating topology for carbon nanotube / any new structure prateeksha s (Wed Dec 19 2007 - 22:21:44 CST)
- fluorescent probes jayant james (Wed Dec 19 2007 - 20:08:33 CST)
- psfgen for pre-equilibrated membrane bilayer Myunggi Yi (Wed Dec 19 2007 - 18:47:10 CST)
- Tcl-forces query Harish Lnu (Wed Dec 19 2007 - 10:23:01 CST)
- Creating topology for carbon nanotube / any new structure prateeksha s (Tue Dec 18 2007 - 22:41:04 CST)
- Re: ABF: split reaction coordinate in widows Subramanian Vaitheeswaran (Tue Dec 18 2007 - 10:40:39 CST)
- ABF: split reaction coordinate in widows Vlad Cojocaru (Tue Dec 18 2007 - 08:01:55 CST)
- namd-l : Topology info - RESidue information for carbon nanotube prateeksha s (Sat Dec 15 2007 - 07:25:19 CST)
- Topology info - RESidue information for carbon nanotube prateeksha s (Sat Dec 15 2007 - 07:23:08 CST)
- ABF - PMF Calculation Jason O'Young (Fri Dec 14 2007 - 10:00:48 CST)
- add Mg2+ Lixia Jin Day (Thu Dec 13 2007 - 11:30:26 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portlandcompilers Philip Peartree (Wed Dec 12 2007 - 15:35:10 CST)
- Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Mon Dec 10 2007 - 21:18:24 CST)
- re: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Tue Dec 11 2007 - 19:19:02 CST)
- Re: Scripting: Handle for energy terms in the PSF file? Peter Freddolino (Tue Dec 11 2007 - 20:30:22 CST)
- re: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Thu Dec 13 2007 - 13:39:18 CST)
- force field parameters for fullerenes Adam Fraser (Mon Dec 10 2007 - 13:18:16 CST)
- SMD question Qiang Zhong (Sat Dec 08 2007 - 19:26:03 CST)
- Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 09:20:23 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 15:22:14 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 16:54:09 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 17:47:59 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 07:29:01 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 12:52:44 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 16:01:56 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Dow_Hurst (Sat Dec 15 2007 - 21:49:11 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Sat Dec 15 2007 - 22:04:08 CST)
- Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 15:22:14 CST)
- Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 09:20:23 CST)
- nonbonded interactions Xu, Jiancong (Fri Dec 07 2007 - 13:34:46 CST)
- ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 08:55:48 CST)
- MD runs at different clusters Monika Sharma (Fri Dec 07 2007 - 04:04:35 CST)
- force dcd files?? Thomas C. Bishop (Thu Dec 06 2007 - 15:22:49 CST)
- SYSTEM ENERGY MINIMIZATION Samuel Morales (Thu Dec 06 2007 - 12:40:54 CST)
- Simple TCL (Forces) question - defining bond vector Jim Pfaendtner (Thu Dec 06 2007 - 09:33:59 CST)
- SYSTEM ENERGY MINIMIZATION El Escuchado por DIOS (Wed Dec 05 2007 - 15:06:48 CST)
- Generating a gromacs topology file for analyzing NAMD trajectories patrick wintrode (Wed Dec 05 2007 - 14:15:11 CST)
- Re: Generating a gromacs topology file for analyzing NAMD trajectories L. Michel Espinoza-Fonseca (Wed Dec 05 2007 - 14:52:52 CST)
- Re: Generating a gromacs topology file for analyzing NAMD trajectories Giovanni Bellesia (Wed Dec 05 2007 - 15:25:42 CST)
- RE: Generating a gromacs topology file for analyzing NAMD trajectories Xu, Jiancong (Thu Dec 06 2007 - 09:41:22 CST)
- simulation of fullerenes Adam Fraser (Wed Dec 05 2007 - 12:16:39 CST)
- Convergence of ABF calculation: n_samples Subramanian Vaitheeswaran (Wed Dec 05 2007 - 08:39:47 CST)
- DEN residue name in Amber prateeksha s (Wed Dec 05 2007 - 00:10:42 CST)
- Protein hydrogens causing "Atoms too fast" error Christopher Gillespie (Mon Dec 03 2007 - 18:03:59 CST)
- ABF fullsamples Jason O'Young (Mon Dec 03 2007 - 13:18:40 CST)
- different 1-4scaling values for different atom types? cong chen (Sun Dec 02 2007 - 23:51:11 CST)
- ABF Output File Jason Wyonn O'Young (Sun Dec 02 2007 - 12:47:26 CST)
- Re: how to perform MD with two proteins Richard Wood (Sun Dec 02 2007 - 10:00:43 CST)
- how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 09:12:28 CST)
- how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 08:37:18 CST)
- how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 07:35:14 CST)
- Re: tip4p - namd follwup luca (Sat Dec 01 2007 - 03:45:35 CST)
- About para file format cong chen (Sat Dec 01 2007 - 00:14:36 CST)
- Unsubscribe Raja Natesan (Fri Nov 30 2007 - 23:44:12 CST)
- Periodic boundary conditions Gianluca Interlandi (Fri Nov 30 2007 - 19:20:07 CST)
- paratool for MG Tianjiao Wang (Fri Nov 30 2007 - 12:48:05 CST)
- tip4p - namd follwup Bishop, Thomas C (Fri Nov 30 2007 - 10:37:24 CST)
- Parameter or patch for thioester Jianping Lin (Fri Nov 30 2007 - 12:23:52 CST)
- Re: PME on a negatively charged system Hai Long (Fri Nov 30 2007 - 11:09:35 CST)
- SMD ensemble? gian peralta (Thu Nov 29 2007 - 17:49:09 CST)
- Pressure fluctuations Ayþe Özlem Sezerman (Fri Nov 30 2007 - 10:50:32 CST)
- TMD and RMSD constrained dynamcs M. Madhu (Fri Nov 30 2007 - 10:22:48 CST)
- How is the maximum velocity limit set? Yinglong Miao (Fri Nov 30 2007 - 10:22:40 CST)
- Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 09:01:39 CST)
- PME on a negatively charged system. Richard Swenson (Thu Nov 29 2007 - 14:53:18 CST)
- tcl script for applying constraints Pijush Ghosh (Thu Nov 29 2007 - 14:35:13 CST)
- problems replicating a DOPC membrane regafan_at_usc.es (Thu Nov 29 2007 - 12:26:29 CST)
- abf: multiple distance Luca Bellucci (Thu Nov 29 2007 - 04:18:19 CST)
- Re: Parameters for NH3, NH4+, and CO2 Ilya Chorny (Wed Nov 28 2007 - 20:31:09 CST)
- uncharged ends Xavier GALLET (Wed Nov 28 2007 - 09:46:22 CST)
- problem with *.pdb and *.psf jose correa (Wed Nov 28 2007 - 08:16:38 CST)
- Flying ions jia (Tue Nov 27 2007 - 21:00:32 CST)
- REMD Dirar Homouz (Tue Nov 27 2007 - 14:33:46 CST)
- Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 06:07:57 CST)
- Re: SMD Constant Velocity: Force Vamshi Gangupomu (Mon Nov 26 2007 - 09:33:51 CST)
- Avoiding self-interaction with PME. Niels Christensen (Sun Nov 25 2007 - 09:59:57 CST)
- SMD Constant Velocity: Force Vamshi Gangupomu (Sun Nov 25 2007 - 00:33:24 CST)
- replica exchange trajectories Raul Alcantara (Fri Nov 23 2007 - 13:12:48 CST)
- energy per residue Xavier GALLET (Fri Nov 23 2007 - 09:15:49 CST)
- minimization-problem jose correa (Thu Nov 22 2007 - 08:13:51 CST)
- PO3 psf Ahlam Al-Rawi (Wed Nov 21 2007 - 16:06:22 CST)
- ABF : dihedral-com.tcl Subramanian Vaitheeswaran (Wed Nov 21 2007 - 09:59:37 CST)
- SMD behavior Adam Fraser (Wed Nov 21 2007 - 09:47:54 CST)
- Dixitpd wants to Share Favorites with you dixitpd_at_gmail.com (Tue Nov 20 2007 - 22:05:54 CST)
- How to freeze some atoms cong chen (Tue Nov 20 2007 - 20:11:24 CST)
- New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 15:56:20 CST)
- MD of DNA lily jin (Tue Nov 20 2007 - 10:31:39 CST)
- RE: ABF calculations jia (Tue Nov 20 2007 - 09:14:42 CST)
- Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 07:54:29 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 09:14:47 CST)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 10:53:04 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 11:48:58 CST)
- Re: Is there solution to numerical inaccuracy David Hardy (Wed Nov 21 2007 - 09:54:41 CST)
- Re: Is there solution to numerical inaccuracy Himanshu Khandelia (Thu Nov 22 2007 - 02:19:55 CST)
- Re: Is there solution to numerical inaccuracy David Hardy (Thu Nov 22 2007 - 07:35:01 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Thu Nov 22 2007 - 09:15:29 CST)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Mon Nov 26 2007 - 04:54:22 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Nov 26 2007 - 14:08:16 CST)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Thu Nov 29 2007 - 12:04:50 CST)
- Re: Is there solution to numerical inaccuracy Ilya Chorny (Thu Nov 29 2007 - 13:24:50 CST)
- Re: Is there solution to numerical inaccuracy Ilya Chorny (Thu Nov 29 2007 - 13:53:47 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Thu Nov 29 2007 - 13:25:35 CST)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Mon Dec 03 2007 - 12:49:50 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Dec 03 2007 - 17:02:51 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Nov 26 2007 - 14:16:40 CST)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Fri Nov 23 2007 - 12:14:01 CST)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 10:53:04 CST)
- Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 09:14:47 CST)
- About RMSD cong chen (Tue Nov 20 2007 - 03:29:32 CST)
- psfGen error Joseph Heil (Mon Nov 19 2007 - 22:00:57 CST)
- ABF calculations jia (Mon Nov 19 2007 - 14:33:51 CST)
- Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Mon Nov 19 2007 - 10:52:44 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 09:19:33 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 10:10:52 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 11:20:39 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Victor Ovchinnikov (Tue Nov 20 2007 - 11:35:51 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 12:46:10 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 10:10:52 CST)
- Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 09:19:33 CST)
- Does rmsd is the judge of system equilibrium in all conditions? cong chen (Mon Nov 19 2007 - 06:08:12 CST)
- Installing NAMD brmorgan_at_clarku.edu (Fri Nov 16 2007 - 11:28:47 CST)
- ABF or SMD jia (Fri Nov 16 2007 - 11:26:20 CST)
- Fw: What is an IC table in the .inp files char_at_ks.uiuc.edu (Thu Nov 15 2007 - 21:10:29 CST)
- [Fwd: Re: What is an IC table in the .inp files] Victor Ovchinnikov (Thu Nov 15 2007 - 21:00:51 CST)
- What is an IC table in the .inp files Ilya Chorny (Thu Nov 15 2007 - 19:02:07 CST)
- Using NAMD DCD in CHARMM Ahlam Al-Rawi (Thu Nov 15 2007 - 13:38:58 CST)
- question switching function Peter Kiss (Thu Nov 15 2007 - 12:12:08 CST)
- user defined restraint in ABF Vlad Cojocaru (Thu Nov 15 2007 - 10:15:17 CST)
- howcan I use amber forcefield in NAMD? mashaojie163 (Wed Nov 14 2007 - 21:58:39 CST)
- RE: howcan I use amber forcefield in NAMD? Irene Newhouse (Thu Nov 15 2007 - 00:51:41 CST)
- Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 06:23:49 CST)
- RE: howcan I use amber forcefield in NAMD? Huy N. Ha (Thu Nov 15 2007 - 17:24:36 CST)
- Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 20:55:53 CST)
- Re: howcan I use amber forcefield in NAMD? Richard Wood (Thu Nov 15 2007 - 21:33:00 CST)
- RE: howcan I use amber forcefield in NAMD? JC Gumbart (Thu Nov 15 2007 - 22:01:54 CST)
- Re: howcan I use amber forcefield in NAMD? Richard Wood (Thu Nov 15 2007 - 22:32:56 CST)
- Re: howcan I use amber forcefield in NAMD? Floris Buelens (Fri Nov 16 2007 - 05:19:37 CST)
- Re: howcan I use amber forcefield in NAMD? mashaojie163 (Sat Nov 17 2007 - 01:28:51 CST)
- Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 06:23:49 CST)
- RE: howcan I use amber forcefield in NAMD? Irene Newhouse (Thu Nov 15 2007 - 00:51:41 CST)
- Ligand Bound. kparra_at_mail.usf.edu (Wed Nov 14 2007 - 12:30:27 CST)
- OPLS Lipid topology/potenital for NAMD Ilya Chorny (Tue Nov 13 2007 - 16:44:02 CST)
- Replica Exchange NAMD Dirar Homouz (Tue Nov 13 2007 - 12:09:52 CST)
- Problem in Running namd2 Sanjay H A (Tue Nov 13 2007 - 01:23:09 CST)
- loadtotalforces error Pijush Ghosh (Mon Nov 12 2007 - 19:14:25 CST)
- ANN: MDAnalysis 0.3 python library nmichaud_at_jhu.edu (Mon Nov 12 2007 - 16:01:11 CST)
- change center of spherical BC during sim paco ty (Mon Nov 12 2007 - 14:33:34 CST)
- Vega ZZ Script for calculating area/lipid. Ilya Chorny (Mon Nov 12 2007 - 13:15:07 CST)
- DCD trajectories produced by SMD simulation Vlad Cojocaru (Mon Nov 12 2007 - 07:43:55 CST)
- Re: DCD trajectories produced by SMD simulation Peter Freddolino (Mon Nov 12 2007 - 11:32:09 CST)
- Re: DCD trajectories produced by SMD simulation Vlad Cojocaru (Tue Nov 13 2007 - 04:05:14 CST)
- Re: DCD trajectories produced by SMD simulation Peter Freddolino (Thu Nov 15 2007 - 00:17:01 CST)
- Re: DCD trajectories produced by SMD simulation Marcos Sotomayor (Thu Nov 15 2007 - 00:23:02 CST)
- Re: DCD trajectories produced by SMD simulation Vlad Cojocaru (Thu Nov 15 2007 - 07:49:58 CST)
- Re: DCD trajectories produced by SMD simulation Peter Freddolino (Thu Nov 15 2007 - 09:46:47 CST)
- Re: DCD trajectories produced by SMD simulation Vlad Cojocaru (Tue Nov 13 2007 - 04:05:14 CST)
- Re: DCD trajectories produced by SMD simulation Peter Freddolino (Mon Nov 12 2007 - 11:32:09 CST)
- serine phosphorylation modeling Wei Liu (Sat Nov 10 2007 - 11:22:36 CST)
- NAMD Installation Problem Sanjay H A (Fri Nov 09 2007 - 20:11:17 CST)
- NAMD Carbohydrate Simulations Niels Johan Christensen (Fri Nov 09 2007 - 06:39:10 CST)
- about signal 11 received,exiting mashaojie163 (Fri Nov 09 2007 - 10:11:15 CST)
- Question on SMD simulation in spheric water . cgji (Fri Nov 09 2007 - 02:46:03 CST)
- (no subject) cgji (Fri Nov 09 2007 - 02:43:27 CST)
- Getting density of water.. Arun Krishnan (Fri Nov 09 2007 - 01:24:36 CST)
- [Fwd: Re: VMD/psfgen scripting: undefined variable] Victor Ovchinnikov (Fri Nov 09 2007 - 00:33:00 CST)
- VMD/psfgen scripting: undefined variable Richard Baxter (Thu Nov 08 2007 - 22:30:12 CST)
- Re: vmd-l: merging two pdb files Neelanjana Sengupta (Thu Nov 08 2007 - 09:29:54 CST)
- ABF application Vlad Cojocaru (Thu Nov 08 2007 - 08:28:23 CST)
- NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Karol Kaszuba (Thu Nov 08 2007 - 06:00:33 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield JC Gumbart (Fri Nov 09 2007 - 12:05:54 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Himanshu Khandelia (Fri Nov 09 2007 - 13:57:10 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Richard Wood (Fri Nov 09 2007 - 16:31:13 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Richard Wood (Sat Nov 10 2007 - 07:43:09 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield L. Michel Espinoza-Fonseca (Sat Nov 10 2007 - 19:29:31 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Himanshu Khandelia (Sun Nov 11 2007 - 05:04:33 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Jerome Henin (Sun Nov 11 2007 - 14:40:16 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Karol Kaszuba (Mon Nov 12 2007 - 04:57:58 CST)
- Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield JC Gumbart (Fri Nov 09 2007 - 12:05:54 CST)
- saving the coordinates for huge trajectory file ramya narasimhan (Tue Nov 06 2007 - 23:19:50 CST)
- NAMD on Abe Richard Swenson (Tue Nov 06 2007 - 19:17:38 CST)
- Re: problem with NAMD RNA run Samuel Coulbourn Flores (Tue Nov 06 2007 - 18:31:04 CST)
- NAMD on Abe Richard Swenson (Tue Nov 06 2007 - 15:54:05 CST)
- Free energy perturbation of a double mutant jia (Tue Nov 06 2007 - 16:37:35 CST)
- problem with NAMD RNA run Samuel Coulbourn Flores (Tue Nov 06 2007 - 15:11:04 CST)
- Strange termination-possible load ballancing issues Richard Swenson (Tue Nov 06 2007 - 10:13:02 CST)
- (no subject) Demet Akten (Tue Nov 06 2007 - 03:26:52 CST)
- to heat up the system lily jin (Mon Nov 05 2007 - 13:51:39 CST)
- compiling namd2 hazards_at_musc.edu (Mon Nov 05 2007 - 10:18:22 CST)
- The experimental data of POPE? Ming (Mon Nov 05 2007 - 02:55:43 CST)
- Area per lipid. Ming (Mon Nov 05 2007 - 01:02:53 CST)
- Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count Shulin Zhuang (Sun Nov 04 2007 - 21:01:45 CST)
- forces on atom Pijush Ghosh (Sun Nov 04 2007 - 09:22:00 CST)
- Re: charmrun: execve failed to start; intel dual core Redhat Richard Baxter (Sat Nov 03 2007 - 23:24:50 CDT)
- Re: Potential function (force field) in NAMD Rahul Bhowmik (Sat Nov 03 2007 - 10:43:57 CDT)
- length of an ABF simulation Vlad Cojocaru (Sat Nov 03 2007 - 09:41:43 CDT)
- charmrun: execve failed to start; intel dual core Redhat Richard Baxter (Thu Nov 01 2007 - 16:42:55 CDT)
- TMD in NAMD: cannot reach target lily jin (Fri Nov 02 2007 - 10:43:55 CDT)
- residue_rmsd.tcl question Christian Blouin (Fri Nov 02 2007 - 08:12:51 CDT)
- How to evaluate the area per lipid and thickness of a lipid bilayer? Ming (Thu Nov 01 2007 - 22:24:03 CDT)
- POPE/protein simuliation. Ming (Thu Nov 01 2007 - 20:06:37 CDT)
- Will reducing the cell basis vector in X and Y force my lipids to pack Ilya Chorny (Thu Nov 01 2007 - 18:59:42 CDT)
- force constant matrix Ahlam Al-Rawi (Thu Nov 01 2007 - 08:29:23 CDT)
- Membrnae (POPE)/protein simuliation. ÁõÃ÷ (Thu Nov 01 2007 - 07:44:10 CDT)
- TMD in NAMD: cannot reach target lily jin (Thu Nov 01 2007 - 13:13:23 CDT)
- FW: Controlling the area per lipid Richard Swenson (Thu Nov 01 2007 - 11:53:28 CDT)
- heat flux when using langevin dynamics Philipp Schön (Thu Nov 01 2007 - 09:12:56 CDT)
- Light dummy atoms (source code question) Tom Joseph (Wed Oct 31 2007 - 20:58:30 CDT)
- Controlling the area per lipid Ilya Chorny (Wed Oct 31 2007 - 20:23:44 CDT)
- Re: Controlling the area per lipid JC Gumbart (Thu Nov 01 2007 - 00:56:27 CDT)
- Re: Controlling the area per lipid Ilya Chorny (Thu Nov 01 2007 - 01:45:31 CDT)
- Re: Controlling the area per lipid Himanshu Khandelia (Thu Nov 01 2007 - 06:20:10 CDT)
- Re: Controlling the area per lipid Ilya Chorny (Thu Nov 01 2007 - 10:32:50 CDT)
- Potential function (force field) in NAMD rahul.bhowmik_at_ndsu.edu (Fri Nov 02 2007 - 18:49:27 CDT)
- replicating a DOPC membrane regafan_at_usc.es (Fri Nov 23 2007 - 12:30:30 CST)
- Re: Controlling the area per lipid Ilya Chorny (Thu Nov 01 2007 - 01:45:31 CDT)
- Re: Controlling the area per lipid JC Gumbart (Thu Nov 01 2007 - 00:56:27 CDT)
- timestep in TMD lily jin (Wed Oct 31 2007 - 14:02:58 CDT)
- scripting in namd Adam Fraser (Wed Oct 31 2007 - 07:39:36 CDT)
- How can I get parameters of unknown residues dongsheng lei (Wed Oct 31 2007 - 04:26:16 CDT)
- Accepted temperature and pressure oscillation cong chen (Wed Oct 31 2007 - 03:14:55 CDT)
- NAMD to CHARMM unit cell information in DCD François Marchand (Tue Oct 30 2007 - 14:29:41 CDT)
- NAMDEnergy lily jin (Tue Oct 30 2007 - 12:00:57 CDT)
- Replica exchange error message Dirar Homouz (Mon Oct 29 2007 - 19:05:24 CDT)
- apply force along an internally defined direction Vlad Cojocaru (Mon Oct 29 2007 - 07:24:02 CDT)
- looking for paramter snoze pa (Sun Oct 28 2007 - 20:04:31 CDT)
- NAMD cg configuration file Alexe Bojovschi (Sun Oct 28 2007 - 19:02:44 CDT)
- Building Charm .. mpi-linux-amd64-ifort/tmp/traceCore.h .. and .. mpi-linux-amd64-ifort/tmp/MsgPacker.h Graham Jenkins (Sat Oct 27 2007 - 15:56:34 CDT)
- RE: how to restart FEP jia (Fri Oct 26 2007 - 15:29:12 CDT)
- how to restart FEP jia (Fri Oct 26 2007 - 13:50:44 CDT)
- restart a NAMD simulation after coordinate transformation in VMD Vlad Cojocaru (Fri Oct 26 2007 - 04:47:11 CDT)
- Help with TCl script Ilya Chorny (Thu Oct 25 2007 - 23:44:49 CDT)
- NCSA Abe versus TACC Lonestar Gianluca Interlandi (Thu Oct 25 2007 - 19:47:48 CDT)
- abf - zeros as output Per Jr. Greisen (Tue Oct 23 2007 - 12:49:45 CDT)
- printing and global variables within TclBC script Leandro Martínez (Tue Oct 23 2007 - 01:55:23 CDT)
- Errors during equilibration: segmentation fault and bad global exclusion count Ambrish (Tue Oct 23 2007 - 01:45:05 CDT)
- (no subject) ramya narasimhan (Tue Oct 23 2007 - 00:45:16 CDT)
- Applying conformational constraints during simulation poker_at_physics.usyd.edu.au (Mon Oct 22 2007 - 22:08:46 CDT)
- ABF - stretching deca-alanine Per Jr. Greisen (Mon Oct 22 2007 - 06:34:25 CDT)
- How to get around with "atoms moving too fast" Yinglong Miao (Fri Oct 19 2007 - 11:45:50 CDT)
- Re: how to apply different damping coefficients simultaneously to different atoms in the same system. Wang, Boyang (Thu Oct 18 2007 - 22:44:09 CDT)
- how to apply different damping coefficients simultaneously to different atoms in the same system. Wang, Boyang (Thu Oct 18 2007 - 20:25:36 CDT)
- Interrupted system call claudia (Thu Oct 18 2007 - 08:25:22 CDT)
- pmf segname for amber ff. MAIN? George Madalin Giambasu (Thu Oct 18 2007 - 00:51:36 CDT)
- For slowly heating, temperature reassignment or Temperature coupling Shulin Zhuang (Tue Oct 16 2007 - 14:41:41 CDT)
- parameterizing a beta aminocyclohexanecarboxylic acid regafan_at_usc.es (Tue Oct 16 2007 - 05:30:36 CDT)
- Drift in performance Jerome Henin (Mon Oct 15 2007 - 12:02:32 CDT)
- Converting a PSF file from one forcefield top another Ilya Chorny (Sat Oct 13 2007 - 13:14:30 CDT)
- Scaling the Tiny benchmark Dow_Hurst (Sat Oct 13 2007 - 11:20:16 CDT)
- Re: vmd-l: Small molecules Christopher Harrison (Fri Oct 12 2007 - 23:41:23 CDT)
- Membrane Protein Simulation Problems Ilya Chorny (Fri Oct 12 2007 - 22:31:28 CDT)
- Re: Membrane Protein Simulation Problems Richard Law (Sat Oct 13 2007 - 03:05:02 CDT)
- Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 10:07:59 CDT)
- Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 10:13:56 CDT)
- Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 10:36:06 CDT)
- Re: Membrane Protein Simulation Problems L. Michel Espinoza-Fonseca (Sat Oct 13 2007 - 11:01:02 CDT)
- Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 11:17:49 CDT)
- Re: Membrane Protein Simulation Problems L. Michel Espinoza-Fonseca (Sat Oct 13 2007 - 11:41:19 CDT)
- Re: Membrane Protein Simulation Problems Peter Freddolino (Sat Oct 13 2007 - 15:29:19 CDT)
- Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:26:57 CDT)
- Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 11:53:03 CDT)
- Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:57:56 CDT)
- Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 13:51:01 CDT)
- Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:37:09 CDT)
- Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 10:13:56 CDT)
- 2-D periodic boundary condition Rahul Bhownik (Fri Oct 12 2007 - 13:00:09 CDT)
- Large Benchmarks Philip Peartree (Thu Oct 11 2007 - 13:50:39 CDT)
- Multiple constraint file Pijush Ghosh (Wed Oct 10 2007 - 17:13:47 CDT)
- lock / unlock threads paul.dalhaimer_at_yale.edu (Wed Oct 10 2007 - 13:27:47 CDT)
- .xsc file and .restart.xsc file lily jin (Tue Oct 09 2007 - 12:06:22 CDT)
- Howto lengthen a collagen strand (which tool to use) QMarcus_R=F6lz=22?= (Tue Oct 09 2007 - 07:23:03 CDT)
- ptraj Ambrish (Mon Oct 08 2007 - 18:30:59 CDT)
- Molecule drifts and high average RMSD per residue Ambrish (Mon Oct 08 2007 - 11:02:49 CDT)
- Re: Molecule drifts and high average RMSD per residue E. Prabhu Raman (Mon Oct 08 2007 - 14:57:00 CDT)
- Re: Molecule drifts and high average RMSD per residue Ilya Chorny (Mon Oct 08 2007 - 16:17:33 CDT)
- Re: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:45:23 CDT)
- Re: vmd-l: Re: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:51:07 CDT)
- Re: Molecule drifts and high average RMSD per residue Ilya Chorny (Tue Oct 09 2007 - 09:53:50 CDT)
- Re: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:58:06 CDT)
- Re: Molecule drifts and high average RMSD per residue Luis Gracia (Tue Oct 09 2007 - 15:15:08 CDT)
- Re: Molecule drifts and high average RMSD per residue Richard Wood (Mon Oct 08 2007 - 18:01:18 CDT)
- Re: Molecule drifts and high average RMSD per residue Ilya Chorny (Mon Oct 08 2007 - 16:17:33 CDT)
- Re: Molecule drifts and high average RMSD per residue Ambrish (Tue Oct 09 2007 - 15:53:31 CDT)
- Re: Molecule drifts and high average RMSD per residue E. Prabhu Raman (Mon Oct 08 2007 - 14:57:00 CDT)
- Charmm 22 vs Charmm 27 Ilya Chorny (Fri Oct 05 2007 - 14:13:33 CDT)
- C1 splitting documentation Floris Buelens (Fri Oct 05 2007 - 08:10:21 CDT)
- all atom simulations with explicit water molecules and langevin thermostat Margaret S. Cheung (Thu Oct 04 2007 - 16:28:14 CDT)
- Initial and final state fix MD Ugur Akgun (Thu Oct 04 2007 - 16:21:25 CDT)
- solvating long protein Dhiraj Srivastava (Wed Oct 03 2007 - 13:54:47 CDT)
- Free energy Calculations alex digenova bravo (Mon Oct 01 2007 - 17:59:34 CDT)
- Question regarding SETTLE (RigidWater) Siddharth (Mon Oct 01 2007 - 17:02:11 CDT)
- extracting interaction energies Narender Singh Maan (Mon Oct 01 2007 - 15:20:36 CDT)
- Problems with Mutator1.1, mutations and FEP SvenBlumenschein_at_gmx.de (Mon Oct 01 2007 - 08:58:06 CDT)
- ABF parameters Subramanian Vaitheeswaran (Mon Oct 01 2007 - 08:45:12 CDT)
- Binding free energy by LIE Narender Singh Maan (Fri Sep 28 2007 - 14:21:21 CDT)
- Globus-WS Submission of a NAMD Job .. Graham Jenkins (Fri Sep 28 2007 - 02:19:28 CDT)
- restraining backbone atoms san_namd roy (Fri Sep 28 2007 - 00:59:09 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 11:22:57 CDT)
- Re: Determining Transition State from an Unfolding Simulation Christopher Harrison (Thu Sep 27 2007 - 11:45:16 CDT)
- Re: Determining Transition State from an Unfolding Simulation Thomas Gaillard (Thu Sep 27 2007 - 12:29:08 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 13:24:13 CDT)
- Re: Determining Transition State from an Unfolding Simulation Neema Salimi (Thu Sep 27 2007 - 13:22:08 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 14:28:49 CDT)
- Re: Determining Transition State from an Unfolding Simulation Christopher Harrison (Thu Sep 27 2007 - 15:43:54 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 16:34:20 CDT)
- restarting an AMBER simulation (truncated octahedron PBC) in NAMD fails Vlad Cojocaru (Thu Sep 27 2007 - 08:45:34 CDT)
- Determining Transition State from an Unfolding Simulation paco ty (Thu Sep 27 2007 - 04:35:14 CDT)
- for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Shulin Zhuang (Wed Sep 26 2007 - 17:08:20 CDT)
- Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Ilya Chorny (Wed Sep 26 2007 - 18:20:36 CDT)
- Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Victor Ovchinnikov (Thu Sep 27 2007 - 19:11:27 CDT)
- Fwd: Determining Transition State from an Unfolding Simulation Arun Krishnan (Wed Sep 26 2007 - 08:19:13 CDT)
- Meaning of lines in "run" part of log file. Audrey Salazar (Tue Sep 25 2007 - 20:08:31 CDT)
- Re: Meaning of lines in "run" part of log file. Audrey Salazar (Tue Sep 25 2007 - 22:24:48 CDT)
- Re: Meaning of lines in "run" part of log file. Richard Wood (Tue Sep 25 2007 - 22:58:19 CDT)
- Re: Meaning of lines in "run" part of log file. Brian Bennion (Wed Sep 26 2007 - 00:01:53 CDT)
- Re: Meaning of lines in "run" part of log file. Arun Krishnan (Wed Sep 26 2007 - 00:38:00 CDT)
- Re: Meaning of lines in "run" part of log file. Audrey Salazar (Wed Sep 26 2007 - 09:55:42 CDT)
- Re: Meaning of lines in "run" part of log file. Subramanian Vaitheeswaran (Wed Sep 26 2007 - 07:04:26 CDT)
- Re: Meaning of lines in "run" part of log file. Audrey Salazar (Tue Sep 25 2007 - 22:24:48 CDT)
- Determining Transition State from an Unfolding Simulation Arun Krishnan (Sun Sep 23 2007 - 15:57:17 CDT)
- Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Sun Sep 23 2007 - 18:32:34 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Wed Sep 26 2007 - 11:13:40 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Wed Sep 26 2007 - 15:30:58 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Wed Sep 26 2007 - 17:30:51 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 07:34:06 CDT)
- Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 07:24:20 CDT)
- Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Sun Sep 23 2007 - 18:33:44 CDT)
- Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Sun Sep 23 2007 - 21:43:36 CDT)
- Re: Determining Transition State from an Unfolding Simulation Arun Krishnan (Tue Sep 25 2007 - 23:56:52 CDT)
- Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Wed Sep 26 2007 - 08:09:07 CDT)
- Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Wed Sep 26 2007 - 10:44:58 CDT)
- Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Wed Sep 26 2007 - 12:24:03 CDT)
- Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Sun Sep 23 2007 - 21:43:36 CDT)
- Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Sun Sep 23 2007 - 18:32:34 CDT)
- Re: NAMD on dual quad-core Xeon's with Infiniband backbone Dow_Hurst (Sat Sep 22 2007 - 18:28:17 CDT)
- NAMD on dual quad-core Xeon's with Infiniband backbone Carsten Olbrich (Sat Sep 22 2007 - 06:44:29 CDT)
- NAMD on dual quad-core Xeon's with Infiniband backbone Stephen M. Dutz (Fri Sep 21 2007 - 14:02:21 CDT)
- Switching Function Jason O'Young (Thu Sep 20 2007 - 13:00:10 CDT)
- effects of box size Narender Singh Maan (Thu Sep 20 2007 - 10:31:02 CDT)
- How to restart a simulation Audrey Salazar (Thu Sep 20 2007 - 10:25:10 CDT)
- FATAL ERROR: called "save_callback" with too many arguments when running replica exchange Ana Vila Verde (Wed Sep 19 2007 - 11:23:50 CDT)
- psfgen: merging of 2 dna chains Carsten Olbrich (Wed Sep 19 2007 - 08:19:09 CDT)
- ABF question Matthew Davies (Wed Sep 19 2007 - 06:45:05 CDT)
- Charmm to Namd!! priyanka srivastava (Wed Sep 19 2007 - 05:49:22 CDT)
- namdenergy strange behaviour !!! paco ty (Wed Sep 19 2007 - 03:20:44 CDT)
- running_NAMD_on_ALPHA_workstation Karol Kaszuba (Tue Sep 18 2007 - 05:43:58 CDT)
- Performance Problems on Linux Cluster / Bad Scaling QMarcus_R=F6lz=22?= (Tue Sep 18 2007 - 08:17:15 CDT)
- Charmrun and ssh problem Andrea Cristiani (Tue Sep 18 2007 - 04:50:23 CDT)
- Re: Charmm format topology and parameter files for FAD Richard Wood (Mon Sep 17 2007 - 17:30:59 CDT)
- NAD topology and parameter file Dhiraj Srivastava (Mon Sep 17 2007 - 16:30:20 CDT)
- TOTAL energy increase Dirar Homouz (Mon Sep 17 2007 - 15:26:10 CDT)
- Charmm format topology and parameter files for FAD mon_sharma_at_research.iiit.ac.in (Mon Sep 17 2007 - 14:17:26 CDT)
- namdenergy strange behaviour !!! paco ty (Mon Sep 17 2007 - 09:49:33 CDT)
- Question for 2D periodic boundary condition Chin_Wei (Mon Sep 17 2007 - 09:18:13 CDT)
- OPLS force field in namd Adam Fraser (Fri Sep 14 2007 - 17:11:15 CDT)
- protonation of some histidine residues mdametto_at_mail.usf.edu (Fri Sep 14 2007 - 16:05:53 CDT)
- the size of membrane? youbin tu (Fri Sep 14 2007 - 14:02:43 CDT)
- Running Error: The periodicity of dihedral #2 is zero Jianhui Tian (Fri Sep 14 2007 - 11:14:36 CDT)
- Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" maria goranovic (Thu Sep 13 2007 - 05:01:18 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Thu Sep 13 2007 - 07:24:42 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Richard Wood (Thu Sep 13 2007 - 08:00:09 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" maria goranovic (Thu Sep 13 2007 - 08:39:46 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Thu Sep 13 2007 - 11:13:44 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Peter Freddolino (Thu Sep 13 2007 - 20:40:46 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Fri Sep 14 2007 - 04:13:04 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Peter Freddolino (Fri Sep 14 2007 - 07:19:38 CDT)
- Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Thu Sep 13 2007 - 07:24:42 CDT)
- ------------- Processor 0 Exiting: Called CmiAbort ------------ jestin mandumpal (Thu Sep 13 2007 - 02:57:50 CDT)
- NAMD run Ahlam Al-Rawi (Mon Sep 10 2007 - 10:32:56 CDT)
- PMF of SMD using CHARMM generated trajectories Rathinavelan, Thenmalarchelvi (Mon Sep 10 2007 - 12:31:56 CDT)
- STRIDE Algorithm Yu Liu (Mon Sep 10 2007 - 09:22:09 CDT)
- The charged states of histidines in green fluorescent protein. Wang, Boyang (Sun Sep 09 2007 - 19:47:33 CDT)
- Patch needed for tuple is missing Error with POPC bilayer maria goranovic (Sun Sep 09 2007 - 07:37:50 CDT)
- How to load velocities during simulations. Wang, Boyang (Sat Sep 08 2007 - 19:56:55 CDT)
- Potentials of mean force using ABF Subramanian Vaitheeswaran (Sat Sep 08 2007 - 17:06:57 CDT)
- atoms moving fast Xiang Mao (Sat Sep 08 2007 - 08:31:30 CDT)
- Re: RATTLE failure Philip Peartree (Fri Sep 07 2007 - 16:43:57 CDT)
- NAMD on dual quad-core Xeon's with Infiniband backbone Stephen M. Dutz (Fri Sep 07 2007 - 14:32:55 CDT)
- Switching PSF files during a run. Wang, Boyang (Fri Sep 07 2007 - 11:35:35 CDT)
- One question about running NAMD Wang, Boyang (Fri Sep 07 2007 - 09:48:39 CDT)
- Freezing point Dr. Tamal Banerjee (Fri Sep 07 2007 - 08:22:05 CDT)
- Two NICs on each node? paco ty (Fri Sep 07 2007 - 02:55:35 CDT)
- Reason: FATAL ERROR: Simulation config file is not accessible. Dirar Homouz (Thu Sep 06 2007 - 15:51:52 CDT)
- FEP question Matthew WIlce (Thu Sep 06 2007 - 08:32:09 CDT)
- A basic question? Dr. Tamal Banerjee (Thu Sep 06 2007 - 05:33:09 CDT)
- How to access energies after MD step with Tcl ? Arturas Ziemys (Wed Sep 05 2007 - 11:30:31 CDT)
- Temperature dependent unfolding.. Arun Krishnan (Tue Sep 04 2007 - 20:13:35 CDT)
- Re: Temperature dependent unfolding.. Monika Sharma (Wed Sep 05 2007 - 04:00:51 CDT)
- Re: Temperature dependent unfolding.. Fabio Passetti (Wed Sep 05 2007 - 07:41:39 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 08:37:45 CDT)
- Re: Temperature dependent unfolding.. Peter Freddolino (Wed Sep 05 2007 - 09:06:31 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 09:26:26 CDT)
- Re: Temperature dependent unfolding.. Peter Freddolino (Wed Sep 05 2007 - 10:37:32 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 11:02:21 CDT)
- Re: Temperature dependent unfolding.. Peter Freddolino (Wed Sep 05 2007 - 11:32:58 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 11:40:56 CDT)
- Re: Temperature dependent unfolding.. Neema Salimi (Wed Sep 05 2007 - 12:19:13 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 12:21:55 CDT)
- Re: Temperature dependent unfolding.. Neema Salimi (Wed Sep 05 2007 - 12:30:29 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Thu Sep 06 2007 - 20:09:46 CDT)
- Re: Temperature dependent unfolding.. Giovanni Settanni (Thu Sep 06 2007 - 06:34:51 CDT)
- Re: Temperature dependent unfolding.. Neema Salimi (Thu Sep 06 2007 - 12:45:22 CDT)
- Re: Temperature dependent unfolding.. gs_at_mrc-lmb.cam.ac.uk (Thu Sep 06 2007 - 14:21:34 CDT)
- Re: Temperature dependent unfolding.. Giovanni Settanni (Thu Sep 06 2007 - 04:04:46 CDT)
- Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 10:56:56 CDT)
- Re: Temperature dependent unfolding.. Richard Wood (Thu Sep 06 2007 - 15:41:21 CDT)
- Re: Temperature dependent unfolding.. Richard Wood (Thu Sep 06 2007 - 21:55:44 CDT)
- Re: Temperature dependent unfolding.. Richard Wood (Fri Sep 07 2007 - 07:20:40 CDT)
- Re: Temperature dependent unfolding.. Monika Sharma (Wed Sep 05 2007 - 04:00:51 CDT)
- scaling issues in distributed environment Viral D. Tejani (Tue Sep 04 2007 - 15:34:20 CDT)
- transmembrane electrical potential gradient in NAMD maria goranovic (Tue Sep 04 2007 - 11:03:31 CDT)
- question about ACE and NME patch Xiang Mao (Tue Sep 04 2007 - 10:10:30 CDT)
- system density Adam Fraser (Tue Sep 04 2007 - 10:04:40 CDT)
- Best NAMD version for Rocks 4.3 IBM xseries 3665 andrea carotti (Tue Sep 04 2007 - 06:06:32 CDT)
- RATTLE failure Philip Peartree (Tue Sep 04 2007 - 06:54:56 CDT)
- Implicit solvent simulation Cesar Avila (Mon Sep 03 2007 - 08:45:16 CDT)
- question regarding nearest-image resolution in NAMD Vincent Kraeutler (Mon Sep 03 2007 - 03:23:24 CDT)
- calculate interaction energies for a system with amber forcefield Rima Chaudhuri (Sat Sep 01 2007 - 19:15:36 CDT)
- Total external work calculation in SMD-PMF calculation Rathinavelan, Thenmalarchelvi (Sat Sep 01 2007 - 17:53:55 CDT)
- Recommended solvation box size Philip Peartree (Wed Aug 29 2007 - 05:33:36 CDT)
- Compiling NAMD 2.6 from Source: no charm-5.9.tar Audrey Salazar (Tue Aug 28 2007 - 13:42:14 CDT)
- Re: biotin charmm topology/parameters Barry Isralewitz (Tue Aug 28 2007 - 10:00:21 CDT)
- About QM-MM Francesco Pietra (Tue Aug 28 2007 - 08:18:18 CDT)
- Re: About QM-MM Ilya Chorny (Tue Aug 28 2007 - 10:21:24 CDT)
- Re: About QM-MM Christopher Harrison (Tue Aug 28 2007 - 12:42:51 CDT)
- Re: About QM-MM Francesco Pietra (Tue Aug 28 2007 - 15:19:05 CDT)
- Re: About QM-MM Eduardo Tejera (Tue Aug 28 2007 - 18:26:48 CDT)
- Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 01:38:17 CDT)
- Re: About QM-MM Dhiraj Srivastava (Wed Aug 29 2007 - 11:31:00 CDT)
- Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:34:45 CDT)
- Re: About QM-MM Ilya Chorny (Wed Aug 29 2007 - 12:26:19 CDT)
- Re: About QM-MM Dhiraj Srivastava (Wed Aug 29 2007 - 11:45:39 CDT)
- Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:59:28 CDT)
- Re: About QM-MM Dhiraj Srivastava (Wed Aug 29 2007 - 12:05:26 CDT)
- Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:54:12 CDT)
- Re: About QM-MM Francesco Pietra (Tue Aug 28 2007 - 15:19:05 CDT)
- biotin charmm topology/parameters Matthew Wilce (Mon Aug 27 2007 - 18:41:46 CDT)
- Problem en equilibration Protein into a bilayer membrane POPC Gabriel J (Mon Aug 27 2007 - 17:50:49 CDT)
- pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 15:54:40 CDT)
- Building 64-bit NAMD Warner Yuen (Mon Aug 27 2007 - 10:23:58 CDT)
- biotin charmm topology/parameters Matthew Wilce (Mon Aug 27 2007 - 01:48:13 CDT)
- size of water box Mehmet Sen (Fri Aug 24 2007 - 23:47:41 CDT)
- Re: Copper and Zinc: top_all27_prot_lipid.inp Harish Lnu (Fri Aug 24 2007 - 12:22:11 CDT)
- Running thermal unfolding with nose hoover langevin piston Zhang, Wei (Fri Aug 24 2007 - 11:53:25 CDT)
- Copper and Zinc: top_all27_prot_lipid.inp Deepangi Pandit (Fri Aug 24 2007 - 11:51:39 CDT)
- Re: question about equilibration step Audrey Salazar (Fri Aug 24 2007 - 09:04:28 CDT)
- Re: question about equilibration step Peter Freddolino (Fri Aug 24 2007 - 10:09:39 CDT)
- Re: question about equilibration step Richard Wood (Fri Aug 24 2007 - 11:22:01 CDT)
- Re: question about equilibration step Richard Wood (Fri Aug 24 2007 - 11:59:22 CDT)
- Re: question about equilibration step Richard Wood (Fri Aug 24 2007 - 14:45:31 CDT)
- Re: Error bad vdW format in Charmm parameter file Subramanian Vaitheeswaran (Fri Aug 24 2007 - 07:54:41 CDT)
- The algorithm of nose hoover langevin pressure control Zhang, Wei (Thu Aug 23 2007 - 21:47:54 CDT)
- question about equilibration step Audrey Salazar (Thu Aug 23 2007 - 17:33:03 CDT)
- Just can't seem to compile charm++ Dale Marinenko (Thu Aug 23 2007 - 17:01:53 CDT)
- Error bad vdW format in Charmm parameter file shyamala iyer (Thu Aug 23 2007 - 14:09:30 CDT)
- error message Ahlam Al-Rawi (Wed Aug 22 2007 - 19:49:12 CDT)
- How to implement an additional interaction potential? Philipp Schön (Thu Aug 23 2007 - 07:00:12 CDT)
- COM restraint in NAMD Victor Ovchinnikov (Wed Aug 22 2007 - 10:55:56 CDT)
- Re: Charm++ Compilation Dow_Hurst (Wed Aug 22 2007 - 09:58:56 CDT)
- Charm++ Compilation Philip Peartree (Wed Aug 22 2007 - 08:35:00 CDT)
- How to include parameters from stream files in calculations Spiro Pavlopoulos (Tue Aug 21 2007 - 15:02:39 CDT)
- Dihedral Parameterization Venky (Mon Aug 20 2007 - 19:17:28 CDT)
- setting solvent density during solvation Adam Fraser (Mon Aug 20 2007 - 11:23:58 CDT)
- drift in protein membrane simulation. membrane and protein one way, water the other way maria goranovic (Mon Aug 20 2007 - 05:20:06 CDT)
- energy drift in NVE Victor Ovchinnikov (Sun Aug 19 2007 - 15:21:22 CDT)
- binaryoutput option doesn't work for dcd file Devendra (Sat Aug 18 2007 - 09:26:28 CDT)
- Latency vs Bandwidth over Infiniband Dow_Hurst (Fri Aug 17 2007 - 17:37:07 CDT)
- seperate files-par, top and pdb files for solvents, needed? jestin mandumpal (Fri Aug 17 2007 - 04:53:00 CDT)
- Number of atoms to high for mdenergy Marek Dynowski (Thu Aug 16 2007 - 07:41:51 CDT)
- Code question: Partitioning the patch contents into water and non-water Vincent Kraeutler (Fri Aug 17 2007 - 04:01:24 CDT)
- Building NAMD with Myrinet MX Warner Yuen (Wed Aug 15 2007 - 15:59:24 CDT)
- SAMs using NAMD Yu Liu (Wed Aug 15 2007 - 15:17:25 CDT)
- Storing atom coordinates at each time step Audrey Salazar (Wed Aug 15 2007 - 15:03:37 CDT)
- NAMD: Exiting Prematurely Arun Krishnan (Tue Aug 14 2007 - 19:59:54 CDT)
- Re: NAMD: Exiting Prematurely Arun Krishnan (Wed Aug 15 2007 - 00:58:25 CDT)
- new spam filtering Jim Phillips (Tue Aug 14 2007 - 18:07:32 CDT)
- RE: How to use NPT ensemble to fix water density Irene Newhouse (Tue Aug 14 2007 - 14:59:59 CDT)
- water molecules and silicon wall Yu Liu (Tue Aug 14 2007 - 14:53:47 CDT)
- How to use NPT ensemble to fix water density Adam Fraser (Tue Aug 14 2007 - 14:28:18 CDT)
- Don't get mad, get Val1um! Jarred Whitlock (Mon Aug 13 2007 - 22:47:48 CDT)
- Re: Your Pharm4cy 0rder #3728660 Lelia Frost (Mon Aug 13 2007 - 21:57:15 CDT)
- One Year written repl1ca w4tches warranty Simone Darling (Mon Aug 13 2007 - 18:42:22 CDT)
- Very peculiar problem while using bigdcd. Help ! maria goranovic (Mon Aug 13 2007 - 08:47:00 CDT)
- How to avoid => ERROR: Step 100920 cell rescaling factor limited. Philipp Schön (Mon Aug 13 2007 - 07:28:39 CDT)
- Hoe to create psf file of C-terminous of protein? Qiang Zhong (Mon Aug 13 2007 - 06:53:13 CDT)
- FIXED atoms not included as described in the documentation Joshua D. Moore (Mon Aug 13 2007 - 04:49:03 CDT)
- cis/trans prolyl sfrickenhaus (Sat Aug 11 2007 - 03:40:55 CDT)
- Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC) Joshua D. Moore (Sat Aug 11 2007 - 01:33:01 CDT)
- Prescr1ption med1cations... without a prescr1ption! Mercedes Dougherty (Sat Aug 11 2007 - 01:19:45 CDT)
- Famous repl1ca w4tches r0lex Cartier Bvlgari Goldie Huffman (Sat Aug 11 2007 - 01:24:31 CDT)
- CHARMRUN vs MPI Jason O'Young (Fri Aug 10 2007 - 13:14:22 CDT)
- Margin Error Hsing Pao (Fri Aug 10 2007 - 12:43:20 CDT)
- bilayer thickness in simulation of POPC membranes Vlad Cojocaru (Fri Aug 10 2007 - 10:56:41 CDT)
- Minimization using Fixed Atoms Rita Cassia (Fri Aug 10 2007 - 05:16:48 CDT)
- bunch of water molecules sathish kumar gurupatham (Thu Aug 09 2007 - 13:39:51 CDT)
- Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 10:56:33 CDT)
- Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 15:26:21 CDT)
- Re: Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 17:59:26 CDT)
- Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 18:22:18 CDT)
- Re: Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 18:50:06 CDT)
- Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 20:09:29 CDT)
- Re: Multiplicity of Parameters Philip Peartree (Fri Aug 10 2007 - 07:25:33 CDT)
- Re: Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 17:59:26 CDT)
- Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 15:26:21 CDT)
- Storage of large files Monika Sharma (Thu Aug 09 2007 - 01:47:57 CDT)
- Temperature Control: Rescaling and Reassignment Adilah Hussein (Wed Aug 08 2007 - 12:43:00 CDT)
- Temperature Control: Rescaling and Reassignment Adilah Hussien (Wed Aug 08 2007 - 04:52:16 CDT)
- How to construct .prm file of phospho-THR? Qiang Zhong (Tue Aug 07 2007 - 08:55:52 CDT)
- NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error Jim Pfaendtner (Mon Aug 06 2007 - 11:51:41 CDT)
- Finding size of water box Audrey Salazar (Mon Aug 06 2007 - 11:15:41 CDT)
- Building NAMD/CHARM++ Mac OS X Intel Warner Yuen (Mon Aug 06 2007 - 10:52:19 CDT)
- attractive harmonic potential between 2 molecules Adam Fraser (Mon Aug 06 2007 - 10:25:29 CDT)
- Constructing a small molecule Yu Liu (Sun Aug 05 2007 - 20:41:58 CDT)
- Building NAMD 64-bit Mac OSX with GCC Warner Yuen (Sun Aug 05 2007 - 15:17:02 CDT)
- Is very slow heating "bad"? Arun Krishnan (Sat Aug 04 2007 - 01:49:14 CDT)
- no effect on velocity scaling Philipp Schön (Fri Aug 03 2007 - 02:36:19 CDT)
- How to calculate the C alpha RMSD from NAMD trajectory Shulin Zhuang (Fri Aug 03 2007 - 02:31:22 CDT)
- Unfolding protocol.. Arun Krishnan (Fri Aug 03 2007 - 00:58:58 CDT)
- TEMPERATURE and TEMPAVG : nan Andrea Diaz (Thu Aug 02 2007 - 16:58:39 CDT)
- bad global exclusion count error Jim Pfaendtner (Thu Aug 02 2007 - 15:56:18 CDT)
- Steered MD with NAMD? List (Wed Aug 01 2007 - 15:05:48 CDT)
- multiple tcouples? Jonathan Lee (Thu Aug 02 2007 - 13:17:12 CDT)
- job stall w/ incresed cpu usage jfgaff_at_ncsu.edu (Thu Aug 02 2007 - 12:23:36 CDT)
- Re: how to restart/continue NAMD run maruthi_at_imsc.res.in (Thu Aug 02 2007 - 04:05:52 CDT)
- BigDCD Per Jr. Greisen (Thu Aug 02 2007 - 03:40:13 CDT)
- Pairinteractions Ilya Chorny (Wed Aug 01 2007 - 16:43:12 CDT)
- NAMD/Infinipath installations Jason Russler (Wed Aug 01 2007 - 08:54:08 CDT)
- about 'loadforces' command...help! hl332_at_drexel.edu (Tue Jul 31 2007 - 15:00:17 CDT)
- vdW parameter for atom type CN7 in ATP Veronika Brazdova (Tue Jul 31 2007 - 05:55:10 CDT)
- RE: extracting coordinates from dcd file M. Madhu (Mon Jul 30 2007 - 23:31:27 CDT)
- extracting coordinates from dcd file M. Madhu (Mon Jul 30 2007 - 13:50:00 CDT)
- NAMD on dual core, dual processor machine? Brian Genge (Mon Jul 30 2007 - 10:23:31 CDT)
- FATAL ERROR: Unable to open extended system file. Arun Krishnan (Mon Jul 30 2007 - 02:27:49 CDT)
- 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Sun Jul 29 2007 - 22:54:57 CDT)
- Q=D4=D7=C5=D4:__128+_proccessor_jobs_on_64bit_?= Widows hang upon completion of the simulation. Alexandre A. Vakhrouchev (Mon Jul 30 2007 - 04:20:41 CDT)
- Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Eric Bohm (Mon Jul 30 2007 - 08:09:28 CDT)
- Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 10:19:15 CDT)
- Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Eric Bohm (Mon Jul 30 2007 - 10:26:01 CDT)
- Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 10:46:48 CDT)
- Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Eric Bohm (Mon Jul 30 2007 - 11:13:09 CDT)
- Re: Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 16:36:02 CDT)
- Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 10:19:15 CDT)
- *.dcd and *.dcd.BAK Per Jr. Greisen (Sun Jul 29 2007 - 10:08:04 CDT)
- Residue name for Dimethyl sulfoxide jestin mandumpal (Sun Jul 29 2007 - 05:00:46 CDT)
- RE: NAMD crashes on winx64 during parallel run. Ilya Chorny (Sat Jul 28 2007 - 09:52:15 CDT)
- guesscoord fails, hydrogen adding problem, output pdb is all zeros Venky (Sat Jul 28 2007 - 03:45:05 CDT)
- SIDECHAIN _RMSD Karol Kaszuba (Fri Jul 27 2007 - 13:56:22 CDT)
- Downloading CHARMM Parameter and Topology Files Audrey Salazar (Fri Jul 27 2007 - 11:31:54 CDT)
- wrapping Arturas Ziemys (Thu Jul 26 2007 - 10:59:38 CDT)
- pairinteractions dimka (Wed Jul 25 2007 - 17:03:37 CDT)
- Help Needed>Compiling source namd mpi enabled for a linux cluster Daniel.G.Roberts_at_sanofi-aventis.com (Wed Jul 25 2007 - 16:31:35 CDT)
- PDB residue renumbering snoze pa (Wed Jul 25 2007 - 16:29:54 CDT)
- Question regarding NAMD nonbonded routines Vincent Kraeutler (Wed Jul 25 2007 - 11:55:40 CDT)
- Re: Question regarding NAMD nonbonded routines Peter Freddolino (Wed Jul 25 2007 - 20:48:19 CDT)
- Re: Question regarding NAMD nonbonded routines Floris Buelens (Thu Jul 26 2007 - 05:04:55 CDT)
- Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Thu Jul 26 2007 - 12:27:29 CDT)
- Re: Question regarding NAMD nonbonded routines Peter Freddolino (Fri Jul 27 2007 - 11:41:08 CDT)
- Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Fri Jul 27 2007 - 12:57:28 CDT)
- Can NAMD be used as for general Newtonian mechanics simulations? Arneh Babakhani (Fri Jul 27 2007 - 15:21:20 CDT)
- Re: Can NAMD be used as for general Newtonian mechanics simulations? Vincent Kraeutler (Sat Jul 28 2007 - 07:11:27 CDT)
- Re: Question regarding NAMD nonbonded routines Peter Freddolino (Mon Jul 30 2007 - 21:21:01 CDT)
- Re: Question regarding NAMD nonbonded routines Peter Freddolino (Wed Jul 25 2007 - 20:48:19 CDT)
- Can I do ¡°accelerated molecular dynamics¡±in NAMD? Qiang Zhong (Wed Jul 25 2007 - 08:22:49 CDT)
- A serious problem of NAMD output. Wang, Boyang (Tue Jul 24 2007 - 17:35:08 CDT)
- Is it possible to compile NAMD win64 with MPI (windows MPI) Ilya Chorny (Tue Jul 24 2007 - 16:52:09 CDT)
- temperature control for small molecule simulations in vacuum Floris Buelens (Tue Jul 24 2007 - 06:50:01 CDT)
- Net charge of the system is not zero utiramerur_at_ecr6.ohio-state.edu (Mon Jul 23 2007 - 08:28:25 CDT)
- FATAL ERROR: Bad global improper count! andrea carotti (Mon Jul 23 2007 - 03:47:16 CDT)
- Unit cell angles information Andrea Diaz (Sat Jul 21 2007 - 16:46:41 CDT)
- Simulated annealing out of mainstream Francesco Pietra (Sat Jul 21 2007 - 08:18:25 CDT)
- spherical boundary conditions jfgaff_at_ncsu.edu (Fri Jul 20 2007 - 13:03:45 CDT)
- Parameter snoze pa (Fri Jul 20 2007 - 12:03:12 CDT)
- Treatment of a Neutral N-terminus Maria Bagonis (Fri Jul 20 2007 - 11:51:32 CDT)
- Can I use FEP in NAMD for reaction of ATP with Kinase? Qiang Zhong (Fri Jul 20 2007 - 06:46:38 CDT)
- free energy,energy,entropy calculation for pushing ATP to active site of kinase! Qiang Zhong (Fri Jul 20 2007 - 06:40:44 CDT)
- NAMD message snoze pa (Thu Jul 19 2007 - 17:44:48 CDT)
- RE: molecule leaves water box during md Irene Newhouse (Thu Jul 19 2007 - 16:40:36 CDT)
- charmm str file snoze pa (Thu Jul 19 2007 - 15:04:22 CDT)
- molecule leaves water box during md Irene Newhouse (Thu Jul 19 2007 - 13:38:02 CDT)
- ATP molecule snoze pa (Thu Jul 19 2007 - 10:22:43 CDT)
- Re: free energy,energy,entropy calculation for pushing ATP to active site of kinase! Dong Luo (Thu Jul 19 2007 - 09:15:13 CDT)
- free energy,energy,entropy calculation for pushing ATP to active site of kinase! Qiang Zhong (Thu Jul 19 2007 - 06:11:39 CDT)
- CHARMM forcefield is free? wavedalla\_at_libero\.it (Thu Jul 19 2007 - 01:12:35 CDT)
- Restarting calculation missmatches Alexandre A. Vakhrouchev (Thu Jul 19 2007 - 00:59:36 CDT)
- NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 Deepangi Pandit (Wed Jul 18 2007 - 13:39:18 CDT)
- NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 Deepangi Pandit (Wed Jul 18 2007 - 13:20:19 CDT)
- Extended System Conservation jadelman_at_berkeley.edu (Wed Jul 18 2007 - 13:02:31 CDT)
- Vanishing bonds in small molecule during psf generation. Christian Blouin (Wed Jul 18 2007 - 08:58:13 CDT)
- NAMD in Solaris X86 Allen Chen (Tue Jul 17 2007 - 17:01:50 CDT)
- namddat syntax error Sayan Bagchi (Tue Jul 17 2007 - 12:35:47 CDT)
- FW: <no subject> Grabe, Michael David (Mon Jul 16 2007 - 14:49:23 CDT)
- how to kill namd job in TCL FORCES Script? hl332_at_drexel.edu (Mon Jul 16 2007 - 12:22:50 CDT)
- removing waters from big dcd files regafan_at_usc.es (Mon Jul 16 2007 - 11:08:57 CDT)
- How to build the psf file and the parameter file of a ligand taojinwuhan_at_sohu.com (Mon Jul 16 2007 - 03:08:33 CDT)
- SGE and NAMD Kevin Jander (Fri Jul 13 2007 - 14:14:05 CDT)
- water HOH angle of 102 defrees Alessio Alexiadis (Fri Jul 13 2007 - 13:13:23 CDT)
- balck box: what is the coupling constant when using langenvinFile? Philipp Schön (Fri Jul 13 2007 - 06:53:38 CDT)
- eq. info. shivam ghosh (Fri Jul 13 2007 - 00:53:05 CDT)
- Push ATP to active site of kinase! Qiang Zhong (Thu Jul 12 2007 - 22:20:43 CDT)
- tclforces: force not a vector maria goranovic (Thu Jul 12 2007 - 01:53:57 CDT)
- Force field for coarse grained simulations (and other questions) patrick wintrode (Wed Jul 11 2007 - 16:20:20 CDT)
- tracing not available with CMK_OPTIMIZE jfgaff_at_ncsu.edu (Wed Jul 11 2007 - 13:10:08 CDT)
- FATAL ERROR: Tried to find atom type on node other than node 0 Jeffrey J. Potoff (Wed Jul 11 2007 - 11:28:31 CDT)
- TCL: force not a vector Peter Jones (Tue Jul 10 2007 - 21:39:04 CDT)
- UNC Paths in the configuration parameters Ilya Chorny (Tue Jul 10 2007 - 15:46:47 CDT)
- Velocity Units Jason O'Young (Mon Jul 09 2007 - 20:57:18 CDT)
- Problems with using multiple Tclforces scripts sequentially maria goranovic (Tue Jul 10 2007 - 12:46:48 CDT)
- can i somehow use reassigntemp for selected atoms only? Philipp Schön (Tue Jul 10 2007 - 11:06:51 CDT)
- NAMD-lite - Heun's method implementation Nick Schafer (Tue Jul 10 2007 - 11:01:36 CDT)
- rmsd_fullthrotle script problem priti arora (Tue Jul 10 2007 - 07:28:34 CDT)
- Writing to DCD file error - pelase help Istomin, Andrei (Mon Jul 09 2007 - 22:16:54 CDT)
- Hydrogen Atoms and Water Molecules Yu Liu (Mon Jul 09 2007 - 21:21:38 CDT)
- Velocity Units Jason Wyonn O'Young (Mon Jul 09 2007 - 20:58:11 CDT)
- Error compiling NAMD with MPI Kevin Jander (Mon Jul 09 2007 - 16:07:16 CDT)
- Did anybody really use TIP4P? Alessio Alexiadis (Mon Jul 09 2007 - 09:52:47 CDT)
- namd2 installation.. Arun Krishnan (Mon Jul 09 2007 - 01:20:19 CDT)
- Unfolding simulations Arun Krishnan (Mon Jul 09 2007 - 01:18:26 CDT)
- Do we need to renumber atoms after solvate? Arun Krishnan (Sun Jul 08 2007 - 20:31:20 CDT)
- centre of mass fixed Moumita Maiti (Sun Jul 08 2007 - 11:29:50 CDT)
- Re: Charmrun issues and namd on Win 64 Ilya Chorny (Fri Jul 06 2007 - 14:51:50 CDT)
- ABF - changing the reaction coordinate Per Jr. Greisen (Fri Jul 06 2007 - 10:18:00 CDT)
- TIP4P examples Alessio Alexiadis (Fri Jul 06 2007 - 01:31:37 CDT)
- Installing NAMD 2.6 on SMP machine... charm++ install errors Arun Krishnan (Fri Jul 06 2007 - 01:29:25 CDT)
- RATTLE error and GROMACS parameters Jason O'Young (Thu Jul 05 2007 - 11:39:50 CDT)
- TMPyP4 force field parameters Francesco Iori (Thu Jul 05 2007 - 10:21:42 CDT)
- ABF restrain alex digenova bravo (Wed Jul 04 2007 - 15:31:19 CDT)
- problems with mutation in psfgen L. Michel Espinoza-Fonseca (Wed Jul 04 2007 - 15:18:45 CDT)
- SMD of proteins in water box without PBC dora guzman (Wed Jul 04 2007 - 11:56:46 CDT)
- vdw parameter priti arora (Wed Jul 04 2007 - 09:31:25 CDT)
- Building a pdb file Audrey Salazar (Tue Jul 03 2007 - 16:14:41 CDT)
- Count protein solvent HBs? paco ty (Tue Jul 03 2007 - 13:10:51 CDT)
- Re: Compilation on IBM-Power (Linux) Monika Sharma (Tue Jul 03 2007 - 13:00:18 CDT)
- problem with periodic boundaries Philipp Schön (Tue Jul 03 2007 - 10:13:04 CDT)
- mismatch of topology with parameter file Moumita Maiti (Tue Jul 03 2007 - 05:28:30 CDT)
- problem in running equilibration shivam ghosh (Tue Jul 03 2007 - 00:02:53 CDT)
- Charm compile: "xlC: command not found" Jianhui Tian (Mon Jul 02 2007 - 09:55:36 CDT)
- compile NAMD on Intel-64 Wei Liu (Mon Jul 02 2007 - 09:38:31 CDT)
- Compilation on IBM-Power (Linux) Monika Sharma (Mon Jul 02 2007 - 06:10:20 CDT)
- Re: Re: Can NAMD perform random expulsion moleculardynamics(REMD)? Sting (Sat Jun 30 2007 - 21:12:50 CDT)
- Can NAMD perform random expulsion molecular dynamics(REMD)? Sting (Sat Jun 30 2007 - 09:03:02 CDT)
- about normal mode analisys S³awek Or³owski (Fri Jun 29 2007 - 04:00:35 CDT)
- (no subject) mashaojienuaa (Fri Jun 29 2007 - 08:52:35 CDT)
- Re: constructing a topology entry for hexadecane Adam Fraser (Fri Jun 29 2007 - 08:31:57 CDT)
- TIP4P in NAMD? Alessio Alexiadis (Fri Jun 29 2007 - 07:52:57 CDT)
- constructing a topology entry for hexadecane Adam Fraser (Thu Jun 28 2007 - 18:25:27 CDT)
- SPC/E water model Anuradha Mittal (Thu Jun 28 2007 - 09:15:13 CDT)
- tcl forces help hl332_at_drexel.edu (Wed Jun 27 2007 - 14:53:47 CDT)
- finding free energy at a time step using abf rmsmith_at_iastate.edu (Wed Jun 27 2007 - 13:24:47 CDT)
- Re: force on SMD atom Moumita Maiti (Wed Jun 27 2007 - 01:10:06 CDT)
- Re: Diffusion of Protein through the membrane Ilya Chorny (Tue Jun 26 2007 - 22:12:22 CDT)
- Determining Equillibration of a membrane protein Ilya Chorny (Tue Jun 26 2007 - 18:57:32 CDT)
- NNB in PSF and alchemify Luca Bellucci (Tue Jun 26 2007 - 10:27:25 CDT)
- abf "force not a vector" error maria goranovic (Tue Jun 26 2007 - 10:31:58 CDT)
- working with non-protein files Adam Fraser (Mon Jun 25 2007 - 21:57:31 CDT)
- has anyone patched NAG to ASN? Irene Newhouse (Mon Jun 25 2007 - 20:57:03 CDT)
- CellBasisVector jfgaff_at_ncsu.edu (Mon Jun 25 2007 - 19:53:47 CDT)
- barostats in NAMD Audrey Salazar (Mon Jun 25 2007 - 18:41:55 CDT)
- Re: Re£º Re: heat diffusion Jonathan Lee (Mon Jun 25 2007 - 12:38:12 CDT)
- turn off intermolecular interaction milton sonoda (Mon Jun 25 2007 - 11:52:28 CDT)
- PMF, defining end point Per Jr. Greisen (Sun Jun 24 2007 - 10:34:28 CDT)
- problem with ABF "can't read forces(80)" maria goranovic (Sun Jun 24 2007 - 07:30:05 CDT)
- High background load warning message Cesar Luis Avila (Sat Jun 23 2007 - 19:12:32 CDT)
- force on SMD atom Moumita Maiti (Fri Jun 22 2007 - 14:43:27 CDT)
- RE: namddat Irene Newhouse (Fri Jun 22 2007 - 01:29:08 CDT)
- negative force shivam ghosh (Fri Jun 22 2007 - 00:42:24 CDT)
- replies Richard Wood (Thu Jun 21 2007 - 11:11:21 CDT)
- ABF inFiles Subramanian Vaitheeswaran (Thu Jun 21 2007 - 11:03:47 CDT)
- TMD David Wright (Thu Jun 21 2007 - 06:03:07 CDT)
- namddat Irene Newhouse (Thu Jun 21 2007 - 02:01:54 CDT)
- SMD atoms are not moving in accordance with steering parameters! Gungor Ozer (Wed Jun 20 2007 - 22:35:59 CDT)
- heat diffusion Jonathan Lee (Wed Jun 20 2007 - 17:39:22 CDT)
- [Fwd: Re: Using CHARMM27] Victor Ovchinnikov (Wed Jun 20 2007 - 11:49:36 CDT)
- extracting forces from dcd files Todd Trimble (Wed Jun 20 2007 - 12:31:49 CDT)
- namd-l-outgoing2@halifax.ks.uiuc.edu sanghyuk_at_ewha.ac.kr (Wed Jun 20 2007 - 12:03:59 CDT)
- Using CHARMM27 alsalazar_at_northwestern.edu (Wed Jun 20 2007 - 10:27:53 CDT)
- Using CHARMM27 Audrey Salazar (Wed Jun 20 2007 - 09:48:45 CDT)
- Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Tue Jun 19 2007 - 10:59:16 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Thu Jun 21 2007 - 01:33:30 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles Peter Freddolino (Thu Jun 21 2007 - 09:06:00 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Sun Jun 24 2007 - 07:06:32 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles Jerome Henin (Sun Jun 24 2007 - 11:37:53 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Mon Jun 25 2007 - 07:06:28 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles Peter Freddolino (Thu Jun 21 2007 - 09:06:00 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles Subramanian Vaitheeswaran (Thu Jun 21 2007 - 11:29:40 CDT)
- Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Thu Jun 21 2007 - 01:33:30 CDT)
- How could I find which part of the protein became more flexible Yuxiao Wang (Tue Jun 19 2007 - 07:56:23 CDT)
- Error in equlibration Wei Liu (Tue Jun 19 2007 - 06:50:12 CDT)
- About pmf Sting (Mon Jun 18 2007 - 23:00:38 CDT)
- Re: Differences between 32bit and 64bit version of NAMD? Carsten Olbrich (Mon Jun 18 2007 - 13:34:45 CDT)
- Normal mode analysis Raul Araya Secchi (Mon Jun 18 2007 - 13:18:43 CDT)
- Differences between 32bit and 64bit version of NAMD? Carsten Olbrich (Mon Jun 18 2007 - 11:04:30 CDT)
- Temperature Control accomp lin (Mon Jun 18 2007 - 09:31:53 CDT)
- NAMD Parameter File Creation Peter Murphy (Sun Jun 17 2007 - 12:04:51 CDT)
- Re: Re: About smd Sting (Sat Jun 16 2007 - 04:14:57 CDT)
- Error: Compile charm-5.9 on Fedora core 6? Qiang Zhong (Fri Jun 15 2007 - 22:13:19 CDT)
- heat diffusion calculation Jonathan Lee (Fri Jun 15 2007 - 17:40:52 CDT)
- Gas phase minimization Purushottam Dixit (Fri Jun 15 2007 - 16:58:44 CDT)
- charmrun simulations over macpros pedro.borkowski_at_utoronto.ca (Fri Jun 15 2007 - 13:07:02 CDT)
- About smd Sting (Fri Jun 15 2007 - 04:46:54 CDT)
- affecting the atom velocities Philipp Schoen1 (Fri Jun 15 2007 - 02:20:55 CDT)
- About pmf Sting (Thu Jun 14 2007 - 21:49:03 CDT)
- checkpoint / revert Arturas Ziemys (Thu Jun 14 2007 - 13:09:24 CDT)
- help!! shivam ghosh (Thu Jun 14 2007 - 06:43:31 CDT)
- Reassign temperature for selected atoms? Philipp Schoen1 (Thu Jun 14 2007 - 04:03:46 CDT)
- Stationary temperature gradient - defining 2 langevinFiles? Philipp Schoen1 (Wed Jun 13 2007 - 09:50:21 CDT)
- Turning off tcl forces Cesar Luis Avila (Wed Jun 13 2007 - 09:42:28 CDT)
- RE: margin value M. Madhu (Tue Jun 12 2007 - 17:19:26 CDT)
- minLineGoal comannd Raul Araya Secchi (Tue Jun 12 2007 - 16:13:53 CDT)
- (no subject) Raul Araya Secchi (Tue Jun 12 2007 - 16:10:48 CDT)
- FATAL ERROR: Bad global exclusion count Idit Buch (Tue Jun 12 2007 - 09:04:17 CDT)
- CNT modeling Jonathan Lee (Tue Jun 12 2007 - 15:29:49 CDT)
- Nobody will know about your problems. Adam Sosa (Tue Jun 12 2007 - 13:05:30 CDT)
- margin value M. Madhu (Tue Jun 12 2007 - 08:58:11 CDT)
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- Want to be on the top all night long? Michael Rich (Sun Jun 10 2007 - 18:26:46 CDT)
- Orgasm power Kristen Kemp (Sun Jun 10 2007 - 16:20:44 CDT)
- steered md with a constant velocity pulling Moumita Maiti (Sun Jun 10 2007 - 14:45:49 CDT)
- Crazy defoliator Allison Chan (Sun Jun 10 2007 - 14:18:35 CDT)
- Penis Launcher Stephanie Dodson (Sun Jun 10 2007 - 09:49:07 CDT)
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- FYEO Zachary Tyson (Fri Jun 08 2007 - 13:28:09 CDT)
- rmsd calculation for RNA Moumita Maiti (Fri Jun 08 2007 - 11:48:58 CDT)
- Parameter file for Gold ? utiramerur_at_ecr6.ohio-state.edu (Fri Jun 08 2007 - 08:51:36 CDT)
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- Report Richard Justice (Thu Jun 07 2007 - 23:37:01 CDT)
- Straining yourself when you are with a woman? Friedrick Mcdowell (Thu Jun 07 2007 - 17:49:13 CDT)
- problem building Namd frm source... hl332_at_drexel.edu (Thu Jun 07 2007 - 12:32:18 CDT)
- Want to be a hero in bed? Amanda Chase (Thu Jun 07 2007 - 11:46:40 CDT)
- Say "NO" to erectile dysfunction! Amanda Pearson (Thu Jun 07 2007 - 06:48:07 CDT)
- nonbonded interpolation Roy Kimura (Thu Jun 07 2007 - 06:14:57 CDT)
- Tired of your poor health? Steven Bowen (Thu Jun 07 2007 - 00:59:57 CDT)
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- Solvating protein with ions B.R.Silver_at_warwick.ac.uk (Wed Jun 06 2007 - 15:20:43 CDT)
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- To buy or not to buy? Renee Gilmore (Tue Jun 05 2007 - 18:27:11 CDT)
- Error on the constraints Jianping Lin (Tue Jun 05 2007 - 16:27:10 CDT)
- convergence monitoring... Raul Araya Secchi (Tue Jun 05 2007 - 14:52:57 CDT)
- Improve your sexual life and save up to 80% Matthew Hughes (Tue Jun 05 2007 - 12:16:03 CDT)
- Rattle Error Ilya Chorny (Tue Jun 05 2007 - 10:45:33 CDT)
- Water molecules inside protein? hl332_at_drexel.edu (Tue Jun 05 2007 - 10:23:13 CDT)
- Re: Water molecules inside protein? Stephen Hicks (Tue Jun 05 2007 - 21:07:47 CDT)
- Re: Water molecules inside protein? Stephen Hicks (Tue Jun 05 2007 - 11:09:19 CDT)
- TMD: different behaviour between serial and mpi versions Thomas Gaillard (Tue Jun 05 2007 - 09:57:20 CDT)
- Sexual power Teresa Jackson (Tue Jun 05 2007 - 07:33:37 CDT)
- Running NAMD on Cluster machine with Myrinet network with MPI and PBS Alessio Alexiadis (Tue Jun 05 2007 - 05:23:38 CDT)
- Wet miracle Amy Mccormick (Tue Jun 05 2007 - 01:45:44 CDT)
- Want to be a hero in bed? Violet Calderon (Mon Jun 04 2007 - 14:18:55 CDT)
- load balancing question Stern, Julie (Mon Jun 04 2007 - 09:39:21 CDT)
- Report Peter Forbes (Mon Jun 04 2007 - 09:22:19 CDT)
- Hymen destroyer George Benton (Mon Jun 04 2007 - 06:25:11 CDT)
- POPC bilayer- System size Purushottam Dixit (Sun Jun 03 2007 - 17:46:09 CDT)
- NAMD plot plugin Richard Casey (Sun Jun 03 2007 - 10:08:48 CDT)
- combine pdb files Richard Casey (Sun Jun 03 2007 - 07:24:35 CDT)
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- sugar topology files Richard Casey (Sat Jun 02 2007 - 11:02:14 CDT)
- faulty kernel? Brian Bennion (Fri Jun 01 2007 - 10:59:39 CDT)
- Pressure calculation method Alexandre A. Vakhrouchev (Fri Jun 01 2007 - 09:05:46 CDT)
- apply periodic boundary condition in one direction ali alizadeh (Thu May 31 2007 - 07:53:37 CDT)
- clustermatic 4 Peter Jones (Wed May 30 2007 - 21:18:26 CDT)
- surface tension Giovanni Bellesia (Wed May 30 2007 - 19:06:42 CDT)
- Tcl callback, run, revert, measure Xiuping Tao (Wed May 30 2007 - 10:08:55 CDT)
- Replica exchange MD L. Michel Espinoza-Fonseca (Tue May 29 2007 - 12:47:34 CDT)
- temperature and pressure control Alessio Alexiadis (Tue May 29 2007 - 00:40:02 CDT)
- Re: Energy shift during simulation hl332_at_drexel.edu (Mon May 28 2007 - 17:47:44 CDT)
- Energy shift during simulation Cesar Luis Avila (Mon May 28 2007 - 16:21:29 CDT)
- NAMD on Power5 Joachim Hein (Mon May 28 2007 - 11:29:17 CDT)
- constraints on zinc ions Wei Liu (Mon May 28 2007 - 07:42:17 CDT)
- Protein in/out of box Monika Sharma (Mon May 28 2007 - 06:10:43 CDT)
- charm installation problem Govardhan Reddy (Sun May 27 2007 - 16:43:43 CDT)
- how to simulate sugars Richard Casey (Sun May 27 2007 - 12:21:26 CDT)
- About cutoff parameter for real space calculation in PME xiaojing gong (Sun May 27 2007 - 06:47:26 CDT)
- Pressure calculation method Alexandre A. Vakhrouchev (Sat May 26 2007 - 22:42:36 CDT)
- Re: Laptop for Molecular Dynamics - Summary Deepangi Pandit (Fri May 25 2007 - 20:39:45 CDT)
- Running NVT simulations Eric Perim (Fri May 25 2007 - 18:03:48 CDT)
- GPU acceleration press Jim Phillips (Fri May 25 2007 - 14:00:42 CDT)
- heating system baxy (Fri May 25 2007 - 13:06:50 CDT)
- force-field parameters for glycoproteins Gaurav Sharma (Fri May 25 2007 - 13:14:33 CDT)
- Fortran and tclForces Luca Bellucci (Fri May 25 2007 - 03:22:11 CDT)
- Re: UAB BlueGene Thomas Caulfield (Thu May 24 2007 - 15:39:31 CDT)
- Laptop for Molecular Dynamics Deepangi Pandit (Thu May 24 2007 - 13:09:55 CDT)
- help Sathish Kumar Gurupatham (Thu May 24 2007 - 11:31:39 CDT)
- Temperature Coupling Alessio Alexiadis (Thu May 24 2007 - 02:59:31 CDT)
- basic pdb file run with namd and vmd Kayode Karunwi (Wed May 23 2007 - 16:05:01 CDT)
- namd crash: Signal: segmentation violation Leandro Martínez (Wed May 23 2007 - 14:30:05 CDT)
- NAMD on RedHat Linux godawr_at_rpi.edu (Wed May 23 2007 - 10:04:22 CDT)
- How could I fixed the system just in Z-coordinate? ali alizadeh (Wed May 23 2007 - 09:34:32 CDT)
- No effect of periodic boundary conditions? Philipp Schoen1 (Wed May 23 2007 - 09:12:13 CDT)
- Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Wed May 23 2007 - 08:06:04 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Wed May 23 2007 - 11:15:42 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Eric Cyr (Wed May 23 2007 - 13:20:34 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Wed May 23 2007 - 13:32:25 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Gianluca Interlandi (Wed May 23 2007 - 18:05:18 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Thu May 24 2007 - 08:46:59 CDT)
- RE: Why is SHAKE not being used in typical NAMD simulations ? Ana Celia Araujo Vila Verde (Thu May 24 2007 - 10:42:30 CDT)
- RE: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Fri May 25 2007 - 04:05:26 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Peter Freddolino (Fri May 25 2007 - 09:52:47 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Fri May 25 2007 - 10:07:55 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Gianluca Interlandi (Sat May 26 2007 - 00:16:30 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Gianluca Interlandi (Sat May 26 2007 - 01:03:25 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Sat May 26 2007 - 05:44:38 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Peter Freddolino (Sat May 26 2007 - 11:10:34 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Sun May 27 2007 - 05:53:31 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Peter Freddolino (Sun May 27 2007 - 12:01:30 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Sun May 27 2007 - 12:49:54 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Wed May 23 2007 - 13:30:11 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? Eric Cyr (Wed May 23 2007 - 13:20:34 CDT)
- Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Wed May 23 2007 - 11:15:42 CDT)
- FullSamples variable in ABF alex digenova bravo (Tue May 22 2007 - 23:50:36 CDT)
- load balance strategy query hl332_at_drexel.edu (Mon May 21 2007 - 11:49:22 CDT)
- Can´t use charmm to perform dcd analysis Victor Capistrán (Sun May 20 2007 - 22:56:18 CDT)
- problems compiling NAMD on SCALI architecture satya work (Sun May 20 2007 - 05:56:54 CDT)
- Overlaoded processors when running NAMD on NCSA Altix Gianluca Interlandi (Sat May 19 2007 - 20:06:08 CDT)
- OPLS dihedrals Arturas Ziemys (Sat May 19 2007 - 10:47:16 CDT)
- NAMD question Cheri McFerrin (Sat May 19 2007 - 08:11:57 CDT)
- q=D8=B8=B4=A3=BA=20Re:=20=BB=D8=B8=B4=A3=BA=20Re:=20?= qHow=20to=20compile=20NAMD2.6=20on=20core2=20operons,=20x86=5F?= 64-redhat-linux,which is the proper choice in Arch .?= xiaojing gong (Fri May 18 2007 - 19:28:14 CDT)
- namd.conf with OPLS options Alexis Salas (Fri May 18 2007 - 17:43:52 CDT)
- improper torsion Hidekazu WATANABE (Fri May 18 2007 - 04:56:37 CDT)
- pdb file Sathish Kumar Gurupatham (Thu May 17 2007 - 15:32:58 CDT)
- Re: namd crash: Signal: segmentation violation Brian Bennion (Thu May 17 2007 - 15:25:48 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Thu May 17 2007 - 15:39:56 CDT)
- Re: namd crash: Signal: segmentation violation Brian Bennion (Thu May 17 2007 - 17:06:15 CDT)
- Re: namd crash: Signal: segmentation violation Brian Bennion (Fri May 18 2007 - 10:25:46 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 12:41:24 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 13:53:15 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 14:49:06 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 15:13:00 CDT)
- Re: namd crash: Signal: segmentation violation Gengbin Zheng (Fri May 18 2007 - 15:30:34 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 12:41:24 CDT)
- Re: namd crash: Signal: segmentation violation Brian Bennion (Fri May 18 2007 - 15:43:20 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 16:19:33 CDT)
- Re: namd crash: Signal: segmentation violation Gengbin Zheng (Fri May 18 2007 - 16:28:54 CDT)
- Re: namd crash: Signal: segmentation violation Brian Bennion (Tue May 22 2007 - 10:53:59 CDT)
- Re: namd crash: Signal: segmentation violation Brian Bennion (Tue May 22 2007 - 14:39:43 CDT)
- Re: namd crash: Signal: segmentation violation Leandro Martínez (Wed May 23 2007 - 13:00:28 CDT)
- namd crash: Signal: segmentation violation Leandro Martínez (Thu May 17 2007 - 13:34:43 CDT)
- Re: Sulphate Ion Parameters (fwd) Parminder Mankoo (Thu May 17 2007 - 10:00:18 CDT)
- double precision numerical accuracy issue Himanshu Khandelia (Thu May 17 2007 - 08:51:36 CDT)
- Re: Sulphate Ion Parameters Arturas Ziemys (Thu May 17 2007 - 08:42:09 CDT)
- Sulphate Ion Parameters Maria Bagonis (Thu May 17 2007 - 07:47:38 CDT)
- problems compiling NAMD on SCALI architecture satya work (Thu May 17 2007 - 05:49:58 CDT)
- System charge Ayþe Özlem Sezerman (Thu May 17 2007 - 04:02:50 CDT)
- Tcl in NAMD (math::interpolate) Chi-Cheng Chiu (Wed May 16 2007 - 13:03:03 CDT)
- How to unsubscribe ? Viswanadham Sridhara (Wed May 16 2007 - 12:30:38 CDT)
- Minimization Rita Cassia (Wed May 16 2007 - 12:19:51 CDT)
- Conversion of .dcd into .xtc format priti arora (Wed May 16 2007 - 07:03:11 CDT)
- Specified Electric Field accomp lin (Wed May 16 2007 - 06:41:22 CDT)
- compiling namd intel 9.1 Alberto Santana (Wed May 16 2007 - 06:06:35 CDT)
- How to link two proteins olivier walker (Wed May 16 2007 - 02:50:00 CDT)
- q=D8=B8=B4=A3=BA=20Re:=20=20How=20to=20compile=20NAMD?= 2.6 on core2 operons, x86_64-redhat-linux,which isqthe=20proper=20choice=20in=20Arch.?= xiaojing gong (Wed May 16 2007 - 01:42:59 CDT)
- User defined potentials of Lennard-Jones type possible? Philipp Schoen1 (Tue May 15 2007 - 09:23:51 CDT)
- how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Tue May 15 2007 - 09:21:33 CDT)
- How to compile NAMD2.6 on core2 operons, x86_64-redhat-linux,which is the proper choice in Arch. xiaojing gong (Mon May 14 2007 - 21:41:43 CDT)
- simulation problems baxy (Mon May 14 2007 - 16:42:44 CDT)
- Deformations under constant strain rates Andrea Diaz (Mon May 14 2007 - 12:28:18 CDT)
- DPMTA instead of PME without PBC possible? Philipp Schoen1 (Mon May 14 2007 - 07:15:52 CDT)
- TCL script for umbrella sampling arijit_r_at_chem.iitkgp.ernet.in (Mon May 14 2007 - 05:07:01 CDT)
- how to caculate the hydrogen bonds occupancy? lnubiofox (Sun May 13 2007 - 09:36:35 CDT)
- recalculating energies dimka (Fri May 11 2007 - 12:19:27 CDT)
- Fast routines for distance evaluations using PBC. Arturas Ziemys (Fri May 11 2007 - 11:52:49 CDT)
- about PMF and MCTI Luca Bellucci (Fri May 11 2007 - 09:02:33 CDT)
- Zn parameters Fabio Passetti (Fri May 11 2007 - 08:17:31 CDT)
- files for air SMAHANE CHALABI (Fri May 11 2007 - 04:01:27 CDT)
- water models: a basic question Alessio Alexiadis (Thu May 10 2007 - 06:31:26 CDT)
- fixed system just in Z direction ali alizadeh (Thu May 10 2007 - 03:36:04 CDT)
- Question about ABF German Saavedra (Wed May 09 2007 - 19:09:45 CDT)
- Re: query about wrapped coordinates: Problem SOLVED hl332_at_drexel.edu (Wed May 09 2007 - 09:22:29 CDT)
- "Timeout waiting for node-program to connect" error, only sometimes Himanshu Khandelia (Wed May 09 2007 - 02:58:29 CDT)
- first aid Francesco Pietra (Tue May 08 2007 - 16:46:29 CDT)
- my simulation dont be minimized when I fixed the channel ali alizadeh (Tue May 08 2007 - 09:48:35 CDT)
- Harmonic dihedral restraints Christopher Rowley (Mon May 07 2007 - 16:57:08 CDT)
- Simulating air with NAMD Lechuga, Javier (Sun May 06 2007 - 10:05:04 CDT)
- Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 12:11:51 CDT)
- RE: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 14:37:03 CDT)
- Re: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 19:09:03 CDT)
- Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 20:18:57 CDT)
- Re: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 21:14:56 CDT)
- Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 21:20:14 CDT)
- Re: Simulating air with NAMD Jeffrey J. Potoff (Sun May 06 2007 - 21:38:35 CDT)
- Re: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 19:09:03 CDT)
- Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 14:54:20 CDT)
- Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 17:53:42 CDT)
- Re: query about wrapped coordinates hl332_at_drexel.edu (Mon May 07 2007 - 16:09:07 CDT)
- Re: query about wrapped coordinates hl332_at_drexel.edu (Mon May 07 2007 - 19:05:40 CDT)
- Re: query about wrapped coordinates hl332_at_drexel.edu (Tue May 08 2007 - 13:15:34 CDT)
- query about wrapped coordinates hl332_at_drexel.edu (Fri May 04 2007 - 13:00:07 CDT)
- Timestep Mustapha Hamdi (Fri May 04 2007 - 12:48:18 CDT)
- Help RICARDO VAZQUEZ (Thu May 03 2007 - 18:26:06 CDT)
- error messages in log file Stern, Julie (Fri May 04 2007 - 10:41:14 CDT)
- Regarding Trajectory analysis priti arora (Fri May 04 2007 - 09:45:14 CDT)
- Problems with version 2.6 for amd64 Carsten Olbrich (Fri May 04 2007 - 03:37:08 CDT)
- System Charge alex digenova bravo (Thu May 03 2007 - 18:26:39 CDT)
- water and air box by VMD SMAHANE CHALABI (Thu May 03 2007 - 02:36:36 CDT)
- "RESTARTING CONJUGATE GRADIENT ALGORITHM" Ugur Akgun (Wed May 02 2007 - 11:14:10 CDT)
- abrupt deviation in rmsd values Monika Sharma (Wed May 02 2007 - 10:35:38 CDT)
- Re: dcd binary file format Jeffrey A Tibbitt (Tue May 01 2007 - 16:57:47 CDT)
- dcd binary file format Jianhui Tian (Tue May 01 2007 - 14:41:53 CDT)
- Parameterizing ligands with protein Lakshmi Dharmarajan (Tue May 01 2007 - 00:17:37 CDT)
- Calculating macroscopic properties poker_at_physics.usyd.edu.au (Mon Apr 30 2007 - 21:38:37 CDT)
- Re: Calculating macroscopic properties Mark Abraham (Mon Apr 30 2007 - 21:51:49 CDT)
- RE: Calculating macroscopic properties JC Gumbart (Tue May 01 2007 - 01:13:35 CDT)
- Re: Calculating macroscopic properties Marcos Sotomayor (Tue May 01 2007 - 11:49:44 CDT)
- Re: Calculating macroscopic properties poker_at_physics.usyd.edu.au (Wed May 02 2007 - 22:00:28 CDT)
- dcd trajectory format Jianhui Tian (Mon Apr 30 2007 - 11:26:31 CDT)
- NAMD on CELL BE Alexandre A. Vakhrouchev (Fri Apr 27 2007 - 09:52:50 CDT)
- Amber PARM Input File Example? Huy N. Ha (Fri Apr 27 2007 - 00:51:37 CDT)
- Polarizable force fields dtmirij (Fri Apr 27 2007 - 00:44:13 CDT)
- Troubles with Free Energy of Conformation Change Masya Mix (Thu Apr 26 2007 - 14:23:13 CDT)
- Fep questions about FepEquilSteps alex digenova bravo (Wed Apr 25 2007 - 14:50:43 CDT)
- PBC related query hl332_at_drexel.edu (Wed Apr 25 2007 - 09:49:09 CDT)
- a topology file in VMD SMAHANE CHALABI (Wed Apr 25 2007 - 02:57:42 CDT)
- Problem for to use/compile NAMD with mpiexec Nicolas Sapay (Tue Apr 24 2007 - 17:20:52 CDT)
- a topology file in VMD SMAHANE CHALABI (Tue Apr 24 2007 - 10:28:07 CDT)
- COntraints for lipid bilayer simulation priti arora (Tue Apr 24 2007 - 05:56:12 CDT)
- errors in energy minimization Wei Liu (Tue Apr 24 2007 - 05:27:52 CDT)
- units of OutputMomenta Stern, Julie (Mon Apr 23 2007 - 12:28:09 CDT)
- topology file SMAHANE CHALABI (Mon Apr 23 2007 - 08:40:54 CDT)
- Run NAMD in loops Neelanjana Sengupta (Sun Apr 22 2007 - 05:36:33 CDT)
- segmentation fault: Please Help hl332_at_drexel.edu (Fri Apr 20 2007 - 11:22:09 CDT)
- Periodic Run Crash hl332_at_drexel.edu (Fri Apr 20 2007 - 09:37:39 CDT)
- Re: namd: DSPC and DAPC for a phospholipid bilayer SMAHANE CHALABI (Fri Apr 20 2007 - 09:10:28 CDT)
- abf output Christine Horejs (Fri Apr 20 2007 - 07:19:12 CDT)
- namd: DSPC and DAPC for a phospholipid bilayer SMAHANE CHALABI (Fri Apr 20 2007 - 04:55:21 CDT)
- PMF Christine Horejs (Fri Apr 20 2007 - 03:59:11 CDT)
- Charges in NAMD topology file Jawahar Neelankatan (Thu Apr 19 2007 - 16:51:08 CDT)
- Membrame Volume Increasing after restart Vamshi Gangupomu (Thu Apr 19 2007 - 13:24:24 CDT)
- Announcement: QM/MM Workshop Jerome Henin (Thu Apr 19 2007 - 13:13:36 CDT)
- general question on protein-membrane simulations -complete message! L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 11:38:10 CDT)
- general question on protein-membrane simulations L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 11:26:46 CDT)
- pure TIP5P water system with AMBER7 parameters satya work (Wed Apr 18 2007 - 11:23:26 CDT)
- question on heating L. Michel Espinoza-Fonseca (Tue Apr 17 2007 - 15:59:12 CDT)
- hexagonal box dimka (Tue Apr 17 2007 - 12:11:09 CDT)
- pmf calculation Christine Horejs (Tue Apr 17 2007 - 08:20:41 CDT)
- 2 proteins Christine Horejs (Tue Apr 17 2007 - 04:59:11 CDT)
- different results for parallel vs serial runs for NAMD Yousung Jung (Mon Apr 16 2007 - 23:04:56 CDT)
- cubic periodic boundary box: what happen if I use a rectangular box? Margaret S. Cheung (Mon Apr 16 2007 - 14:43:13 CDT)
- How to make alkaline ph pgn file ravi sharma (Mon Apr 16 2007 - 14:11:47 CDT)
- total force on atom Todd Trimble (Mon Apr 16 2007 - 14:59:13 CDT)
- TMD constrained energy M. Madhu (Mon Apr 16 2007 - 11:31:11 CDT)
- how to kill namd2 child process after power cut Philipp Schoen1 (Fri Apr 13 2007 - 03:16:59 CDT)
- infinite layer Nicolas Belloy (Thu Apr 12 2007 - 11:59:26 CDT)
- which charm paco ty (Thu Apr 12 2007 - 10:41:48 CDT)
- namd seg fault on Intel cluster Smith, Ian (Thu Apr 12 2007 - 10:20:40 CDT)
- returning the host list where NAMD runs from an LSF batch system Vlad Cojocaru (Thu Apr 12 2007 - 09:16:41 CDT)
- compiling NAMD on an elan-linux-ia64 arch Vlad Cojocaru (Thu Apr 12 2007 - 04:51:41 CDT)
- How to define a spatial grid for a temperature landscape/contour Philipp Schoen1 (Thu Apr 12 2007 - 04:36:31 CDT)
- RATTLE algorithm error Marcelo Puiatti (Wed Apr 11 2007 - 09:46:38 CDT)
- "binaryoutput no" doesn't work Philipp Schoen1 (Wed Apr 11 2007 - 05:55:02 CDT)
- Minimizer Ayþe Özlem Sezerman (Wed Apr 11 2007 - 05:38:48 CDT)
- problem about pairlistdistance... hl332_at_drexel.edu (Tue Apr 10 2007 - 11:24:15 CDT)
- zCoord-1atom German Saavedra (Tue Apr 10 2007 - 11:24:05 CDT)
- How to build charm++ on core2 processor xiaojing gong (Tue Apr 10 2007 - 07:12:40 CDT)
- help! How to build charm++ on core 2 computer processor xiaojing gong (Tue Apr 10 2007 - 06:29:09 CDT)
- warning about pairlistdist: hl332_at_drexel.edu (Mon Apr 09 2007 - 23:35:22 CDT)
- unsubscribe Xiongce Zhao (Mon Apr 09 2007 - 09:29:55 CDT)
- I'm sorry ... please ignore the junk !! Vlad Cojocaru (Mon Apr 09 2007 - 05:50:54 CDT)
- Vlad has Tagged you! :) Vlad Cojocaru (Mon Apr 09 2007 - 05:06:40 CDT)
- namd 2.6 installation on i686 problems Stern, Julie (Sun Apr 08 2007 - 15:30:00 CDT)
- wrong velocity in steered molecular dynamics Ana Celia Araujo Vila Verde (Sat Apr 07 2007 - 14:29:18 CDT)
- equilibration of "big" membrane L. Michel Espinoza-Fonseca (Sat Apr 07 2007 - 13:49:05 CDT)
- can someone comment? hl332_at_drexel.edu (Fri Apr 06 2007 - 22:17:32 CDT)
- Pressure fluctuations Cyril Falvo (Thu Apr 05 2007 - 14:30:13 CDT)
- error on running NAMD on a large cluster with prun Vlad Cojocaru (Thu Apr 05 2007 - 04:14:33 CDT)
- NAMD 2.6 installation problem Stern, Julie (Wed Apr 04 2007 - 15:06:50 CDT)
- Translation to NAMD psf file. Hidekazu WATANABE (Wed Apr 04 2007 - 08:17:05 CDT)
- Atoms mooving too fast ... still the problem Andrea Diaz (Tue Apr 03 2007 - 19:51:39 CDT)
- RE:Re: Help !!! ERROR: Atoms mooving too fast Andrea Diaz (Tue Apr 03 2007 - 14:46:36 CDT)
- read dcd binary trajectory milton sonoda (Mon Apr 02 2007 - 14:25:03 CDT)
- membrane simulation: pressure control parameters Vlad Cojocaru (Mon Apr 02 2007 - 06:55:10 CDT)
- Creating PDB from PSF and COOR files Vamshi Gangupomu (Fri Mar 30 2007 - 16:08:16 CDT)
- MM works MD does not in Fixed system Pedro Borkowski (Fri Mar 30 2007 - 15:45:42 CDT)
- Problem about momentum correction hl332_at_drexel.edu (Fri Mar 30 2007 - 12:11:59 CDT)
- How can I use TIP4-P water model with NAMD? Nils Zimmermann (Fri Mar 30 2007 - 04:29:01 CDT)
- Coarse-grained Modeling/User defined FF Joshua Adelman (Thu Mar 29 2007 - 13:13:17 CDT)
- It doesn't work with using amber files. Hidekazu WATANABE (Thu Mar 29 2007 - 07:09:25 CDT)
- libstdc++.so.5 Stern, Julie (Wed Mar 28 2007 - 18:15:13 CDT)
- unsubscribe Xiongce Zhao (Wed Mar 28 2007 - 16:07:17 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 12:40:23 CDT)
- Re: Pressure Discrepancy Marcos Sotomayor (Wed Mar 28 2007 - 13:16:47 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 15:00:51 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 15:50:13 CDT)
- Re: Pressure Discrepancy Richard Wood (Wed Mar 28 2007 - 18:23:22 CDT)
- Re: Pressure Discrepancy Sterling Paramore (Wed Mar 28 2007 - 22:19:36 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Thu Mar 29 2007 - 13:18:06 CDT)
- Re: Pressure Discrepancy Sterling Paramore (Thu Mar 29 2007 - 13:39:15 CDT)
- Re: Pressure Discrepancy Peter Freddolino (Thu Mar 29 2007 - 13:41:29 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Thu Mar 29 2007 - 16:29:04 CDT)
- Re: Pressure Discrepancy Peter Freddolino (Thu Mar 29 2007 - 16:52:02 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Thu Mar 29 2007 - 17:00:14 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Tue Apr 03 2007 - 11:39:08 CDT)
- Re: Pressure Discrepancy Sterling Paramore (Tue Apr 03 2007 - 20:44:36 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Thu Apr 19 2007 - 16:05:05 CDT)
- Re: Pressure Discrepancy Sterling Paramore (Thu Apr 19 2007 - 22:16:04 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 10:56:07 CDT)
- Re: Pressure Discrepancy Sterling Paramore (Fri Apr 20 2007 - 11:18:39 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 12:30:37 CDT)
- Re: Pressure Discrepancy Peter Freddolino (Wed Mar 28 2007 - 23:07:44 CDT)
- Re: Pressure Discrepancy Sterling Paramore (Wed Mar 28 2007 - 22:19:36 CDT)
- Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 20:47:16 CDT)
- Re: Pressure Discrepancy Richard Wood (Wed Mar 28 2007 - 22:33:48 CDT)
- Re: Pressure Discrepancy Richard Wood (Thu Mar 29 2007 - 17:38:49 CDT)
- Re: Pressure Discrepancy Richard Wood (Thu Mar 29 2007 - 17:44:41 CDT)
- Re: Pressure Discrepancy Richard Wood (Fri Apr 20 2007 - 06:01:44 CDT)
- Re: Pressure Discrepancy Richard Wood (Fri Apr 20 2007 - 15:23:18 CDT)
- NAMD2.6 requirments on p690 Dong Luo (Wed Mar 28 2007 - 10:47:11 CDT)
- dcd file produced with NAMD can be used with AMBER? Rita Cassia (Wed Mar 28 2007 - 04:11:56 CDT)
- RE: Difficulties is minimizing capped peptides - solution kate.nairn_at_csiro.au (Tue Mar 27 2007 - 19:59:03 CDT)
- Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:21:05 CDT)
- Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:17:29 CDT)
- multiple time stepping in namd: Query hl332_at_drexel.edu (Tue Mar 27 2007 - 14:54:33 CDT)
- Pressure Discrepancy Morad Alawneh (Tue Mar 27 2007 - 13:23:42 CDT)
- unsubscribe vmd-l Narender Singh Maan (Tue Mar 27 2007 - 11:39:36 CDT)
- NAMD fails with LAM (can't run example) Smith, Ian (Tue Mar 27 2007 - 10:13:54 CDT)
- How to use the transformation matrix in VMD to obtain the tetramer xiaojing gong (Tue Mar 27 2007 - 07:22:47 CDT)
- charmrun + NAMD on dual quad-core intel procs Ravinder Abrol (Mon Mar 26 2007 - 15:39:09 CDT)
- the relationship between system size and cpu numbers Dong Luo (Tue Mar 27 2007 - 10:28:54 CDT)
- ERROR: Number of pdb and psf atoms are not the same! Arturas Ziemys (Mon Mar 26 2007 - 14:08:36 CDT)
- Periodic Boundary Conditions Per Jr. Greisen (Mon Mar 26 2007 - 02:26:19 CDT)
- protein/lipid simulation Stephen M. Dutz (Sun Mar 25 2007 - 20:41:23 CDT)
- viarecv.c rhandle->len' failed. on infiniband Rene Salmon (Fri Mar 23 2007 - 17:44:59 CDT)
- How to "twist" a molecule? (resubmit) Margaret S. Cheung (Fri Mar 23 2007 - 11:05:16 CDT)
- Re: How to "twist" a molecule? (resubmit) JC Gumbart (Sun Mar 25 2007 - 00:33:00 CDT)
- Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Mar 26 2007 - 08:51:16 CDT)
- Re: How to "twist" a molecule? (resubmit) Grzegorz Jezierski (Mon Mar 26 2007 - 04:46:53 CDT)
- Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Mar 26 2007 - 08:49:42 CDT)
- Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Mar 26 2007 - 14:09:33 CDT)
- Re: How to "twist" a molecule? (resubmit) Grzegorz Jezierski (Wed Mar 28 2007 - 04:56:42 CDT)
- Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Jun 11 2007 - 17:49:57 CDT)
- Re: How to "twist" a molecule? (resubmit) Victor Ovchinnikov (Mon Jun 11 2007 - 20:21:35 CDT)
- Re: How to "twist" a molecule? (resubmit) Margaret.Cheung_at_mail.uh.edu (Tue Jun 12 2007 - 11:19:36 CDT)
- Re: How to "twist" a molecule? (resubmit) JC Gumbart (Sun Mar 25 2007 - 00:33:00 CDT)
- equilibration amit dong (Fri Mar 23 2007 - 11:30:06 CDT)
- restart NAMD job Jianhui Tian (Fri Mar 23 2007 - 09:03:38 CDT)
- Extraction of force data Viral D. Tejani (Thu Mar 22 2007 - 22:12:02 CDT)
- How to "twist" a molecule? Margaret S. Cheung (Thu Mar 22 2007 - 18:02:57 CDT)
- unsubscribe Jonathan D. Proulx (Wed Mar 21 2007 - 14:44:47 CDT)
- distance constraints with an upper bound Neema Salimi (Wed Mar 21 2007 - 13:19:19 CDT)
- Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" namd vmd (Wed Mar 21 2007 - 12:38:42 CDT)
- Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" Cesar Luis Avila (Wed Mar 21 2007 - 13:54:47 CDT)
- Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" namd vmd (Thu Mar 22 2007 - 07:55:00 CDT)
- Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" Peter Freddolino (Thu Mar 22 2007 - 19:24:26 CDT)
- hexagonal crystal Allison Langham (Wed Mar 21 2007 - 11:22:26 CDT)
- Re: user defined L-J parameters Arturas Ziemys (Wed Mar 21 2007 - 08:59:21 CDT)
- user defined L-J parameters Alessio Alexiadis (Wed Mar 21 2007 - 05:18:17 CDT)
- Dihedral restraints do not work Neelanjana Sengupta (Tue Mar 20 2007 - 10:44:10 CDT)
- query about thermostat.. hl332_at_drexel.edu (Mon Mar 19 2007 - 14:01:43 CDT)
- parameters for GABA (gamma-amino butyric acid) namd vmd (Sun Mar 18 2007 - 07:33:57 CDT)
- problem with namddat_unix: Plz help... hl332_at_drexel.edu (Fri Mar 16 2007 - 12:10:13 CDT)
- applying experimental constraints to a MD simulation L. Michel Espinoza-Fonseca (Fri Mar 16 2007 - 11:31:41 CDT)
- psfgen and bond topology specification Neelanjana Sengupta (Thu Mar 15 2007 - 16:20:24 CDT)
- Why is water density not 1.0g/cm3? lw257_at_email.med.yale.edu (Wed Mar 14 2007 - 18:57:06 CDT)
- Problem with NVE run: Help hl332_at_drexel.edu (Thu Mar 15 2007 - 14:19:55 CDT)
- Third node stops the simulation paco ty (Thu Mar 15 2007 - 12:45:46 CDT)
- Re: Water density is not 1.0g/cm3 Peter Freddolino (Thu Mar 15 2007 - 12:25:44 CDT)
- Why is water density not 1.0g/cm3? Liguo Wang (Thu Mar 15 2007 - 14:01:12 CDT)
- Warning: overloaded due to high background load Jianhui Tian (Thu Mar 15 2007 - 10:15:57 CDT)
- how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 06:50:45 CDT)
- Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 07:59:01 CDT)
- Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 09:56:03 CDT)
- Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 15:06:16 CDT)
- Re: how to convert dcd files from namd to charmm Peter Freddolino (Thu Mar 15 2007 - 15:16:25 CDT)
- Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 15:33:41 CDT)
- Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 15:34:31 CDT)
- Re: how to convert dcd files from namd to charmm Peter Freddolino (Thu Mar 15 2007 - 15:49:06 CDT)
- Re: how to convert dcd files from namd to charmm L. Michel Espinoza-Fonseca (Thu Mar 15 2007 - 16:20:40 CDT)
- Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 15:38:37 CDT)
- Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 09:56:03 CDT)
- Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 08:08:25 CDT)
- Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 07:59:01 CDT)
- Why minimization before Molecular Dynamics? Pedro Borkowski (Thu Mar 15 2007 - 04:25:05 CDT)
- non-parallel NAMD compilation Xiuping Tao (Tue Mar 13 2007 - 15:07:47 CDT)
- Re: Incorrect Atom Count vivek behera (Tue Mar 13 2007 - 23:22:16 CDT)
- protein spinning and total enegy not constant in NVE hl332_at_drexel.edu (Tue Mar 13 2007 - 14:06:07 CDT)
- Kinetic Energy frm MDEnergy (energy evaluation tool) Rahul Bhowmik (Mon Mar 12 2007 - 18:11:36 CDT)
- Free Energy/ ERROR Arturas Ziemys (Mon Mar 12 2007 - 15:37:31 CDT)
- Free Energy of Conformation Change Arturas Ziemys (Mon Mar 12 2007 - 13:16:57 CDT)
- applying experimental constraints to a MD simulation L. Michel Espinoza-Fonseca (Sun Mar 11 2007 - 18:14:16 CDT)
- DMPC Atoms moving too fast ! mustapha.hamdi_at_ensi-bourges.fr (Sat Mar 10 2007 - 10:08:08 CST)
- question about the influence of water box size in FEP jieru.zheng_at_duke.edu (Fri Mar 09 2007 - 09:30:40 CST)
- topology problem! ramya wwjd (Fri Mar 09 2007 - 03:04:58 CST)
- multiple timestep and dcdfreq Luca Muccioli (Thu Mar 08 2007 - 07:27:32 CST)
- Premature stop paco ty (Thu Mar 08 2007 - 03:57:15 CST)
- protein diffuses to boundary.. hl332_at_drexel.edu (Wed Mar 07 2007 - 16:21:24 CST)
- firstLdbStep and ldbPeriod Gianluca Interlandi (Wed Mar 07 2007 - 13:11:37 CST)
- *** topology file for AMP? *** Daniel Keedy (Tue Mar 06 2007 - 15:50:56 CST)
- DCD for windows lily jin (Tue Mar 06 2007 - 15:25:40 CST)
- Configuration file Rita Cassia (Tue Mar 06 2007 - 07:54:51 CST)
- Problems with energy conservation in NVE dynamics with 2fs timestep ahenneck_at_ix.urz.uni-heidelberg.de (Tue Mar 06 2007 - 04:27:03 CST)
- Changing the protonation states of residues Nabajyoti Goswami (Mon Mar 05 2007 - 03:27:07 CST)
- Problem with water box ramya wwjd (Fri Mar 02 2007 - 06:50:26 CST)
- Difficulties is minimizing capped peptides kate.nairn_at_csiro.au (Mon Mar 05 2007 - 21:18:01 CST)
- distance restraint w/upper bound example Neema Salimi (Mon Mar 05 2007 - 15:27:05 CST)
- how to get the velocities from the dcd file Alessio Alexiadis (Mon Mar 05 2007 - 09:25:49 CST)
- restraining parts of a molecule Stern, Julie (Sun Mar 04 2007 - 21:20:28 CST)
- reproduciblity between software Stern, Julie (Fri Mar 02 2007 - 10:43:23 CST)
- dimer minimization ayk_at_mail.ecc.u-tokyo.ac.jp (Wed Feb 28 2007 - 03:54:40 CST)
- Crystal Structure Analysis pedro.borkowski_at_utoronto.ca (Tue Feb 27 2007 - 12:02:23 CST)
- different output in processors dora guzman (Tue Feb 27 2007 - 14:18:24 CST)
- Incorrect Atom Count vivek behera (Tue Feb 27 2007 - 09:02:17 CST)
- Periodic Cell error on CO2 MD Ugur Akgun (Mon Feb 26 2007 - 16:32:24 CST)
- Tcl: callback, run, revert, measure Tao, Xiuping (Sun Feb 25 2007 - 22:25:41 CST)
- Restraints and System COM Drift Philip Blood (Mon Feb 26 2007 - 13:48:01 CST)
- Tcl: callback, run, revert, measure Xiuping Tao (Mon Feb 26 2007 - 12:50:28 CST)
- Re: uses of patches for changing the protonation states of residues Peter Freddolino (Mon Feb 26 2007 - 08:40:24 CST)
- namd2 run error Moumita Maiti (Mon Feb 26 2007 - 07:14:20 CST)
- Varying Force Simulations Viral D. Tejani (Sat Feb 24 2007 - 19:47:23 CST)
- aligning ligands Narender Singh Maan (Fri Feb 23 2007 - 12:39:45 CST)
- TMD and TclForces Jeff Wereszczynski (Fri Feb 23 2007 - 10:56:55 CST)
- RDF.tcl question Jianhui Tian (Wed Feb 21 2007 - 12:43:24 CST)
- Does pair interaction calculations uses PBC ? Arturas Ziemys (Wed Feb 21 2007 - 11:18:22 CST)
- Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 21:58:54 CST)
- TOTAL, TOTAL2 and TOTAL3 Alessandro Cembran (Mon Feb 19 2007 - 11:36:16 CST)
- NVE ensemble configuration file Lechuga, Javier (Mon Feb 19 2007 - 06:11:29 CST)
- Parallel performance on Intel Woodcrest Himanshu Khandelia (Sun Feb 18 2007 - 15:19:20 CST)
- const vel SMD Narender Singh Maan (Fri Feb 16 2007 - 14:03:40 CST)
- Problem about cellBasisVector Jianhui Tian (Fri Feb 16 2007 - 09:14:00 CST)
- Error compile charm++ Jianhui Tian (Thu Feb 15 2007 - 12:40:22 CST)
- NAMD Integration algorithm Nava Whiteford (Thu Feb 15 2007 - 07:44:03 CST)
- tabulated potentials? Nicolas Bock (Tue Feb 13 2007 - 15:35:03 CST)
- Temperature problem Al-Rawi, Ahlam (Tue Feb 13 2007 - 14:05:35 CST)
- Velocities of different Atoms Rahul Bhowmik (Tue Feb 13 2007 - 09:18:28 CST)
- ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 10:58:32 CST)
- Re: vmd-l: ionize (big, big, big system!) Peter Freddolino (Mon Feb 12 2007 - 11:07:50 CST)
- Re: vmd-l: ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 11:19:57 CST)
- Re: Re: vmd-l: ionize (big, big, big system!) Alessandro Cembran (Mon Feb 12 2007 - 11:37:20 CST)
- Re: Re: vmd-l: ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 17:49:25 CST)
- Re: Re: vmd-l: ionize (big, big, big system!) Alessandro Cembran (Mon Feb 12 2007 - 18:57:05 CST)
- Re: vmd-l: ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 11:19:57 CST)
- Re: ionize (big, big, big system!) Cesar Luis Avila (Mon Feb 12 2007 - 12:58:11 CST)
- Re: ionize (big, big, big system!) Jacob Poehlsgaard (Tue Feb 13 2007 - 02:22:23 CST)
- Re: vmd-l: ionize (big, big, big system!) Peter Freddolino (Mon Feb 12 2007 - 11:07:50 CST)
- Protein partially denatures during pulling Gianluca Interlandi (Sun Feb 11 2007 - 01:01:40 CST)
- Re: SMD and CPT? (fwd) Gianluca Interlandi (Fri Feb 09 2007 - 13:52:23 CST)
- DMPC psf. mustapha.hamdi_at_ensi-bourges.fr (Fri Feb 09 2007 - 10:10:24 CST)
- SMD and CPT? Gianluca Interlandi (Fri Feb 09 2007 - 00:49:45 CST)
- tclForces: relation between force and velocity Westley A Sherman (Thu Feb 08 2007 - 12:55:19 CST)
- force constant for zer-velocity SMD namd vmd (Thu Feb 08 2007 - 06:35:53 CST)
- pH in NAMD Per Jr. Greisen (Thu Feb 08 2007 - 05:37:39 CST)
- Re: pH in NAMD Mark Abraham (Thu Feb 08 2007 - 06:20:06 CST)
- Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 09:36:19 CST)
- Re: pH in NAMD Jerome Henin (Thu Feb 08 2007 - 09:58:50 CST)
- Re: pH in NAMD Jan Saam (Thu Feb 08 2007 - 11:21:02 CST)
- Re: pH in NAMD Mark Abraham (Thu Feb 08 2007 - 19:12:40 CST)
- Re: pH in NAMD MW Van der Kamp, School of Chemistry (Fri Feb 09 2007 - 02:48:48 CST)
- Re: pH in NAMD Mark Abraham (Fri Feb 09 2007 - 09:54:34 CST)
- Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 10:24:29 CST)
- Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 13:13:52 CST)
- Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 09:36:19 CST)
- Re: pH in NAMD Peter Freddolino (Thu Feb 08 2007 - 10:29:44 CST)
- Re: pH in NAMD Mark Abraham (Thu Feb 08 2007 - 06:20:06 CST)
- tclbc example scripts namd vmd (Thu Feb 08 2007 - 04:46:54 CST)
- Compiling Questions Joshua D. Moore (Wed Feb 07 2007 - 23:55:39 CST)
- Problem compiling NAMD on BlueGene Jianhui Tian (Tue Feb 06 2007 - 13:08:06 CST)
- Pressure problem when using restart file Jacob Poehlsgaard (Tue Feb 06 2007 - 10:11:53 CST)
- fixing internal coordinates Martin McCullagh (Mon Feb 05 2007 - 14:01:55 CST)
- too large an area/lipid in POPE bilayers using membrane plugin Himanshu Khandelia (Mon Feb 05 2007 - 11:50:04 CST)
- Calculation of CHARMM Parameters from GAMESS Output. Klon, Anthony (Mon Feb 05 2007 - 09:27:09 CST)
- problems running more than 9 Replicas in replica exchange simulations Ana Celia Araujo Vila Verde (Sun Feb 04 2007 - 14:33:41 CST)
- Error: parameter multiplicity.plz reply. hl332_at_drexel.edu (Sat Feb 03 2007 - 12:36:45 CST)
- NAMD - Pronunciation? Shirley Hui (Fri Feb 02 2007 - 19:57:47 CST)
- Energy Minimization Shirley Hui (Fri Feb 02 2007 - 14:23:01 CST)
- "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Fri Feb 02 2007 - 07:31:53 CST)
- Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Fri Feb 02 2007 - 09:29:44 CST)
- Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Sat Feb 03 2007 - 01:21:35 CST)
- Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Sat Feb 03 2007 - 08:38:58 CST)
- Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Sun Feb 04 2007 - 06:11:03 CST)
- Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Sun Feb 04 2007 - 08:15:38 CST)
- Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Thu Feb 08 2007 - 15:04:12 CST)
- Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Sat Feb 03 2007 - 01:21:35 CST)
- Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Fri Feb 02 2007 - 09:29:44 CST)
- flexiblecell and constant ratio regafan_at_usc.es (Fri Feb 02 2007 - 06:09:00 CST)
- DNA hydrogen bonds Maxim Karachevtsev (Fri Feb 02 2007 - 02:00:46 CST)
- (no subject) Maxim Karachevtsev (Fri Feb 02 2007 - 02:00:12 CST)
- Binding Free Energy Shirley Hui (Thu Feb 01 2007 - 15:40:27 CST)
- Question about compiling NAMD Jianhui Tian (Thu Feb 01 2007 - 14:44:15 CST)
- DNA H-bonds Maxim Karachevtsev (Thu Feb 01 2007 - 03:51:26 CST)
- problems running Replica Exchange simulations using SSH to spawn the processes Ana Celia Araujo Vila Verde (Thu Feb 01 2007 - 13:28:06 CST)
- DNA and low pH Gaurav Sharma (Wed Jan 31 2007 - 15:06:46 CST)
- MPI compile of NAMD runs on dual core machines but not quad core machines Joshua D. Moore (Wed Jan 31 2007 - 14:47:14 CST)
- peptide conformation search examples Andrew D. Fant (Tue Jan 30 2007 - 14:21:49 CST)
- DNA helix model lily jin (Tue Jan 30 2007 - 13:26:26 CST)
- a philosophical question... Richard Wood (Tue Jan 30 2007 - 12:21:06 CST)
- Re: a philosophical question... L. Michel Espinoza-Fonseca (Tue Jan 30 2007 - 12:54:06 CST)
- Re: a philosophical question... Richard Wood (Tue Jan 30 2007 - 13:35:25 CST)
- Re: a philosophical question... Richard Wood (Wed Jan 31 2007 - 18:01:46 CST)
- Re: a philosophical question... Richard Wood (Mon Feb 19 2007 - 17:16:52 CST)
- Re: a philosophical question... Richard Wood (Mon Feb 19 2007 - 18:19:46 CST)
- Re: a philosophical question... L. Michel Espinoza-Fonseca (Tue Jan 30 2007 - 12:54:06 CST)
- Questions re: protein-DNA complex Shirley Hui (Mon Jan 29 2007 - 16:20:02 CST)
- FAO developers: vdW energies, forces and derivatives Floris Buelens (Mon Jan 29 2007 - 05:23:43 CST)
- constant velocity SMD Narender Singh Maan (Fri Jan 26 2007 - 11:11:39 CST)
- constant velocity SMD Narender Singh Maan (Fri Jan 26 2007 - 11:44:41 CST)
- Re: constant velocity SMD JC Gumbart (Fri Jan 26 2007 - 11:59:46 CST)
- Re: constant velocity SMD Cesar Luis Avila (Fri Jan 26 2007 - 12:34:36 CST)
- force field for H2PO4- and HPO4(-2) ions Pawel Weronski (Sat Feb 24 2007 - 10:01:43 CST)
- Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sat Feb 24 2007 - 10:20:05 CST)
- Re: force field for H2PO4- and HPO4(-2) ions Richard Wood (Sat Feb 24 2007 - 15:42:55 CST)
- Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sat Feb 24 2007 - 17:44:13 CST)
- Re: force field for H2PO4- and HPO4(-2) ions Richard Wood (Sat Feb 24 2007 - 20:35:13 CST)
- Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sun Feb 25 2007 - 00:35:35 CST)
- Re: force field for H2PO4- and HPO4(-2) ions George Madalin Giambasu (Sat Feb 24 2007 - 14:33:16 CST)
- Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sat Feb 24 2007 - 10:20:05 CST)
- minimization error - high IMPRP energy Richard Lonsdale (Fri Jan 26 2007 - 10:31:44 CST)
- compilation of charm++ L. Michel Espinoza-Fonseca (Fri Jan 26 2007 - 06:53:47 CST)
- Simulations with large number of constraints crash at startup phase 1 on Indiana's Bigred Philip Blood (Thu Jan 25 2007 - 13:42:20 CST)
- membrane constraints on thickness Himanshu Khandelia (Thu Jan 25 2007 - 11:58:39 CST)
- Re: membrane constraints on thickness Peter Freddolino (Thu Jan 25 2007 - 13:24:21 CST)
- Re: membrane constraints on thickness Himanshu Khandelia (Fri Jan 26 2007 - 03:45:40 CST)
- Re: membrane constraints on thickness Peter Freddolino (Fri Jan 26 2007 - 07:01:35 CST)
- Re: membrane constraints on thickness Himanshu Khandelia (Fri Jan 26 2007 - 07:27:21 CST)
- Re: membrane constraints on thickness Peter Freddolino (Fri Jan 26 2007 - 08:18:24 CST)
- Re: membrane constraints on thickness Morad Alawneh (Fri Jan 26 2007 - 09:25:12 CST)
- Re: membrane constraints on thickness Philip Blood (Fri Jan 26 2007 - 09:52:27 CST)
- Re: membrane constraints on thickness Philip Blood (Fri Jan 26 2007 - 11:09:55 CST)
- Re: membrane constraints on thickness Peter Freddolino (Fri Jan 26 2007 - 07:02:49 CST)
- Re: membrane constraints on thickness Himanshu Khandelia (Fri Jan 26 2007 - 03:45:40 CST)
- Re: membrane constraints on thickness Peter Freddolino (Thu Jan 25 2007 - 13:24:21 CST)
- Replica Exchange (Parallel) M. Madhu (Thu Jan 25 2007 - 11:18:33 CST)
- How to write a new dcd.file by using Tcl xiaojing gong (Thu Jan 25 2007 - 08:28:21 CST)
- 0 coordinates for LES atoms in pdb file after solvation Dhiraj Srivastava (Thu Jan 25 2007 - 01:45:32 CST)
- NAMD install problem. Wang, Boyang (Wed Jan 24 2007 - 12:59:54 CST)
- modified patch to PROline Neelanjana Sengupta (Wed Jan 24 2007 - 12:25:21 CST)
- Tcl Scripting M. Madhu (Wed Jan 24 2007 - 11:01:37 CST)
- Re: minimizing bad system: bad global excl. count Brian Bennion (Tue Jan 23 2007 - 14:35:19 CST)
- minimizing bad system: bad global excl. count Himanshu Khandelia (Tue Jan 23 2007 - 11:32:41 CST)
- Simulation of Eukaryotic membrane protein Aaron Oakley (Sun Jan 21 2007 - 23:23:12 CST)
- heating with restraints AYTUG TUNCEL (Fri Jan 19 2007 - 12:12:05 CST)
- AcetylProlineAmide topology Neelanjana Sengupta (Wed Jan 17 2007 - 12:35:45 CST)
- harmonic distance restraint X Zheng (Tue Jan 16 2007 - 16:02:59 CST)
- fixed atoms appearing on the other side of simulation box Ana Celia Araujo Vila Verde (Tue Jan 16 2007 - 13:38:33 CST)
- SHAKE: Constrain EVERY bond length and bond angle Neelanjana Sengupta (Tue Jan 16 2007 - 13:21:52 CST)
- Constrain EVERY bond length and bond angle Neelanjana Sengupta (Tue Jan 16 2007 - 13:18:59 CST)
- Restart Simulation Karol Kaszuba (Tue Jan 16 2007 - 05:49:34 CST)
- Re: Scalability problem with NAMD2.6 on Intel Xeon EM64T processors Morad Alawneh (Mon Jan 15 2007 - 14:54:38 CST)
- g(r) plugin Ayþe Özlem Sezerman (Mon Jan 15 2007 - 04:09:56 CST)
- C:CA bond getting stretched Dhiraj Srivastava (Mon Jan 15 2007 - 01:45:37 CST)
- Re: Scalability problem with NAMD2.6 on Intel Xeon EM64T processors Morad Alawneh (Sat Jan 13 2007 - 10:18:46 CST)
- Scalability problem with NAMD2.6 on Intel Xeon EM64T processors Morad Alawneh (Fri Jan 12 2007 - 10:56:07 CST)
- FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE Alexander Vaughn (Thu Jan 11 2007 - 19:37:34 CST)
- "CWeb performance data sent to wrong processor..." Jon Halverson (Thu Jan 11 2007 - 15:47:57 CST)
- Replica Exchange MD using Amber parameters Kramer Campen (Thu Jan 11 2007 - 08:39:32 CST)
- H-bond energy amit dong (Thu Jan 11 2007 - 04:24:04 CST)
- experimental phi-values as restraints regafan_at_usc.es (Wed Jan 10 2007 - 10:08:42 CST)
- Stray PME grid charges detected Simon Watson (Tue Jan 09 2007 - 12:06:53 CST)
- Why does lipid move out of water box Nitin Bhardwaj (Tue Jan 09 2007 - 11:29:24 CST)
- generalized born routine Rie Nygaard (Tue Jan 09 2007 - 07:10:18 CST)
- Anyone have catdcd-4.0 for BlueGene? Joshua D. Moore (Mon Jan 08 2007 - 15:34:09 CST)
- Protein, ligand, ion out of the water box. Rima Chaudhuri (Mon Jan 08 2007 - 12:35:07 CST)
- Thermodynamic Integration (free energy of conformation change) Kramer Campen (Mon Jan 08 2007 - 12:11:02 CST)
- ligand parameterization Idit Buch (Mon Jan 08 2007 - 05:26:54 CST)
- topology of carbon dioxide compatible with Charmm arijit_r_at_chem.iitkgp.ernet.in (Mon Jan 08 2007 - 05:06:07 CST)
- The NAMD job do not go forward Fabio Passetti (Fri Jan 05 2007 - 12:43:13 CST)
- "Not all atoms have unique coordinates" Nitin Bhardwaj (Fri Jan 05 2007 - 12:31:18 CST)
- SPC/E water model laura (Fri Jan 05 2007 - 07:05:40 CST)
- Free Energy of Conformation Change Units Kramer Campen (Tue Jan 02 2007 - 15:45:23 CST)
- Tcl_BC: [nexatom] twice in script Arturas Ziemys (Tue Jan 02 2007 - 09:52:53 CST)
- compute nonbonding interactions on bonded atoms Lorant Janosi (Fri Dec 29 2006 - 23:10:12 CST)
- unequal PMEGridSizes Neelanjana Sengupta (Fri Dec 29 2006 - 16:46:56 CST)
- namd question _at_huji.ac.il (Tue Dec 26 2006 - 04:44:42 CST)
- forming disulfide after equilibrating system dora guzman (Fri Dec 22 2006 - 17:24:10 CST)
- PME for a hexagonal system dimka (Fri Dec 22 2006 - 15:17:16 CST)
- loadforces problem Arturas Ziemys (Thu Dec 21 2006 - 13:58:44 CST)
- Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin Nathan H. Cho (Wed Dec 20 2006 - 20:59:20 CST)
- (no subject) Marcelo Puiatti (Wed Dec 20 2006 - 12:30:55 CST)
- NAMD constraint force and energy Floris Buelens (Wed Dec 20 2006 - 04:53:12 CST)
- g(r) Ayþe Özlem Sezerman (Wed Dec 20 2006 - 04:20:51 CST)
- about counterions taojinwuhan_at_sohu.com (Tue Dec 19 2006 - 21:18:19 CST)
- net translation in long simulations Mehdi Bagheri-Hamaneh (Tue Dec 19 2006 - 17:00:59 CST)
- Update on NAMD on BlueGene/TCL Joshua D. Moore (Tue Dec 19 2006 - 15:20:47 CST)
- ZeroMomentum-Please help Mehdi Bagheri-Hamaneh (Tue Dec 19 2006 - 08:20:04 CST)
- ZeroMomentum Mehdi Bagheri-Hamaneh (Mon Dec 18 2006 - 11:09:20 CST)
- simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Mon Dec 18 2006 - 10:16:08 CST)
- outputPressure Morad Alawneh (Fri Dec 15 2006 - 20:50:13 CST)
- Building PDB files for DNA. Wang, Boyang (Fri Dec 15 2006 - 10:29:55 CST)
- addforce Arturas Ziemys (Wed Dec 13 2006 - 14:16:43 CST)
- problems of RATTLE with big systems regafan_at_usc.es (Wed Dec 13 2006 - 12:46:22 CST)
- Problem with equilibration and pressure Jacob Poehlsgaard (Wed Dec 13 2006 - 05:31:49 CST)
- simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 02:01:41 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 07:49:30 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 08:23:15 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 08:25:07 CST)
- Re: simulation of membrane-protein systems Cesar Luis Avila (Wed Dec 13 2006 - 09:14:07 CST)
- Re: simulation of membrane-protein systems Marcos Sotomayor (Wed Dec 13 2006 - 11:02:37 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 11:12:13 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 11:16:21 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 11:19:01 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 11:30:51 CST)
- Re: simulation of membrane-protein systems regafan_at_usc.es (Wed Dec 13 2006 - 13:47:44 CST)
- Re: simulation of membrane-protein systems JC Gumbart (Wed Dec 13 2006 - 13:59:27 CST)
- Re: simulation of membrane-protein systems Marcos Sotomayor (Wed Dec 13 2006 - 11:34:22 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 11:38:11 CST)
- Re: simulation of membrane-protein systems Marcos Sotomayor (Wed Dec 13 2006 - 11:59:53 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Fri Dec 15 2006 - 02:24:01 CST)
- Re: simulation of membrane-protein systems Richard Wood (Wed Dec 13 2006 - 14:21:25 CST)
- Re: simulation of membrane-protein systems JC Gumbart (Wed Dec 13 2006 - 14:42:24 CST)
- Re: simulation of membrane-protein systems Guo Zhi (Wed Dec 13 2006 - 22:00:03 CST)
- RE: simulation of membrane-protein systems JC Gumbart (Wed Dec 13 2006 - 22:28:17 CST)
- Parallelization method Jordi Camps (Thu Dec 14 2006 - 11:33:38 CST)
- Re: Parallelization method JC Gumbart (Thu Dec 14 2006 - 11:45:45 CST)
- RE: Parallelization method Jordi Camps (Thu Dec 14 2006 - 12:04:34 CST)
- Re: simulation of membrane-protein systems Richard Wood (Fri Dec 15 2006 - 05:12:26 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 08:23:15 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 07:49:30 CST)
- Correlation Functions Juan Diaz (Tue Dec 12 2006 - 14:39:52 CST)
- Correlation Functions Juan Diaz (Tue Dec 12 2006 - 14:24:47 CST)
- FEP & different ligands satya work (Mon Dec 11 2006 - 01:20:06 CST)
- how to use reaction field in NAMD xiaojing gong (Sun Dec 10 2006 - 21:21:33 CST)
- problem reading topolgy files Annalisa Marsico (Sun Dec 10 2006 - 06:14:51 CST)
- Re: bug in pressure calculation with E field? Peter Freddolino (Sat Dec 09 2006 - 14:19:01 CST)
- particle access in tclBC Arturas Ziemys (Thu Dec 07 2006 - 13:24:05 CST)
- Tcl_Forces / 'loadcoords' loads NOT wrapped coordinates ? Arturas Ziemys (Thu Dec 07 2006 - 12:19:31 CST)
- Help. Parameters for PSGL needed Cesar Luis Avila (Thu Dec 07 2006 - 09:49:48 CST)
- Reassigning Velocities AYTUG TUNCEL (Thu Dec 07 2006 - 06:47:58 CST)
- NAMD pairInteraction - huge VDW and TOTAL3 Ravinder Abrol (Wed Dec 06 2006 - 18:10:23 CST)
- minimization temperature and constraints AYTUG TUNCEL (Tue Dec 05 2006 - 17:20:22 CST)
- Re: Tcl_Forces = pressure shifts while Langevin Piston is ON Arturas Ziemys (Tue Dec 05 2006 - 13:47:08 CST)
- polyethylene topology Arturas Ziemys (Tue Dec 05 2006 - 12:05:57 CST)
- NAMD-2.6 Insatallation help bertrand russell (Tue Dec 05 2006 - 04:29:43 CST)
- Re: RE: about topology generation Sting (Tue Dec 05 2006 - 01:03:56 CST)
- about topology generation Sting (Mon Dec 04 2006 - 22:18:26 CST)
- Issue with rhombic dodecahedron / CHARMM compatibility Dan Bolintineanu (Mon Dec 04 2006 - 17:03:21 CST)
- Is it equilibrated? taojinwuhan_at_sohu.com (Mon Dec 04 2006 - 01:45:49 CST)
- question about RMSD defined in NAMD Boyang Wang (Sat Dec 02 2006 - 19:46:40 CST)
- Tcl_Forces = pressure shifts while Langevin Piston is ON Arturas Ziemys (Fri Dec 01 2006 - 16:53:01 CST)
- FixedAtomForces and ExcludeFromPressure Vishal Kopardé (Thu Nov 30 2006 - 19:39:49 CST)
- water box deformation AYTUG TUNCEL (Thu Nov 30 2006 - 16:59:15 CST)
- high vdw energy AYTUG TUNCEL (Thu Nov 30 2006 - 16:44:39 CST)
- getbond (Tcl forces) / PBC Arturas Ziemys (Thu Nov 30 2006 - 10:12:32 CST)
- Generalized solvent boundary potential or similar tricks for huge systems in NAMD?? Jacob Poehlsgaard (Thu Nov 30 2006 - 03:15:35 CST)
- problem w/ free energy perturbation OMAR NABEEL ALY DEMERDASH (Wed Nov 29 2006 - 18:51:17 CST)
- RATTLE errors in equilibration regafan_at_usc.es (Wed Nov 29 2006 - 09:46:32 CST)
- is there any maximum limt of atom numbers in VMD or NAMD? youbin tu (Tue Nov 28 2006 - 23:00:41 CST)
- RE: pressure calculation in applied field Todd Trimble (Tue Nov 28 2006 - 17:18:24 CST)
- Re: pressure calculation in applied field Brian Bennion (Tue Nov 28 2006 - 16:06:10 CST)
- protein unfolding -- Phi MD Wei Fu (Tue Nov 28 2006 - 13:59:29 CST)
- pressure calculation in applied field Todd Trimble (Tue Nov 28 2006 - 12:36:51 CST)
- TIP4P water Vishal Kopardé (Mon Nov 27 2006 - 17:53:34 CST)
- error message in free energy pert. OMAR NABEEL ALY DEMERDASH (Sun Nov 26 2006 - 23:36:23 CST)
- help:autopsf changed the structure! taojinwuhan_at_sohu.com (Sun Nov 26 2006 - 19:57:42 CST)
- Harmonic Constraint: 2 types Morad Alawneh (Sun Nov 26 2006 - 19:36:15 CST)
- ABF with z-coord Ugur Akgun (Fri Nov 24 2006 - 20:31:06 CST)
- dcd file format Leandro Martínez (Fri Nov 24 2006 - 05:38:05 CST)
- problems with paralellism Leandro Martínez (Thu Nov 23 2006 - 12:49:39 CST)
- Distance restraint Yao Fan (Wed Nov 22 2006 - 16:50:04 CST)
- Dummy particles Arturas Ziemys (Wed Nov 22 2006 - 14:55:36 CST)
- question on free energy pert. OMAR NABEEL ALY DEMERDASH (Wed Nov 22 2006 - 11:54:21 CST)
- LINE=*CMAP* regafan_at_usc.es (Wed Nov 22 2006 - 08:32:24 CST)
- POPC Matteo Masetti (Wed Nov 22 2006 - 04:43:08 CST)
- Re: How to create repulsive particle ? Arturas Ziemys (Tue Nov 21 2006 - 15:45:01 CST)
- electric field Todd Trimble (Tue Nov 21 2006 - 15:08:11 CST)
- How to create repulsive particle ? Arturas Ziemys (Tue Nov 21 2006 - 13:47:51 CST)
- combine.tcl Annalisa Marsico (Tue Nov 21 2006 - 12:40:00 CST)
- distorsion in hydrogens added regafan_at_usc.es (Tue Nov 21 2006 - 05:47:58 CST)
- Expansion of DCD tamal_at_iitk.ac.in (Mon Nov 20 2006 - 23:20:04 CST)
- Re: compiling charm++ with g++ 4.1 Leandro Martínez (Mon Nov 20 2006 - 14:27:43 CST)
- clustering conformations Dave Venky (Mon Nov 20 2006 - 12:42:58 CST)
- Compile charm++ with icc Shaowen Hu (Sat Nov 18 2006 - 15:42:36 CST)
- compiling charm++ with g++ 4.1 Leandro Martínez (Mon Nov 20 2006 - 10:26:22 CST)
- Tcl Boundary Forces Peter Jones (Sat Nov 18 2006 - 20:31:29 CST)
- bad exclusion count Francesco Iori (Fri Nov 17 2006 - 15:19:37 CST)
- Charged Atoms in External Magnetic Field Westley A Sherman (Thu Nov 16 2006 - 18:50:12 CST)
- electric field Todd Trimble (Thu Nov 16 2006 - 11:57:25 CST)
- strange memory behavior brian (Thu Nov 16 2006 - 11:20:06 CST)
- electric field and MISC Todd Trimble (Wed Nov 15 2006 - 18:20:54 CST)
- Re: vmd-l: PSF files append!! Neelanjana Sengupta (Wed Nov 15 2006 - 14:24:57 CST)
- small query... hl332_at_drexel.edu (Wed Nov 15 2006 - 13:48:39 CST)
- charges in topology regafan_at_usc.es (Wed Nov 15 2006 - 11:34:32 CST)
- NAMD on Linux IBM PowerPC JS20 Cluster sh (Wed Nov 15 2006 - 10:32:59 CST)
- RE: electric field and MISC energy Todd Trimble (Tue Nov 14 2006 - 10:46:19 CST)
- ABF (fwd) Matthew Davies (Tue Nov 14 2006 - 07:40:30 CST)
- Reproducing free energy profile for acetate-guanidinium association Grzegorz Jezierski (Tue Nov 14 2006 - 06:40:04 CST)
- unable to open charmm parameter file in Window bo baker (Tue Nov 14 2006 - 01:16:37 CST)
- electric field and MISC energy Todd Trimble (Mon Nov 13 2006 - 10:44:29 CST)
- recompiling NAMD 2.6 from sources on CentOS-3 x86_64: Charm++ failing test Tru Huynh (Mon Nov 13 2006 - 10:16:46 CST)
- LES / cLES Arturas Ziemys (Mon Nov 13 2006 - 09:40:09 CST)
- dcd file is too large taojinwuhan_at_sohu.com (Mon Nov 13 2006 - 02:52:41 CST)
- atomlist command in matdcd Dhiraj Srivastava (Sun Nov 12 2006 - 02:20:25 CST)
- Unnatural Bond lengths Vinit Rege (Sat Nov 11 2006 - 01:56:35 CST)
- Linux HP Itanium Quadrics Alessandro Cembran (Fri Nov 10 2006 - 17:04:45 CST)
- LES : size Arturas Ziemys (Fri Nov 10 2006 - 12:09:50 CST)
- how to remove translational and rotational motion from dcd file Dhiraj Srivastava (Thu Nov 09 2006 - 14:59:28 CST)
- Question about free energy of conformation change Peiquan Chen (Thu Nov 09 2006 - 02:26:46 CST)
- electric field and MISC energy Todd Trimble (Wed Nov 08 2006 - 16:19:02 CST)
- Another question on Diffusion Vinit Rege (Wed Nov 08 2006 - 13:15:49 CST)
- System of POPC bilayer Vinit Rege (Wed Nov 08 2006 - 12:21:56 CST)
- how long is enough to heat up and equilibrate lily jin (Wed Nov 08 2006 - 11:05:37 CST)
- infinite nanotubes with PBC in NAMD? Nicolas Winter (Wed Nov 08 2006 - 10:33:11 CST)
- PME GridSize Neelanjana Sengupta (Tue Nov 07 2006 - 17:57:24 CST)
- FEP Energy very high: Mutual exclusion of atoms Nitin Bhardwaj (Tue Nov 07 2006 - 17:28:58 CST)
- Trouble with Charmm/PDB? Javad Azadi (Mon Nov 06 2006 - 23:33:21 CST)
- dissociation in NAMD sukesh shenoy (Mon Nov 06 2006 - 11:00:40 CST)
- protein is moving from center to one corner of water box. Dhiraj Srivastava (Mon Nov 06 2006 - 01:06:53 CST)
- residue name LIP ... ! Vinit Rege (Sat Nov 04 2006 - 19:52:26 CST)
- [Fwd: Re: SMD on center of mass] Peter Freddolino (Fri Nov 03 2006 - 14:05:47 CST)
- Warning: 1 processors are overloaded due to high background load Dhiraj Srivastava (Fri Nov 03 2006 - 11:30:34 CST)
- RE: deformations in a water box during equilibration in NAMD regafan_at_usc.es (Fri Nov 03 2006 - 04:28:01 CST)
- production in NVE ensemble after equilibration in NPT ensemble Dhiraj Srivastava (Thu Nov 02 2006 - 23:54:30 CST)
- ABF on a single molecule Ugur Akgun (Thu Nov 02 2006 - 14:26:11 CST)
- Re: ABF on a single molecule Chris Chipot (Sun Nov 05 2006 - 03:26:53 CST)
- Re: ABF on a single molecule Ugur Akgun (Mon Nov 06 2006 - 14:19:04 CST)
- Re: ABF on a single molecule Chris Chipot (Mon Nov 06 2006 - 15:19:17 CST)
- Re: ABF on a single molecule Ugur Akgun (Mon Nov 06 2006 - 16:33:24 CST)
- ABF - zCoord for more than one monomer Ugur Akgun (Thu Nov 09 2006 - 10:19:47 CST)
- Re: ABF - zCoord for more than one monomer Chris Chipot (Mon Nov 13 2006 - 07:47:30 CST)
- Re: ABF on a single molecule Ugur Akgun (Mon Nov 06 2006 - 14:19:04 CST)
- Re: ABF on a single molecule Chris Chipot (Sun Nov 05 2006 - 03:26:53 CST)
- external force Al-Rawi, Ahlam (Thu Nov 02 2006 - 12:16:23 CST)
- deformations in a cubic water box during equilibration in NAMD regafan_at_usc.es (Thu Nov 02 2006 - 08:52:39 CST)
- histidine protonation xiaojing gong (Thu Nov 02 2006 - 08:18:27 CST)
- urestraint for minimizations and MD (no PMF) MW Van der Kamp, School of Chemistry (Thu Nov 02 2006 - 05:46:21 CST)
- namd installation Michal Walczak (Thu Nov 02 2006 - 03:56:21 CST)
- Hydrogens collapsing Vishal Kopardé (Wed Nov 01 2006 - 21:20:50 CST)
- equilibration of protein Dhiraj Srivastava (Wed Nov 01 2006 - 12:31:17 CST)
- rmsd is not stabilizing even after 0.6 ns Dhiraj Srivastava (Tue Oct 31 2006 - 13:41:54 CST)
- namd/charm infiniband build Rene Salmon (Mon Oct 30 2006 - 14:57:30 CST)
- Using NBFIX sukesh shenoy (Sat Oct 28 2006 - 17:59:52 CDT)
- compiling namd Michal Walczak (Sat Oct 28 2006 - 09:43:11 CDT)
- useFlexibleCell olga hrydziuszko (Sat Oct 28 2006 - 09:19:03 CDT)
- changing parameter files during simulation run sukesh shenoy (Fri Oct 27 2006 - 10:18:55 CDT)
- constrained simulation Dhiraj Srivastava (Fri Oct 27 2006 - 03:32:15 CDT)
- Re: Fwd: GRADIENT TOLERANCE: nan Brian Bennion (Thu Oct 26 2006 - 11:29:00 CDT)
- Replica Exchange Arturas Ziemys (Thu Oct 26 2006 - 10:53:16 CDT)
- Using/converting old extended top and par files? Jacob Poehlsgaard (Thu Oct 26 2006 - 05:34:31 CDT)
- Urey-Bradley term and VDW energy Hyonseok Hwang (Wed Oct 25 2006 - 22:41:36 CDT)
- Question about ABF Gaurav Sharma (Wed Oct 25 2006 - 18:03:13 CDT)
- heat capacity: NPT vs. NVT Arturas Ziemys (Wed Oct 25 2006 - 09:53:37 CDT)
- Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 08:37:30 CDT)
- Question about REMD ×Þ¿¡ (Wed Oct 25 2006 - 08:37:00 CDT)
- RATTLE Error Vishal Kopardé (Wed Oct 25 2006 - 06:59:18 CDT)
- error estimate in FEP calculation jz7_at_duke.edu (Tue Oct 24 2006 - 23:18:27 CDT)
- external force Al-Rawi, Ahlam (Tue Oct 24 2006 - 17:30:43 CDT)
- NPT ensemble with Periodic boundary condition Dhiraj Srivastava (Tue Oct 24 2006 - 17:07:38 CDT)
- external force Al-Rawi, Ahlam (Tue Oct 24 2006 - 14:39:42 CDT)
- Waiting for 0-th client to connect. Leandro Martínez (Tue Oct 24 2006 - 12:50:07 CDT)
- deformed water box after heating Dhiraj Srivastava (Mon Oct 23 2006 - 21:40:37 CDT)
- running 2 jobs simutaneously? Ching Wong (Mon Oct 23 2006 - 21:14:41 CDT)
- sphericalBCk1 milton sonoda (Mon Oct 23 2006 - 19:50:01 CDT)
- Replica-Exchange MD E. Prabhu Raman (Mon Oct 23 2006 - 13:53:41 CDT)
- Equilibriation Info tamal_at_iitk.ac.in (Mon Oct 23 2006 - 13:52:14 CDT)
- Re: phi and psi dihedral restraints Neelanjana Sengupta (Mon Oct 23 2006 - 12:20:41 CDT)
- calculation of non-bonded interactions Jindal Shah (Mon Oct 23 2006 - 09:55:59 CDT)
- temperature reassignment Dhiraj Srivastava (Mon Oct 23 2006 - 03:07:28 CDT)
- target molecular moves away from water box laura (Sun Oct 22 2006 - 20:18:11 CDT)
- phi and psi dihedral restraints Neelanjana Sengupta (Sun Oct 22 2006 - 18:24:24 CDT)
- deformed water box during equilibration. Dhiraj Srivastava (Sat Oct 21 2006 - 05:13:35 CDT)
- Problem setting distance restraints MW Van der Kamp, School of Chemistry (Fri Oct 20 2006 - 07:24:04 CDT)
- adding extra ions to neutralize charge on protein Dhiraj Srivastava (Thu Oct 19 2006 - 11:42:48 CDT)
- charge on protein Dhiraj Srivastava (Wed Oct 18 2006 - 21:57:28 CDT)
- Re: Intel Woodcrest version? Jacob Poehlsgaard (Wed Oct 18 2006 - 03:01:33 CDT)
- Hydroxyproline topology Neelanjana Sengupta (Tue Oct 17 2006 - 21:15:25 CDT)
- Intel Woodcrest version? Jacob Poehlsgaard (Tue Oct 17 2006 - 05:50:16 CDT)
- Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006 Jim Phillips (Mon Oct 16 2006 - 16:13:52 CDT)
- rigid protein Mehdi Bagheri-Hamaneh (Mon Oct 16 2006 - 13:00:58 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 08:21:45 CDT)
- Re: rigid protein L. Michel Espinoza-Fonseca (Thu Oct 19 2006 - 10:14:21 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 10:23:16 CDT)
- Re: rigid protein L. Michel Espinoza-Fonseca (Thu Oct 19 2006 - 10:38:33 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 10:50:01 CDT)
- Re: rigid protein Marcos Sotomayor (Thu Oct 19 2006 - 10:55:07 CDT)
- Re: rigid protein JC Gumbart (Thu Oct 19 2006 - 11:04:37 CDT)
- Re: rigid protein Gianluca Interlandi (Thu Oct 19 2006 - 13:12:53 CDT)
- Re: rigid protein Mark Abraham (Thu Oct 19 2006 - 10:44:27 CDT)
- Re: rigid protein Marc Baaden (Thu Oct 19 2006 - 12:29:32 CDT)
- Re: rigid protein Mark Abraham (Thu Oct 19 2006 - 20:20:09 CDT)
- Re: rigid protein Luca Bellucci (Fri Oct 20 2006 - 05:08:50 CDT)
- Re: rigid protein L. Michel Espinoza-Fonseca (Thu Oct 19 2006 - 10:14:21 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 08:21:45 CDT)
- NAMD on Dual processor computer Dhiraj Srivastava (Sun Oct 15 2006 - 14:28:31 CDT)
- problem with reassigning temperature Dhiraj Srivastava (Sat Oct 14 2006 - 21:55:15 CDT)
- CMAP in NAMD simulation Neelanjana Sengupta (Sat Oct 14 2006 - 17:26:23 CDT)
- Multiple tclForcesScript Morad Alawneh (Sat Oct 14 2006 - 14:53:28 CDT)
- simulation in nve ensemble Dhiraj Srivastava (Fri Oct 13 2006 - 21:45:37 CDT)
- about diahedra entry in top_all22_sugar.inp bqluan (Fri Oct 13 2006 - 13:31:35 CDT)
- Comments on 'restart' simulation Pijush Ghosh (Thu Oct 12 2006 - 16:33:10 CDT)
- MD in steps Pijush Ghosh (Thu Oct 12 2006 - 11:21:39 CDT)
- "reinitvel" parameter in config file Dhiraj Srivastava (Wed Oct 11 2006 - 18:34:21 CDT)
- line too long in pdb file restart.coor Dhiraj Srivastava (Wed Oct 11 2006 - 14:28:41 CDT)
- changing velocity during simulation olga hrydziuszko (Wed Oct 11 2006 - 09:05:28 CDT)
- changing velocity during simulation olga hrydziuszko (Wed Oct 11 2006 - 08:10:17 CDT)
- equilibration at three different temperature Dhiraj Srivastava (Tue Oct 10 2006 - 18:00:52 CDT)
- popc pressure profile Allan Haldane (Tue Oct 10 2006 - 11:40:43 CDT)
- Flushing output: MPI version of NAMD on AMD64 Vani Krishna (Tue Oct 10 2006 - 00:00:31 CDT)
- Re: Re: restraining the protein not to move during equilibration Lewyn Li (Mon Oct 09 2006 - 10:52:55 CDT)
- topology & parameters for urea patrick wintrode (Mon Oct 09 2006 - 11:00:44 CDT)
- Atomic partial charge Luca Bellucci (Mon Oct 09 2006 - 05:35:36 CDT)
- restraining the protein not to move during equilibration Dhiraj Srivastava (Sun Oct 08 2006 - 23:30:39 CDT)
- dissociation of water Shenoy, Sukesh (Sun Oct 08 2006 - 18:06:56 CDT)
- restarting the simulation Dhiraj Srivastava (Sun Oct 08 2006 - 16:17:38 CDT)
- value of B column is zero Dhiraj Srivastava (Sun Oct 08 2006 - 00:34:16 CDT)
- zero kinetic energy during minimization Dhiraj Srivastava (Sun Oct 08 2006 - 00:12:39 CDT)
- problem with dihedral restraint Neelanjana Sengupta (Fri Oct 06 2006 - 16:11:43 CDT)
- reflective barrier olga hrydziuszko (Fri Oct 06 2006 - 10:49:33 CDT)
- Installation Problem bertrand russell (Fri Oct 06 2006 - 06:52:00 CDT)
- periodic boundry conditions olga hrydziuszko (Fri Oct 06 2006 - 05:58:45 CDT)
- Re: vmd-l: trace to newcartoon inconsistent display problem Cesar Luis Avila (Thu Oct 05 2006 - 15:58:11 CDT)
- forward and backward pulling curcio (Thu Oct 05 2006 - 10:59:10 CDT)
- PME processors Nicholas M Glykos (Thu Oct 05 2006 - 07:11:46 CDT)
- constraining distance Anahita Tafvizi (Wed Oct 04 2006 - 13:16:29 CDT)
- sialic acid bqluan (Tue Oct 03 2006 - 15:36:00 CDT)
- missing info from NAMD output Neelanjana Sengupta (Tue Oct 03 2006 - 14:27:08 CDT)
- NAMD timestep and numsteps santanu chatterjee (Tue Oct 03 2006 - 12:39:26 CDT)
- "Adaptive" force direction in SMD? HAMON véronique (Tue Oct 03 2006 - 10:00:28 CDT)
- SMD From Force to Free Energy Ugur Akgun (Tue Oct 03 2006 - 09:54:07 CDT)
- Re: How can I do protein complex's simulation? Dhiraj Srivastava (Mon Oct 02 2006 - 19:58:29 CDT)
- How can I do protein complex's simulation? Yuqi Liu (Mon Oct 02 2006 - 18:46:13 CDT)
- Constraining a molecule and measuring the corresponding constraint force Doug Moby (Sat Sep 30 2006 - 08:36:31 CDT)
- trajectory extension E. Prabhu Raman (Fri Sep 29 2006 - 13:39:55 CDT)
- removing bonds in psf luca (Fri Sep 29 2006 - 05:44:13 CDT)
- removing bonds in psf olga hrydziuszko (Fri Sep 29 2006 - 03:45:27 CDT)
- United Atoms in NAMD Rajan Vatassery (Fri Sep 29 2006 - 02:08:12 CDT)
- Qmeasure=22?= command Arturas Ziemys (Wed Sep 27 2006 - 16:30:24 CDT)
- FFTW problem Jyh-Shyong Ho (Wed Sep 27 2006 - 04:02:57 CDT)
- about abf ËïæÃæà (Tue Sep 26 2006 - 08:30:24 CDT)
- force calculation peach gil (Tue Sep 26 2006 - 14:03:10 CDT)
- forces calculation peach gil (Tue Sep 26 2006 - 13:12:16 CDT)
- Namd list administration Cesar Luis Avila (Tue Sep 26 2006 - 10:13:58 CDT)
- redirecting stdout to a file olga hrydziuszko (Tue Sep 26 2006 - 08:11:57 CDT)
- how add bond in psf file? Luca Bellucci (Mon Sep 25 2006 - 08:18:27 CDT)
- imprecision in table energy A. Ozlem T. Bishop (Sun Sep 24 2006 - 09:57:50 CDT)
- checkpoint software for NAMD? Dan Strahs (Thu Sep 21 2006 - 15:37:47 CDT)
- Transition state Luca Bellucci (Thu Sep 21 2006 - 03:45:49 CDT)
- NAMD installation on Cray XD1 (AMD opteron 64-bit) Vani Krishna (Wed Sep 20 2006 - 23:46:37 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Wed Sep 20 2006 - 16:21:16 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Wed Sep 20 2006 - 16:08:07 CDT)
- PBS & local (scratch) space Arturas Ziemys (Wed Sep 20 2006 - 15:42:18 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Wed Sep 20 2006 - 15:40:16 CDT)
- force constant from gaussian to namd Shenoy, Sukesh (Wed Sep 20 2006 - 13:44:12 CDT)
- Water Hole Jacob Poehlsgaard (Tue Sep 19 2006 - 03:00:54 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Mon Sep 18 2006 - 16:20:42 CDT)
- Altix Performance Tuning Alessandro Cembran (Mon Sep 18 2006 - 13:18:52 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Fri Sep 15 2006 - 16:50:14 CDT)
- Water outside protein surface Pijush Ghosh (Fri Sep 15 2006 - 00:06:39 CDT)
- equilibrating the system with constrained Protein Dhiraj Srivastava (Thu Sep 14 2006 - 13:12:31 CDT)
- combined QM/MM calculation with NAMD Dhiraj Srivastava (Thu Sep 14 2006 - 10:35:28 CDT)
- Urea parameter bqluan (Wed Sep 13 2006 - 21:20:05 CDT)
- load balancer, athlon 64 dual core Leandro Martínez (Wed Sep 13 2006 - 07:06:08 CDT)
- top par for NAG, BMA ? Georgios Papadopoulos (Mon Sep 11 2006 - 11:47:38 CDT)
- Recentering the box on target molecule and wraping Arturas Ziemys (Mon Sep 11 2006 - 10:39:55 CDT)
- question regarding the use of reaction coordinate "distance-com" in ABF method Anahita Tafvizi (Sun Sep 10 2006 - 12:51:46 CDT)
- History file of an ABF smiulation Anahita Tafvizi (Sat Sep 09 2006 - 13:55:58 CDT)
- parameter file name E. Prabhu Raman (Fri Sep 08 2006 - 18:46:41 CDT)
- assigning atom type for parameterization Dhiraj Srivastava (Fri Sep 08 2006 - 15:23:02 CDT)
- Constraining angles ?? tamal_at_iitk.ac.in (Fri Sep 08 2006 - 13:36:31 CDT)
- Morse potential? Shenoy, Sukesh (Thu Sep 07 2006 - 21:57:56 CDT)
- Re: clarification(s) Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher Tom Caulfield (Thu Sep 07 2006 - 20:25:27 CDT)
- FW: Compilation problems on intel woodcrest Jacob Poehlsgaard (Thu Sep 07 2006 - 06:51:41 CDT)
- no parameter for CN8-ON6 Dhiraj Srivastava (Wed Sep 06 2006 - 19:45:59 CDT)
- Win64 version Dan Strahs (Wed Sep 06 2006 - 14:50:25 CDT)
- parameterizing novel molecule Dhiraj Srivastava (Wed Sep 06 2006 - 01:52:47 CDT)
- Unit cell information in binary output files Ben Roberts (Tue Sep 05 2006 - 22:23:13 CDT)
- help: how to scale the velocities by a factor for a subset of the system? Yong Zhang (Tue Sep 05 2006 - 21:59:25 CDT)
- Accelerating groups of atoms Cesar Luis Avila (Tue Sep 05 2006 - 15:18:59 CDT)
- atom name based paremeters E. Prabhu Raman (Tue Sep 05 2006 - 14:31:30 CDT)
- mDyne/A to kcal/mol/A2 Shenoy, Sukesh (Tue Sep 05 2006 - 14:29:59 CDT)
- mDyne/A to kcal/mol/A2 Shenoy, Sukesh (Tue Sep 05 2006 - 12:56:27 CDT)
- Re: vmd-l: imposing period boundary conditions in a simulation with a crystal Axel Kohlmeyer (Tue Sep 05 2006 - 12:00:19 CDT)
- wall clock vs secs/step metrics Brian Bennion (Tue Sep 05 2006 - 12:02:29 CDT)
- Re: DPPC.Pdb file needed Elsa S. Henriques (Tue Sep 05 2006 - 08:42:29 CDT)
- calculate potential energy from DCD file casoni\_at_libero\.it (Tue Sep 05 2006 - 07:21:57 CDT)
- DPPC.Pdb file needed Lechuga, Javier (Mon Sep 04 2006 - 11:27:49 CDT)
- minimization of a cyclic peptide with NAMD Idit Buch (Mon Sep 04 2006 - 04:22:03 CDT)
- problem with Dihedral Restraints Neelanjana Sengupta (Mon Sep 04 2006 - 01:13:44 CDT)
- namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher Thomas Caulfield (Sun Sep 03 2006 - 20:54:06 CDT)
- Re: CoordinateTransformation Sting (Sun Sep 03 2006 - 20:17:21 CDT)
- CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:34:48 CDT)
- CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:33:32 CDT)
- pbc_box Maria Gonzalez (Sun Sep 03 2006 - 12:49:09 CDT)
- electric field Ekta Khurana (Sat Sep 02 2006 - 20:17:21 CDT)
- Angles and dihedral generation Cesar Luis Avila (Fri Sep 01 2006 - 20:02:36 CDT)
- mechanical force calculation Gaurav Sharma (Thu Aug 31 2006 - 22:23:55 CDT)
- Minimization algorithms Per Jr. Greisen (Thu Aug 31 2006 - 11:19:19 CDT)
- Patches & psfgen Marcos Sotomayor (Thu Aug 31 2006 - 11:04:03 CDT)
- Trajectory analysis Luca Bellucci (Thu Aug 31 2006 - 08:00:49 CDT)
- mass of atoms changable? E. Prabhu Raman (Wed Aug 30 2006 - 16:19:46 CDT)
- NAMD 2.6 released Jim Phillips (Wed Aug 30 2006 - 15:18:36 CDT)
- Re: vdW parameters Jindal Shah (Wed Aug 30 2006 - 15:04:16 CDT)
- prob. with constraints Neelanjana Sengupta (Wed Aug 30 2006 - 11:08:56 CDT)
- vdW parameters Jindal Shah (Wed Aug 30 2006 - 10:38:19 CDT)
- DPPC.Pdb Lechuga, Javier (Wed Aug 30 2006 - 05:57:38 CDT)
- Counting H-bonds from a dcd file Nitin Bhardwaj (Tue Aug 29 2006 - 17:00:51 CDT)
- Fat node jonathan_at_ibt.unam.mx (Mon Aug 28 2006 - 21:02:13 CDT)
- error in loading "import hessian/charge from single point calculation" in paratool Dhiraj Srivastava (Mon Aug 28 2006 - 17:53:11 CDT)
- Using PsfGen Lechuga, Javier (Mon Aug 28 2006 - 14:29:52 CDT)
- Segmentation violation from APOA1 simulation on AMD64 Cesar Luis Avila (Mon Aug 28 2006 - 13:49:25 CDT)
- About CHARMM charge Luca Bellucci (Mon Aug 28 2006 - 04:10:45 CDT)
- Building molecule from topology file Lechuga, Javier (Sat Aug 26 2006 - 06:57:40 CDT)
- Type of force values in the tclForces script. Boyang Wang (Fri Aug 25 2006 - 11:34:44 CDT)
- Info: Adjusted background load on 11 nodes. Leandro Martínez (Fri Aug 25 2006 - 07:42:28 CDT)
- Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Fri Aug 25 2006 - 08:01:53 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Cesar Luis Avila (Sat Aug 26 2006 - 16:40:15 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Cesar Luis Avila (Sat Aug 26 2006 - 17:00:08 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Mon Aug 28 2006 - 12:21:49 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Tue Aug 29 2006 - 07:13:51 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Cesar Luis Avila (Sat Aug 26 2006 - 16:40:15 CDT)
- Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Fri Aug 25 2006 - 08:01:53 CDT)
- RMSD increases after restarts, decreases at the end of run hodak_at_chips.ncsu.edu (Thu Aug 24 2006 - 17:16:03 CDT)
- SMD of TFIIB! jonas condes (Thu Aug 24 2006 - 13:57:52 CDT)
- N-methylacetamide Neelanjana Sengupta (Tue Aug 22 2006 - 19:21:39 CDT)
- charmm toppology : internal coordinates Arturas Ziemys (Tue Aug 22 2006 - 16:39:00 CDT)
- NAMD 2.6b2 on IBM POWER5 with AIX 5.3 Operating System rossi_at_york.cuny.edu (Tue Aug 22 2006 - 12:45:59 CDT)
- pair interaction cutoff Holly Freedman (Mon Aug 21 2006 - 21:51:30 CDT)
- NAMD2.6b2: Segmentation fault Morad Alawneh (Mon Aug 21 2006 - 12:00:47 CDT)
- Re: NAMD2.6b2: Segmentation fault Jim Phillips (Mon Aug 21 2006 - 15:05:37 CDT)
- why this error? Hamsa Priya Mohana sundaram (Mon Aug 21 2006 - 10:20:46 CDT)
- Lipids into NAMD Lechuga, Javier (Mon Aug 21 2006 - 06:10:30 CDT)
- Lipid into NAMD Lechuga, Javier (Sat Aug 19 2006 - 09:33:26 CDT)
- SMD of TFIIB jonas condes (Fri Aug 18 2006 - 14:40:46 CDT)
- small query... hl332_at_drexel.edu (Fri Aug 18 2006 - 11:17:25 CDT)
- bad global exclusion count in LES Dhiraj Srivastava (Fri Aug 18 2006 - 02:11:11 CDT)
- topology and parameter file for non aromatic nitrogen in ring system. Dhiraj Srivastava (Thu Aug 17 2006 - 22:15:57 CDT)
- Re: long range electrostatics for alchemical transformation nmichaud_at_jhu.edu (Thu Aug 17 2006 - 20:38:13 CDT)
- NAMD OSX Xgrid Matthew Wilce (Thu Aug 17 2006 - 19:45:58 CDT)
- NAMD 2.6b1 released Jim Phillips (Thu Aug 17 2006 - 18:24:22 CDT)
- alchemical transformation Michael A. Wilson (Thu Aug 17 2006 - 12:04:55 CDT)
- deprotonated form of Proline molecule Dhiraj Srivastava (Tue Aug 15 2006 - 14:55:35 CDT)
- n terminal patch on proline Dhiraj Srivastava (Tue Aug 15 2006 - 11:53:47 CDT)
- Pulling of Center of Mass Rahul Bhowmik (Tue Aug 15 2006 - 10:44:07 CDT)
- Building for SunGrid Jonathan D. Proulx (Tue Aug 15 2006 - 09:05:38 CDT)
- negatively charged proline as substrate Dhiraj Srivastava (Mon Aug 14 2006 - 11:08:40 CDT)
- CHARMM top and par files for PO4 Alexe Bojovschi (Mon Aug 14 2006 - 03:53:20 CDT)
- user defined restraints? Georgios Papadopoulos (Fri Aug 11 2006 - 04:41:17 CDT)
- Ion Channel Jarzynski Alessandro Cembran (Thu Aug 10 2006 - 17:56:29 CDT)
- where is PSUL? Heme cystein link question? youbin tu (Thu Aug 10 2006 - 11:01:50 CDT)
- Linking with -memory paranoid Cesar Luis Avila (Thu Aug 10 2006 - 10:49:43 CDT)
- 2D Ewald summation Xiongce Zhao (Thu Aug 10 2006 - 10:08:46 CDT)
- Changes to dihedral angles Neelanjana Sengupta (Wed Aug 09 2006 - 17:14:36 CDT)
- Running NAMD on debug mode Cesar Luis Avila (Wed Aug 09 2006 - 09:46:06 CDT)
- Fwd: extracting waters from DCD yi wang (Tue Aug 08 2006 - 16:50:55 CDT)
- Cham++ errors Kramer Campen (Tue Aug 08 2006 - 15:01:07 CDT)
- extracting waters from DCD Narender Singh Maan (Tue Aug 08 2006 - 14:04:04 CDT)
- Re: extracting waters from DCD Jerome Henin (Tue Aug 08 2006 - 15:55:01 CDT)
- Re: extracting waters from DCD Neelanjana Sengupta (Tue Aug 08 2006 - 15:57:56 CDT)
- Re: extracting waters from DCD Nicholas M Glykos (Wed Aug 09 2006 - 06:54:44 CDT)
- Re: extracting waters from DCD Marc Baaden (Wed Aug 09 2006 - 08:36:03 CDT)
- Re: extracting waters from DCD Joshua A. Speidel (Wed Aug 09 2006 - 09:42:34 CDT)
- Acetaldehyde Dihedral Parameters Kevser Göçmen Topal (Wed Jun 06 2007 - 10:33:14 CDT)
- Re: Acetaldehyde Dihedral Parameters L. Michel Espinoza-Fonseca (Wed Jun 06 2007 - 11:05:20 CDT)
- Re: Acetaldehyde Dihedral Parameters Peter Freddolino (Wed Jun 06 2007 - 11:19:42 CDT)
- Re: Acetaldehyde Dihedral Parameters Peter Freddolino (Wed Jun 06 2007 - 11:51:57 CDT)
- Re: Acetaldehyde Dihedral Parameters L. Michel Espinoza-Fonseca (Wed Jun 06 2007 - 12:21:38 CDT)
- Re: Acetaldehyde Dihedral Parameters Peter Freddolino (Wed Jun 06 2007 - 14:28:20 CDT)
- data structure of neighbor list bqluan (Tue Aug 08 2006 - 10:37:52 CDT)
- questions regarding output data of an ABF simulation Anahita Tafvizi (Mon Aug 07 2006 - 15:27:34 CDT)
- Problem with Alchemical FEP Jawahar Neelankatan (Mon Aug 07 2006 - 09:24:55 CDT)
- atom type HZ4 not found Dhiraj Srivastava (Sat Aug 05 2006 - 13:27:12 CDT)
- pairinteractionSelf Holly Freedman (Thu Aug 03 2006 - 21:41:55 CDT)
- topology file with CT carbon Lacramioara Negureanu (Thu Aug 03 2006 - 19:46:59 CDT)
- Simulation of a 1000 water molecules Shenoy, Sukesh (Thu Aug 03 2006 - 13:19:34 CDT)
- Re: Simulation of a 1000 water molecules L. Michel Espinoza-Fonseca (Thu Aug 03 2006 - 14:34:47 CDT)
- Re: Simulation of a 1000 water molecules griadi_at_utalca.cl (Thu Aug 03 2006 - 15:12:37 CDT)
- Re: Simulation of a 1000 water molecules Brian Bennion (Thu Aug 03 2006 - 15:05:16 CDT)
- Re: Simulation of a 1000 water molecules Neelanjana Sengupta (Thu Aug 03 2006 - 15:11:37 CDT)
- Re: Simulation of a 1000 water molecules Jerome Henin (Thu Aug 03 2006 - 16:35:29 CDT)
- fad topology and parameter file Dhiraj Srivastava (Thu Aug 03 2006 - 02:11:45 CDT)
- FEP implementation in NAMD nmichaud_at_jhu.edu (Wed Aug 02 2006 - 18:17:53 CDT)
- Using LES with AMBER parm files Kramer Campen (Wed Aug 02 2006 - 14:35:05 CDT)
- coordination chemistry with NAMD Gaurav Sharma (Wed Aug 02 2006 - 14:04:04 CDT)
- two chain in pdb file Dhiraj Srivastava (Tue Aug 01 2006 - 01:46:01 CDT)
- missing atoms in pdb file. Dhiraj Srivastava (Tue Aug 01 2006 - 01:36:04 CDT)
- Cell membranes with lipids different from POPC and POPE Lechuga, Javier (Mon Jul 31 2006 - 18:03:59 CDT)
- TeraGrid Efficiency a-yermakova_at_northwestern.edu (Mon Jul 31 2006 - 12:22:41 CDT)
- collision correction of Locally Enhanced Sampling Dhiraj Srivastava (Sun Jul 30 2006 - 15:14:52 CDT)
- Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
- New alchemical FEP tutorial Jerome Henin (Fri Jul 28 2006 - 14:13:40 CDT)
- Alchemical Free Energy Perturbation Simulation Jawahar Neelankatan (Fri Jul 28 2006 - 11:18:20 CDT)
- simple query.. hl332_at_drexel.edu (Thu Jul 27 2006 - 11:06:39 CDT)
- About pressureProfile command for non-equilibrium system. Boyang Wang (Wed Jul 26 2006 - 19:50:20 CDT)
- Equilibration problem pedro mansilla (Wed Jul 26 2006 - 13:47:44 CDT)
- topology files a-yermakova_at_northwestern.edu (Wed Jul 26 2006 - 12:54:21 CDT)
- namdenergy Luca Bellucci (Wed Jul 26 2006 - 10:02:58 CDT)
- simulation crashing with nan Jackie (Wed Jul 26 2006 - 08:49:56 CDT)
- VDW energy in CHARMM force field Gan, Yong (Tue Jul 25 2006 - 15:49:37 CDT)
- NBFix and NAMD Neelanjana Sengupta (Tue Jul 25 2006 - 13:53:48 CDT)
- LES Jackie (Tue Jul 25 2006 - 11:54:51 CDT)
- psfgen gets ATP chiral atoms wrong John Wise (Mon Jul 24 2006 - 15:43:23 CDT)
- InfiniPath and NAMD David Sept (Mon Jul 24 2006 - 14:57:03 CDT)
- temp autocorrelation Swarna Patra (Sun Jul 23 2006 - 20:00:09 CDT)
- Torque aplication with SMD pedro mansilla (Sun Jul 23 2006 - 11:38:44 CDT)
- Queries on patches, GDP-topology gamini_at_ncbs.res.in (Sat Jul 22 2006 - 07:36:15 CDT)
- Autopsf a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 16:00:41 CDT)
- PME grid error during minimization a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 15:05:10 CDT)
- (No subject) a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 15:04:47 CDT)
- unit cell information from dcd file Hamsa Priya Mohana sundaram (Thu Jul 20 2006 - 11:34:51 CDT)
- Tcl parsing of NAMD config file does not work. Klon, Anthony (Thu Jul 20 2006 - 07:43:09 CDT)
- need pair interaction energies, not forces Holly Freedman (Wed Jul 19 2006 - 22:20:06 CDT)
- #QNAN: Please help! a-yermakova_at_northwestern.edu (Wed Jul 19 2006 - 14:09:40 CDT)
- total mol calculation Jackie (Wed Jul 19 2006 - 14:08:07 CDT)
- total mol calculation Jackie (Wed Jul 19 2006 - 14:07:57 CDT)
- bulid psf for structure already with hydrogens Ching Wong (Wed Jul 19 2006 - 14:02:32 CDT)
- Re: About the unit of "efield" a-yermakova_at_northwestern.edu (Wed Jul 19 2006 - 13:24:39 CDT)
- help!!! hl332_at_drexel.edu (Wed Jul 19 2006 - 00:12:23 CDT)
- plz help!! hl332_at_drexel.edu (Tue Jul 18 2006 - 10:30:07 CDT)
- About the unit of "efield" wang (Tue Jul 18 2006 - 00:28:03 CDT)
- FATAL ERROR: pairlist i_upper mismatch! xiaojing gong (Mon Jul 17 2006 - 21:43:46 CDT)
- Minimizing and Equilibrating a-yermakova_at_northwestern.edu (Mon Jul 17 2006 - 13:12:52 CDT)
- linux cluster problems Per Jr. Greisen (Mon Jul 17 2006 - 04:20:57 CDT)
- Restarting velocities Per Jr. Greisen (Sun Jul 16 2006 - 05:47:58 CDT)
- unsubscribe Raj NK (Sat Jul 15 2006 - 21:46:00 CDT)
- Possible bug on NAMD 2.6B1? Cesar Avila (Sat Jul 15 2006 - 11:06:23 CDT)
- linux cluster problems Per Jr. Greisen (Sat Jul 15 2006 - 05:44:28 CDT)
- restart the simulation Tamal Banerjee (Fri Jul 14 2006 - 23:06:25 CDT)
- If I run NAMD on small computer, which processor is the best for NAMD under Linux? xiaojing gong (Fri Jul 14 2006 - 02:25:48 CDT)
- qsub on a linux cluster Per Jr. Greisen (Fri Jul 14 2006 - 02:12:54 CDT)
- splitting up long run leads to very different DNA conformation in E field Todd Trimble (Thu Jul 13 2006 - 18:40:10 CDT)
- log File - pressure not read a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 15:32:37 CDT)
- any SD minimization in NAMD? Ching Wong (Thu Jul 13 2006 - 14:59:57 CDT)
- NAMD on TeraGrid: OpenMP? a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 12:43:53 CDT)
- solvating a protein a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 11:16:04 CDT)
- NAMD on TeraGrid a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 11:04:17 CDT)
- About the module of "External Electric Field " wang (Wed Jul 12 2006 - 01:47:29 CDT)
- third time..can someone help!! hl332_at_drexel.edu (Tue Jul 11 2006 - 22:09:22 CDT)
- Computing Potential of Mean Force --SMD-cv gamini_at_ncbs.res.in (Tue Jul 11 2006 - 15:36:45 CDT)
- force calculation during to conformational change Gaurav Sharma (Tue Jul 11 2006 - 11:38:15 CDT)
- NVT nose-hoover hamiltonian in SMD? interesting.contraceptive_at_gmail.com (Mon Jul 10 2006 - 19:30:56 CDT)
- UseConstantRatio between "run" Alessandro Cembran (Mon Jul 10 2006 - 18:37:38 CDT)
- many short runs or one long run? Ching Wong (Mon Jul 10 2006 - 15:04:42 CDT)
- Protonation state Ching Wong (Mon Jul 10 2006 - 14:49:57 CDT)
- (No subject) a-yermakova_at_northwestern.edu (Mon Jul 10 2006 - 12:50:19 CDT)
- caps AYTUG TUNCEL (Mon Jul 10 2006 - 12:53:23 CDT)
- autoionize plugin.. hl332_at_drexel.edu (Mon Jul 10 2006 - 11:32:18 CDT)
- namdenergy plugin Chandra Ramananjara (Sun Jul 09 2006 - 23:47:10 CDT)
- RNA to DNA nisha_at_ncbs.res.in (Sat Jul 08 2006 - 00:29:24 CDT)
- across the nodes, namd jobs don't get enough CPU! M. Madhu (Fri Jul 07 2006 - 11:00:59 CDT)
- TCL Forces and Help on Script Joshua D. Moore (Thu Jul 06 2006 - 13:52:00 CDT)
- Rattle Algorithm Tamal Banerjee (Thu Jul 06 2006 - 01:52:49 CDT)
- Re: About the error of "Tcl interface" wang (Thu Jul 06 2006 - 00:26:31 CDT)
- About the error of "Tcl interface" wang (Wed Jul 05 2006 - 21:05:27 CDT)
- NAMD to Amber AYTUG TUNCEL (Tue Jul 04 2006 - 18:56:23 CDT)
- unsubscribe Noah Edelson (Tue Jul 04 2006 - 15:12:53 CDT)
- NAMDenergy Holly Freedman (Tue Jul 04 2006 - 12:44:59 CDT)
- OXT in pdb file nisha_at_ncbs.res.in (Tue Jul 04 2006 - 05:09:51 CDT)
- The problem of "SMD and smd.tcl" James W (Mon Jul 03 2006 - 20:33:57 CDT)
- Box size santanu chatterjee (Mon Jul 03 2006 - 16:33:33 CDT)
- Help on mutation Pijush Ghosh (Sun Jul 02 2006 - 01:24:19 CDT)
- Simulation Hangs during minimization Cesar Luis Avila (Mon Jul 03 2006 - 15:20:38 CDT)
- Data from Output file Tamal Banerjee (Mon Jul 03 2006 - 03:01:48 CDT)
- Protonation states Ching Wong (Fri Jun 30 2006 - 19:04:32 CDT)
- Problem equilibrating with low pressure santanu chatterjee (Fri Jun 30 2006 - 16:31:55 CDT)
- Constant Energy Simulations Eric Perim (Fri Jun 30 2006 - 08:42:48 CDT)
- Hi Moumita Maiti (Fri Jun 30 2006 - 04:26:18 CDT)
- what does "syntax error" mean in VMD? and does confinment to some residue will cause error? xiaojing gong (Thu Jun 29 2006 - 23:56:51 CDT)
- RE£º Re: £º Re: problems for runing NAMD on parallel computers xiaojing gong (Thu Jun 29 2006 - 23:32:46 CDT)
- Do I need to use an xsc file to restart a simulation in NVT? Ana Celia Araujo Vila Verde (Wed Jun 28 2006 - 10:41:07 CDT)
- Heating Up a system. Cesar Luis Avila (Thu Jun 29 2006 - 16:06:21 CDT)
- Do I need to use an xsc file to restart a simulation in NVT? Ana Celia Araujo Vila Verde (Wed Jun 28 2006 - 14:05:27 CDT)
- Binary for MacOSX-i686 Mikolai Fajer (Wed Jun 28 2006 - 13:53:00 CDT)
- Pressure control santanu chatterjee (Wed Jun 28 2006 - 13:43:52 CDT)
- problems for runing NAMD on parallel computers xiaojing gong (Wed Jun 28 2006 - 09:15:44 CDT)
- Problem with C++ libraries Baudilio Tejerina (Tue Jun 27 2006 - 10:29:32 CDT)
- psfgen and charmm19: is there any inconsistency? Magali Cottevieille (Tue Jun 27 2006 - 03:18:20 CDT)
- Calculating or Outputing Forces Joshua D. Moore (Mon Jun 26 2006 - 21:00:44 CDT)
- Re: ABF Simulation Tyler Luchko (Mon Jun 26 2006 - 19:45:02 CDT)
- Time of MD edu (Fri Jun 23 2006 - 13:59:54 CDT)
- Question about Van der Waals radii Chandra Ramananjara (Mon Jun 26 2006 - 09:14:10 CDT)
- PME pair interaction analysis Holly Freedman (Sun Jun 25 2006 - 16:17:41 CDT)
- Re: Boiling temperature of water. Boyang Wang (Thu Jun 22 2006 - 21:38:54 CDT)
- Boiling temperature of water. Boyang Wang (Thu Jun 22 2006 - 19:20:09 CDT)
- Autoionize error: spontaneously quits dora guzman (Wed Jun 21 2006 - 18:38:51 CDT)
- Re: NAMD results depend on # of processors!!?? Jan Saam (Wed Jun 21 2006 - 16:25:21 CDT)
- calculation (continue) edu (Wed Jun 21 2006 - 16:03:40 CDT)
- error using Namdenergy Chandra Ramananjara (Wed Jun 21 2006 - 15:04:19 CDT)
- NAMD: run problem bo baker (Wed Jun 21 2006 - 14:53:41 CDT)
- Is clock skew a problem for charm++ Jan Saam (Tue Jun 20 2006 - 17:37:19 CDT)
- Re: Is clock skew a problem for charm++ Jan Saam (Tue Jun 20 2006 - 17:50:46 CDT)
- Re: Re: Is clock skew a problem for charm++ Gengbin Zheng (Wed Jun 21 2006 - 02:08:08 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Wed Jun 21 2006 - 08:52:54 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Wed Jun 21 2006 - 14:38:09 CDT)
- Re: Re: Is clock skew a problem for charm++ Gengbin Zheng (Wed Jun 21 2006 - 23:17:07 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Thu Jun 22 2006 - 06:56:26 CDT)
- Re: Re: Is clock skew a problem for charm++ Sameer Kumar (Thu Jun 22 2006 - 08:04:11 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Thu Jun 22 2006 - 12:54:47 CDT)
- NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jan Saam (Wed Jun 21 2006 - 15:55:13 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Brian Bennion (Wed Jun 21 2006 - 17:24:11 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jan Saam (Thu Jun 22 2006 - 06:36:50 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jerome Henin (Wed Jun 21 2006 - 17:34:23 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jan Saam (Thu Jun 22 2006 - 06:45:47 CDT)
- Re: Re: Is clock skew a problem for charm++ hrh (Wed Jun 21 2006 - 06:33:05 CDT)
- Re: Re: Is clock skew a problem for charm++ Gengbin Zheng (Wed Jun 21 2006 - 02:08:08 CDT)
- Re: Is clock skew a problem for charm++ Jan Saam (Tue Jun 20 2006 - 17:50:46 CDT)
- Conversion for forces Gianluca Interlandi (Tue Jun 20 2006 - 14:05:28 CDT)
- Tcl, minimization and MD (Warning: I am a lazy ignorant) Edelmiro Moman (Tue Jun 20 2006 - 10:20:09 CDT)
- RE: Tcl, minimization and MD (Warning: I am a lazy ignorant) JC Gumbart (Tue Jun 20 2006 - 10:38:17 CDT)
- Re: Tcl, minimization and MD (Warning: I am a lazy ignorant) Peter Freddolino (Tue Jun 20 2006 - 10:40:52 CDT)
- Regarding box-size Moumita Maiti (Tue Jun 20 2006 - 06:32:43 CDT)
- Angle 2, Where is the problem [IMPORTANT] linefinc (Mon Jun 19 2006 - 11:50:41 CDT)
- support TIP5? doubt on high temperature MD Ching Wong (Mon Jun 19 2006 - 20:31:52 CDT)
- extended system or Basis Vector Ching Wong (Mon Jun 19 2006 - 20:29:01 CDT)
- non-cubic boxes for Periodic Boundary Conditions George M. Giambasu (Mon Jun 19 2006 - 17:38:31 CDT)
- Lipid bilayer center go away from center of system. ghg_at_xalt.am (Sun Jun 18 2006 - 10:10:38 CDT)
- chage free energy edu (Fri Jun 16 2006 - 13:58:08 CDT)
- Re. Namd window network problem edu (Fri Jun 16 2006 - 10:33:25 CDT)
- Angle CO2 Problem linefinc (Fri Jun 16 2006 - 06:08:23 CDT)
- Re: free energy calculate Taeho Kim (Fri Jun 16 2006 - 01:30:29 CDT)
- free energy calculate Taeho Kim (Fri Jun 16 2006 - 00:52:16 CDT)
- Vibrational mode analysis Gianluca Interlandi (Thu Jun 15 2006 - 19:31:40 CDT)
- Re: Vibrational mode analysis L. Michel Espinoza-Fonseca (Thu Jun 15 2006 - 19:47:29 CDT)
- Re: Vibrational mode analysis Michael Grabe (Thu Jun 15 2006 - 20:36:16 CDT)
- Re: Vibrational mode analysis Richard Law (Thu Jun 15 2006 - 20:52:18 CDT)
- NAMD: compile problem bo baker (Thu Jun 15 2006 - 19:04:58 CDT)
- problem in minimization while running Moumita Maiti (Thu Jun 15 2006 - 15:59:50 CDT)
- NAMD compile in Mac OSX and IBM XL C/C++ bo baker (Thu Jun 15 2006 - 15:18:56 CDT)
- psfgen: last CTER does not work Morad Alawneh (Thu Jun 15 2006 - 14:30:14 CDT)
- Namd window network problem edu (Thu Jun 15 2006 - 13:55:51 CDT)
- help with adding a new force filed into NAMD liu liuxiandong (Thu Jun 15 2006 - 10:44:10 CDT)
- slow NAMD simulations on a AMD athlon64 in SUSE linux Fam Eklund (Wed Jun 14 2006 - 16:28:38 CDT)
- Compile NAMD on Bluegene Dong Luo (Wed Jun 14 2006 - 16:17:13 CDT)
- Re: Compile NAMD on Bluegene Mgr. Lubos Vrbka (Thu Jun 15 2006 - 01:01:25 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 01:11:34 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Thu Jun 15 2006 - 09:48:32 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 12:16:40 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Thu Jun 15 2006 - 14:16:30 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Fri Jun 16 2006 - 13:56:46 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Thu Jun 15 2006 - 11:35:18 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 12:04:49 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 01:11:34 CDT)
- Re: Compile NAMD on Bluegene Mgr. Lubos Vrbka (Thu Jun 15 2006 - 01:01:25 CDT)
- namd: problem bo baker (Wed Jun 14 2006 - 12:04:47 CDT)
- Superctitiacal CO2 linefinc (Wed Jun 14 2006 - 09:58:58 CDT)
- the patching problem in psfgen Moumita Maiti (Wed Jun 14 2006 - 06:13:20 CDT)
- Altix performances Alessandro Cembran (Tue Jun 13 2006 - 17:40:59 CDT)
- Velocity unit ofvelocity in NAMD the binary files Amin R. Mazloom (Tue Jun 13 2006 - 15:43:09 CDT)
- namd: problem bo baker (Tue Jun 13 2006 - 14:16:56 CDT)
- Unit of Velocity in the Velocity files Amin R. Mazloom (Tue Jun 13 2006 - 11:36:56 CDT)
- Is the GBSA model in NAMD ? wang (Tue Jun 13 2006 - 01:42:14 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Tue Jun 13 2006 - 02:00:01 CDT)
- Re: Is the GBSA model in NAMD ? wang (Tue Jun 13 2006 - 04:03:08 CDT)
- Re: Is the GBSA model in NAMD ? Joshua D. Moore (Tue Jun 13 2006 - 12:32:49 CDT)
- Re: Is the GBSA model in NAMD ? dimka (Tue Jun 13 2006 - 15:17:55 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Tue Jun 13 2006 - 22:24:30 CDT)
- Re: Is the GBSA model in NAMD ? Richard Wood (Wed Jun 14 2006 - 05:22:22 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Wed Jun 14 2006 - 09:00:45 CDT)
- Re: Is the GBSA model in NAMD ? Peter Freddolino (Wed Jun 14 2006 - 09:16:58 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Tue Jun 13 2006 - 02:00:01 CDT)
- (no subject) Michael Grabe (Mon Jun 12 2006 - 20:38:48 CDT)
- setenv: command not found bo baker (Mon Jun 12 2006 - 18:55:39 CDT)
- Pairlist warnings Alessandro Cembran (Sat Jun 10 2006 - 16:58:07 CDT)
- Interrupted system call Edelmiro Moman (Fri Jun 09 2006 - 02:21:25 CDT)
- question on phosphotyrosine parameters from charmm Mao Xiang (Thu Jun 08 2006 - 22:32:06 CDT)
- Re: Some problem on pair force calculation Sting (Thu Jun 08 2006 - 20:40:11 CDT)
- DCD to PDB conversion Edelmiro Moman (Thu Jun 08 2006 - 02:57:31 CDT)
- Constant electric field to selected atoms. hamdi (Wed Jun 07 2006 - 09:08:32 CDT)
- Factorization in PMEGridSize Edelmiro Moman (Wed Jun 07 2006 - 04:36:54 CDT)
- Where to put the "nodelist" file Edelmiro Moman (Wed Jun 07 2006 - 02:45:37 CDT)
- Some problem on pair force calculation Sting (Tue Jun 06 2006 - 22:27:30 CDT)
- TCL forces and boundary conditions Tyler Luchko (Tue Jun 06 2006 - 18:23:27 CDT)
- Re: vmd-l: snoze pa (Tue Jun 06 2006 - 17:47:34 CDT)
- output on Linux-amd64-MPI Seungho Choe (Tue Jun 06 2006 - 15:47:33 CDT)
- Some problem on pair force calculation Sting (Tue Jun 06 2006 - 08:32:48 CDT)
- PMF error wang (Mon Jun 05 2006 - 21:38:18 CDT)
- a error during install charm-5.9 snowyowls (Mon Jun 05 2006 - 18:45:14 CDT)
- CMAP and NAMD L. Michel Espinoza-Fonseca (Mon Jun 05 2006 - 19:16:21 CDT)
- getting #.IND #QNAN after phase 8 Amin R. Mazloom (Mon Jun 05 2006 - 14:25:25 CDT)
- FEP error "atoms moving too fast" jz7_at_duke.edu (Sun Jun 04 2006 - 10:39:37 CDT)
- the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
- Error on renaming file Morad Alawneh (Fri Jun 02 2006 - 10:31:21 CDT)
- A puzzling problem about adsorption energy in solution. Boyang Wang (Thu Jun 01 2006 - 17:39:26 CDT)
- help on compiling error Binquan luan (Thu Jun 01 2006 - 11:32:44 CDT)
- Starting out with NAMD/VMD nisha_at_ncbs.res.in (Thu Jun 01 2006 - 02:22:21 CDT)
- Re: Re: Large energy fluctuation Sting (Tue May 31 2005 - 21:38:38 CDT)
- Free energy from MD Simulation Nitin Bhardwaj (Wed May 31 2006 - 17:13:51 CDT)
- Large energy fluctuation Sting (Mon May 30 2005 - 21:44:44 CDT)
- Density of water santanu chatterjee (Tue May 30 2006 - 14:04:32 CDT)
- parallel NAMD output problem ARTURAS ZIEMYS (Tue May 30 2006 - 11:27:36 CDT)
- Re: ABF: example works; more questions. Jan Saam (Tue May 30 2006 - 11:01:29 CDT)
- SMD Energy Pijush Ghosh (Tue May 30 2006 - 10:47:32 CDT)
- Repeating again: Periodic velocity pulls hl332_at_drexel.edu (Tue May 30 2006 - 09:51:14 CDT)
- ABF: example works now; more questions. Jan Saam (Tue May 30 2006 - 08:57:15 CDT)
- Large energy fluctuation Sting (Fri Apr 08 2005 - 07:09:07 CDT)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CAI Per Jr. Greisen (Tue May 30 2006 - 04:08:56 CDT)
- questions regrading ABF Jan Saam (Mon May 29 2006 - 10:47:48 CDT)
- [Fwd: Re: Specific Heat Calculation with VMD] Ayþe Özlem Sezerman (Mon May 29 2006 - 08:31:31 CDT)
- Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Mon May 29 2006 - 00:49:42 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 00:36:34 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=90=B4=E6=B4=AA=E6=98=8E?= (Mon May 29 2006 - 03:54:12 CDT)
- RE: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 09:51:02 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Tue May 30 2006 - 11:22:42 CDT)
- RE: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 12:01:21 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Wed May 31 2006 - 00:05:38 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Wed May 31 2006 - 03:48:41 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Tue May 30 2006 - 11:47:58 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=90=B4=E6=B4=AA=E6=98=8E?= (Wed May 31 2006 - 01:45:20 CDT)
- RE: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Wed May 31 2006 - 09:19:11 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=90=B4=E6=B4=AA=E6=98=8E?= (Mon May 29 2006 - 03:54:12 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 00:36:34 CDT)
- Periodic cell has become too small santanu chatterjee (Sun May 28 2006 - 17:42:29 CDT)
- Basic question. Taeho Kim (Fri May 26 2006 - 20:24:54 CDT)
- Free energy with amber topology Stefano Corni (Fri May 26 2006 - 02:53:28 CDT)
- Periodic velcoity pulls hl332_at_drexel.edu (Fri May 26 2006 - 12:15:55 CDT)
- [Fwd: Specific Heat Calculation with VMD] Ayþe Özlem Sezerman (Fri May 26 2006 - 09:29:31 CDT)
- Specific Heat Calculation with VMD Ayþe Özlem Sezerman (Fri May 26 2006 - 08:46:02 CDT)
- Remove water to close to the protein? Per Jr. Greisen (Fri May 26 2006 - 07:59:27 CDT)
- Spike during minimization of protein with water Per Jr. Greisen (Fri May 26 2006 - 02:47:01 CDT)
- something about simulation of small molecules in NAMD q=CF=20=B3=C2?= (Thu May 25 2006 - 21:00:43 CDT)
- Water simulation with namd santanu chatterjee (Wed May 24 2006 - 16:32:49 CDT)
- How to make a virtual bond? patrick wintrode (Wed May 24 2006 - 13:27:24 CDT)
- Transition path sampling Hemant Kushwaha (Tue May 23 2006 - 09:11:17 CDT)
- Re: make the helix longer lily jin (Mon May 22 2006 - 15:19:57 CDT)
- make the helix longer lily jin (Mon May 22 2006 - 13:16:06 CDT)
- Saving the coordinates of DCD file in pdb format Ayþe Özlem Sezerman (Mon May 22 2006 - 04:50:45 CDT)
- About loadcoors -- is there a loadvelocity? Boyang Wang (Fri May 19 2006 - 13:01:11 CDT)
- NDON! and NACC! in Parameter Files Joshua D. Moore (Thu May 18 2006 - 19:10:28 CDT)
- DCD file Ayse Ozlem Sezerman (Thu May 18 2006 - 02:09:40 CDT)
- LDB problem on Dual Atlon64 X2 Sebastian Wasilewski (Wed May 17 2006 - 17:07:17 CDT)
- How to turn off electrostatic interactions (PME). Maxim Fedorov (Wed May 17 2006 - 15:58:07 CDT)
- Rigid bonds for United Atom Methylene Chloride CH2Cl2 Joshua D. Moore (Wed May 17 2006 - 15:22:41 CDT)
- pair interaction analysis of multiple trajectories with different timestep Shirley Li (Wed May 17 2006 - 10:18:03 CDT)
- question on the charged system Hyonseok Hwang (Wed May 17 2006 - 01:31:08 CDT)
- SMD lily jin (Tue May 16 2006 - 19:18:28 CDT)
- How to make a disulphide bond lily jin (Tue May 16 2006 - 13:02:51 CDT)
- Re: Simulation on AMD64 Dual Core - threads lose connection Sławek Orłowski (Tue May 16 2006 - 01:04:39 CDT)
- pair interaction Shirley Li (Mon May 15 2006 - 19:13:27 CDT)
- NAMD support for MNDO semi-empirical model Chandra Ramananjara (Mon May 15 2006 - 10:34:07 CDT)
- Cannot open file 'pair.pdb' Sandeep Agrawal (Mon May 15 2006 - 07:32:42 CDT)
- Taurine parameters Morad Alawneh (Sat May 13 2006 - 10:13:50 CDT)
- UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params Sandeep Agrawal (Fri May 12 2006 - 04:17:06 CDT)
- Nose-Hoover langevin piston pressure control and target surface tension Hyonseok Hwang (Thu May 11 2006 - 23:04:55 CDT)
- Water liquid-vapor interface Jindal Shah (Thu May 11 2006 - 13:24:43 CDT)
- cluster / scratch space ziemys_at_ecr6.ohio-state.edu (Thu May 11 2006 - 09:28:06 CDT)
- How to include more parameterfiles in NAMD Per Jr. Greisen (Thu May 11 2006 - 09:36:36 CDT)
- Simulation on AMD64 Dual Core - threads lose connection Sławek Orłowski (Thu May 11 2006 - 02:42:00 CDT)
- explicit hydrogen bonds Matthew Wilce (Thu May 11 2006 - 00:54:20 CDT)
- namd: adding water molecules Sergio Anis (Wed May 10 2006 - 21:12:43 CDT)
- namd: adding water molecules Sergio Anis (Wed May 10 2006 - 21:52:33 CDT)
- CMAP Per Jr. Greisen (Wed May 10 2006 - 12:04:07 CDT)
- periodic cell too small genie lfs (Wed May 10 2006 - 04:48:44 CDT)
- Some basic questions about NAMD Shirley Li (Tue May 09 2006 - 15:01:37 CDT)
- les + conformational free energy L. Michel Espinoza-Fonseca (Tue May 09 2006 - 08:31:51 CDT)
- Re: Heme - Cysteine link Sławek Orłowski (Tue May 09 2006 - 08:20:50 CDT)
- CMAP Per Jr. Greisen (Tue May 09 2006 - 06:16:45 CDT)
- Heme - Cysteine link Muhittin Emre Özdemir (Tue May 09 2006 - 04:06:46 CDT)
- Re: About timestep again. Boyang Wang (Mon May 08 2006 - 17:38:07 CDT)
- About timestep again. -- Fastest motion O-H streching period 10 fs. Boyang Wang (Mon May 08 2006 - 11:14:37 CDT)
- Timestep -- Can I use 2 fs timestep for 50 nanoseconds simulation? Boyang Wang (Mon May 08 2006 - 10:22:05 CDT)
- Timestep. Boyang Wang (Mon May 08 2006 - 10:05:17 CDT)
- hi... Navratna Vajpai (Mon May 08 2006 - 04:36:33 CDT)
- change in Disulphide Patches Navratna Vajpai (Mon May 08 2006 - 03:05:28 CDT)
- Clustermatic and NFS mount Gianluca Interlandi (Sun May 07 2006 - 15:49:40 CDT)
- a basic question Tamal Banerjee (Sun May 07 2006 - 12:04:31 CDT)
- protein moves away from water box Shirley Li (Fri May 05 2006 - 14:25:40 CDT)
- sound velocity of water Binquan luan (Thu May 04 2006 - 18:10:53 CDT)
- Cannot specify both an initial temperature and a velocity file Osman Yogurtcu (Thu May 04 2006 - 06:44:03 CDT)
- MMPBSA... Raul Araya Secchi (Wed May 03 2006 - 16:23:46 CDT)
- Asymmetric water molecule found??? Elsa F. Sousa Henriques (Wed May 03 2006 - 02:59:26 CDT)
- TRIO Gianluca Interlandi (Tue May 02 2006 - 16:55:09 CDT)
- [Fwd: Re: SMD of small molecule dimer] dora guzman (Tue May 02 2006 - 11:59:32 CDT)
- convert .dcd into .trr Shirley Li (Tue May 02 2006 - 12:37:53 CDT)
- one residue rmsd snoze pa (Mon May 01 2006 - 17:49:02 CDT)
- fix atoms in minimisation Maria Gonzalez (Mon May 01 2006 - 10:14:35 CDT)
- about TCL boundary forces gbellesia_at_chem.ucsb.edu (Sat Apr 29 2006 - 17:16:54 CDT)
- parameters for camphor Sergio Anis (Mon May 01 2006 - 12:35:04 CDT)
- SMD of small molecule dimer dora guzman (Fri Apr 28 2006 - 12:05:39 CDT)
- SMD of small molecule dimer dora guzman (Thu Apr 27 2006 - 19:28:20 CDT)
- simulated annealing genie lfs (Mon May 01 2006 - 11:04:35 CDT)
- [Fwd: HD speed ??] Mark Abraham (Sun Apr 30 2006 - 12:28:04 CDT)
- HD speed ?? Georgios Papadopoulos (Sun Apr 30 2006 - 03:13:36 CDT)
- NAD splits up into 3 pieces Per Jr. Greisen (Sun Apr 30 2006 - 07:13:02 CDT)
- simulations of periodic lattice List User (Sun Apr 30 2006 - 02:38:00 CDT)
- Simulation with denaturants? patrick wintrode (Sat Apr 29 2006 - 14:00:02 CDT)
- how long should the simulation be run genie lfs (Sat Apr 29 2006 - 04:33:50 CDT)
- parameter and topology file for ethanol Per Jr. Greisen (Sat Apr 29 2006 - 03:32:42 CDT)
- Re: modeling zinc binding site Jan Kosinski (Fri Apr 28 2006 - 10:25:20 CDT)
- OPLS force field for carbon tetrachloride ( ccl4 ) ? wzhuang (Fri Apr 28 2006 - 02:15:44 CDT)
- why pressure is fluctuating so much Tamal Banerjee (Thu Apr 27 2006 - 22:40:28 CDT)
- error message snoze pa (Thu Apr 27 2006 - 16:15:35 CDT)
- binary.coor to ascII.coor paul.dalhaimer_at_yale.edu (Thu Apr 27 2006 - 12:14:52 CDT)
- how to add charged particles manually. ayhan duzgun (Wed Apr 26 2006 - 21:24:13 CDT)
- two references- I got them, thank you! Ioana Cozmuta (Wed Apr 26 2006 - 16:15:11 CDT)
- two references Ioana Cozmuta (Wed Apr 26 2006 - 15:18:28 CDT)
- NAMD is unstable on myrinet connecting cpus xiaojing gong (Wed Apr 26 2006 - 09:15:21 CDT)
- How to deal with a long path in ABF simulation? Wenyu Zhong (Wed Apr 26 2006 - 09:34:31 CDT)
- question on pulling direction lzshen (Wed Apr 26 2006 - 11:41:46 CDT)
- scaling NAMD2.6B1 on IBM P5 Thomas C. Bishop (Tue Apr 25 2006 - 14:44:33 CDT)
- still on tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 12:34:52 CDT)
- smd dimer dissociation L. Michel Espinoza-Fonseca (Tue Apr 25 2006 - 11:24:12 CDT)
- part of a protein AYTUG TUNCEL (Tue Apr 25 2006 - 02:58:42 CDT)
- error related to tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 00:52:38 CDT)
- modeling zinc binding site Jan Kosinski (Tue Apr 25 2006 - 07:46:30 CDT)
- parameter and topology for cyclodextrin! Íõº£Ãû (Mon Apr 24 2006 - 23:58:57 CDT)
- NAMD configuration files for NVT ensemble Lechuga, Javier (Sat Apr 22 2006 - 12:15:08 CDT)
- simulated annealing with explicit water L. Michel Espinoza-Fonseca (Mon Apr 24 2006 - 05:37:30 CDT)
- Faltal Error. reassignFreq fails Martin Loewer (Fri Apr 21 2006 - 05:50:28 CDT)
- Re: Re: water hole Sting (Thu Apr 20 2006 - 22:15:42 CDT)
- Re: Re: water hole Sting (Sat Apr 20 2002 - 21:28:49 CDT)
- water hole Sting (Fri Apr 19 2002 - 21:45:40 CDT)
- RE: Computing cost of frozen atoms Jacob Pøhlsgaard (Wed Apr 19 2006 - 03:33:28 CDT)
- namd2 on IBM P5 hangs Rene Salmon (Wed Apr 19 2006 - 13:34:16 CDT)
- custom pulling path Raul Alcantara (Wed Apr 19 2006 - 12:30:13 CDT)
- different cutoff for elecstrostatic and VDW interactions Hyonseok Hwang (Tue Apr 18 2006 - 12:53:29 CDT)
- Computing cost of frozen atoms Jacob Pøhlsgaard (Tue Apr 18 2006 - 04:39:20 CDT)
- Multiplicity of parameters Rahul Bhowmik (Tue Apr 18 2006 - 09:36:22 CDT)
- Clustering of conformation Leo.Ghemtio_at_sanofi-aventis.com (Tue Apr 18 2006 - 04:25:02 CDT)
- How to deal with this sugar residues though psfgen? q=E2=BA=E9=C3=F7?= (Tue Apr 18 2006 - 00:51:58 CDT)
- amidated C-terminus (NH2) with OPLS force field Giovanni Bellesia (Mon Apr 17 2006 - 17:34:57 CDT)
- OPLS-AA/L Giovanni Bellesia (Mon Apr 17 2006 - 15:53:34 CDT)
- MD analysis snoze pa (Mon Apr 17 2006 - 14:37:31 CDT)
- FEP, IONS, DUMMY atoms, LARGE numbers Raul Araya Secchi (Mon Apr 17 2006 - 12:32:55 CDT)
- About the command "set z [lindex $coorList($i) 2]". Boyang Wang (Sat Apr 15 2006 - 19:47:04 CDT)
- Re: vmd-l: breaking the DCD file snoze pa (Sun Apr 16 2006 - 17:08:31 CDT)
- Multiple residues at same position snoze pa (Sun Apr 16 2006 - 02:01:35 CDT)
- question about protein leaving water box TZU-LAN YEH (Fri Apr 14 2006 - 21:05:17 CDT)
- tcl boundary forces Giovanni Bellesia (Fri Apr 14 2006 - 13:26:16 CDT)
- vmd-l: Generating PSF for 1JNO.pdb chain A Lin (Fri Apr 14 2006 - 10:29:07 CDT)
- Periodic cell has become too small for original patch grid! lily jin (Thu Apr 13 2006 - 11:40:24 CDT)
- High VDW energies during minimization and dynamics Deva Priyakumar (Thu Apr 13 2006 - 10:23:38 CDT)
- RE: High VDW energies during minimization and dynamics Pijush Ghosh (Thu Apr 13 2006 - 11:52:35 CDT)
- Re: High VDW energies during minimization and dynamics Brian Bennion (Thu Apr 13 2006 - 12:47:30 CDT)
- Re: High VDW energies during minimization and dynamics Peter Freddolino (Thu Apr 13 2006 - 13:22:07 CDT)
- NAMD-L: question about SMDk, the force constant for SMD Margaret Shun Cheung (Wed Apr 12 2006 - 23:27:27 CDT)
- ACE patch paul.dalhaimer_at_yale.edu (Wed Apr 12 2006 - 10:56:46 CDT)
- reconstructing PMF Ioana Cozmuta (Tue Apr 11 2006 - 16:57:02 CDT)
- help on NAMD code Binquan luan (Tue Apr 11 2006 - 13:12:12 CDT)
- General question about psfgen atoms. snoze pa (Tue Apr 11 2006 - 12:27:27 CDT)
- namd + opteron/xeon L. Michel Espinoza-Fonseca (Mon Apr 10 2006 - 11:55:56 CDT)
- Developing topologies for modified NA residues? Jacob Pøhlsgaard (Mon Apr 10 2006 - 08:37:04 CDT)
- About restart.vel.old file. Boyang Wang (Fri Apr 07 2006 - 22:15:58 CDT)
- error about tclForcesScript xiaojing gong (Mon Apr 10 2006 - 09:21:13 CDT)
- How to measure of radius of a molecules? Taeho Kim (Mon Apr 10 2006 - 03:30:28 CDT)
- Constrain only in Z direction xiaojing gong (Sun Apr 09 2006 - 22:32:02 CDT)
- Multimeric protein Gianluca Interlandi (Sat Apr 08 2006 - 16:57:28 CDT)
- system calls inside namd script Himanshu Khandelia (Sat Apr 08 2006 - 16:42:46 CDT)
- NAMD-L: question about harmonic constraints Margaret Shun Cheung (Sat Apr 08 2006 - 13:33:33 CDT)
- RE: NAMD-L: question about harmonic constraints JC Gumbart (Sat Apr 08 2006 - 13:52:02 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Sat Apr 08 2006 - 22:30:13 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Mon Apr 10 2006 - 09:52:05 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Mon Apr 10 2006 - 12:54:57 CDT)
- Re: NAMD-L: question about harmonic constraints JC Gumbart (Mon Apr 10 2006 - 17:50:58 CDT)
- Re: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Mon Apr 10 2006 - 18:26:27 CDT)
- Re: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 17:41:08 CDT)
- Re: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Tue Apr 11 2006 - 21:06:33 CDT)
- RE: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 23:43:40 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 11:25:23 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 13:31:20 CDT)
- RE: NAMD-L: question about harmonic constraints Gianluca Interlandi (Wed Apr 12 2006 - 17:05:24 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 17:29:50 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 22:05:14 CDT)
- RE: NAMD-L: question about harmonic constraints JC Gumbart (Sat Apr 08 2006 - 13:52:02 CDT)
- A strange phenomenon in my dynamics system,any suggestion? ËïÍ¥¹ã (Fri Apr 07 2006 - 21:29:32 CDT)
- How to patch residues in different chains snoze pa (Fri Apr 07 2006 - 18:32:38 CDT)
- difference between reassignfreq and rescalefreq in temperature controls. Margaret Shun Cheung (Fri Apr 07 2006 - 13:13:16 CDT)
- a name quesiton lily jin (Fri Apr 07 2006 - 11:19:41 CDT)
- parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
- RE: Bizarre atom behavior Chang, Christopher (Thu Apr 06 2006 - 16:40:04 CDT)
- Re: vmd-l:namd-l; question about psfgen (param for CT1?) Margaret Shun Cheung (Thu Apr 06 2006 - 15:53:20 CDT)
- Re: vmd-l: dummy atoms and FEP Peter Freddolino (Thu Apr 06 2006 - 11:45:26 CDT)
- dummy atoms and FEP Raul Araya Secchi (Thu Apr 06 2006 - 11:36:57 CDT)
- tcouple vs langevin Margaret Shun Cheung (Thu Apr 06 2006 - 10:53:46 CDT)
- residue name and segment name Tamal Banerjee (Thu Apr 06 2006 - 02:05:07 CDT)
- Bizarre atom behavior Chang, Christopher (Wed Apr 05 2006 - 11:35:54 CDT)
- Problem about the energy change of refold of SMD protein TCWu (Wed Apr 05 2006 - 18:53:35 CDT)
- CMAP in NAMD? mpavlova_at_purdue.edu (Wed Apr 05 2006 - 16:34:58 CDT)
- running NAMD on beowulf cluster Nitin Bhardwaj (Wed Apr 05 2006 - 14:17:31 CDT)
- minimize in FEP.... Raul Araya (Wed Apr 05 2006 - 10:55:56 CDT)
- A possibel wrong coding in Parameters::read_charmm_parameter_file(char *) Qikai Li (Wed Apr 05 2006 - 10:25:56 CDT)
- NAMD-L:density of water molecules in a water sphere Margaret Shun Cheung (Tue Apr 04 2006 - 12:08:01 CDT)
- Tpr Ching Wong (Tue Apr 04 2006 - 10:55:33 CDT)
- help on error message during compiling Binquan luan (Mon Apr 03 2006 - 19:43:14 CDT)
- other crystal types in NAMD ? Himanshu Khandelia (Tue Apr 04 2006 - 10:17:40 CDT)
- Energy due to electric field jcm203_at_soton.ac.uk (Tue Apr 04 2006 - 09:09:18 CDT)
- langevinHydrogen off? Gianluca Interlandi (Mon Apr 03 2006 - 18:15:23 CDT)
- density of water molecules in a water sphere Margaret Shun Cheung (Mon Apr 03 2006 - 13:56:42 CDT)
- restart a simulation lily jin (Mon Apr 03 2006 - 12:25:57 CDT)
- PMEGridSize Anuradha Mittal (Sun Apr 02 2006 - 21:18:38 CDT)
- math formula for spherical boundary conditions. Margaret Shun Cheung (Sun Apr 02 2006 - 15:44:11 CDT)
- questions about the use of HIS residue xiaojing gong (Sun Apr 02 2006 - 08:05:53 CDT)
- TCL energy variables jbelof_at_mail.usf.edu (Sat Apr 01 2006 - 11:29:14 CST)
- dual core processors Leandro Martínez (Fri Mar 31 2006 - 11:04:01 CST)
- Molecular Volume Tamal Banerjee (Thu Mar 30 2006 - 22:22:26 CST)
- RE£º Re: how to plugin catDCD intoqVMD=20of=20windows=20version?= xiaojing gong (Wed Mar 29 2006 - 19:17:03 CST)
- bulk density in RDF.tcl ARTURAS ZIEMYS (Wed Mar 29 2006 - 10:28:44 CST)
- DCD file really corrupt? Lea Thøgersen (Wed Mar 29 2006 - 06:27:09 CST)
- how to plugin catDCD into VMD of windows version xiaojing gong (Wed Mar 29 2006 - 07:07:02 CST)
- Periodic cell has become too small Per Jr. Greisen (Wed Mar 29 2006 - 06:28:28 CST)
- Can I use namd for carbon nanotubes? Rob (Tue Mar 28 2006 - 22:16:44 CST)
- parameter files lily jin (Tue Mar 28 2006 - 14:13:39 CST)
- input file for PO3 lily jin (Tue Mar 28 2006 - 11:02:34 CST)
- Re£º Re: how to constrain a dihedralqangle=3F?= xiaojing gong (Tue Mar 28 2006 - 08:20:02 CST)
- Fwd: Re: vmd-l: Generating PSF for 1JNO.pdb chain A Lin (Mon Mar 27 2006 - 19:18:13 CST)
- force-field parameters for TOAC Gaurav Sharma (Mon Mar 27 2006 - 17:02:31 CST)
- no Na or CLA paramters in par_all22_prot.inp Shulin Zhuang (Mon Mar 27 2006 - 06:54:49 CST)
- psfgen operation for the C terminal of HSE Shulin Zhuang (Mon Mar 27 2006 - 01:46:57 CST)
- How to contract the PBC cell Tamal Banerjee (Mon Mar 27 2006 - 01:21:06 CST)
- about the MSE residue Shulin Zhuang (Sun Mar 26 2006 - 23:42:16 CST)
- MD problem bo baker (Sun Mar 26 2006 - 16:54:38 CST)
- Generating lipid bilayer model Gan, Yong (Sat Mar 25 2006 - 23:31:18 CST)
- MD Run frozen bo baker (Fri Mar 24 2006 - 15:42:47 CST)
- Tcl scripting within NAMD configuration file Chandra Ramananjara (Fri Mar 24 2006 - 09:26:18 CST)
- Simulation failed during the stage of heat Shulin Zhuang (Thu Mar 23 2006 - 23:58:15 CST)
- run frozen bo baker (Thu Mar 23 2006 - 20:08:58 CST)
- how to constrain a dihedral angle? xiaojing gong (Thu Mar 23 2006 - 18:55:34 CST)
- TCL scripting within NAMD Configuration File Chandra Ramananjara (Thu Mar 23 2006 - 09:12:56 CST)
- vmd-l: boubt about consistency of measures Sergio Anis (Thu Mar 23 2006 - 08:19:52 CST)
- force over selection Ioana Cozmuta (Wed Mar 22 2006 - 23:51:46 CST)
- Re: Gigabit ethernet switch for cluster Dow_Hurst (Wed Mar 22 2006 - 21:33:57 CST)
- SMD temperature scaling Christopher Calderon (Wed Mar 22 2006 - 17:09:44 CST)
- Use extendedSystem or cellBasisVector? Ching Wong (Wed Mar 22 2006 - 16:45:45 CST)
- energy calculation in VMD lily jin (Wed Mar 22 2006 - 16:41:45 CST)
- Can someone PLEASE explain the "firsttimestep" parameter ? Himanshu Khandelia (Wed Mar 22 2006 - 14:49:03 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Sterling Paramore (Wed Mar 22 2006 - 15:40:02 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Marcos Sotomayor (Wed Mar 22 2006 - 15:53:16 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? snoze pa (Wed Mar 22 2006 - 16:24:49 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Himanshu Khandelia (Wed Mar 22 2006 - 16:45:17 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? surendra negi (Wed Mar 22 2006 - 18:19:39 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Marcos Sotomayor (Wed Mar 22 2006 - 15:53:16 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Brian Bennion (Wed Mar 22 2006 - 16:43:18 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Sterling Paramore (Wed Mar 22 2006 - 15:40:02 CST)
- using restart file or .coor/.vel file xiaojing gong (Wed Mar 22 2006 - 08:44:57 CST)
- Gigabit ethernet switch for cluster Cesar Luis Avila (Tue Mar 21 2006 - 14:43:45 CST)
- VMD Command Pijush Ghosh (Tue Mar 21 2006 - 00:00:42 CST)
- question about the parameter "exclude" xiaojing gong (Tue Mar 21 2006 - 07:20:31 CST)
- Re:Re:error caused by lipid membrane xiaojing gong (Mon Mar 20 2006 - 20:33:42 CST)
- error caused by atoms of lipid membrane xiaojing gong (Mon Mar 20 2006 - 06:27:07 CST)
- what does "patch" mean? xiaojing gong (Sun Mar 19 2006 - 20:04:25 CST)
- Re: error in membrane producing xiaojing gong (Sun Mar 19 2006 - 18:00:04 CST)
- the "firsttimestep" conundrum Himanshu Khandelia (Sun Mar 19 2006 - 15:20:47 CST)
- Building cluster Cesar Luis Avila (Sat Mar 18 2006 - 12:54:38 CST)
- error in membrane producing xiaojing gong (Fri Mar 17 2006 - 21:21:15 CST)
- error in membrane producing xiaojing gong (Fri Mar 17 2006 - 19:30:25 CST)
- Memory requirements for clusters Naresh (Fri Mar 17 2006 - 18:24:57 CST)
- problems with .conf script Pedro Borkowski (Fri Mar 17 2006 - 13:13:17 CST)
- Question about memory usage Joshua D. Moore (Fri Mar 17 2006 - 12:03:59 CST)
- timestep in namd snoze pa (Thu Mar 16 2006 - 12:34:10 CST)
- farnesyl&retinal Magda W (Thu Mar 16 2006 - 02:44:08 CST)
- Dihedral parameters for multiple minima Chang, Christopher (Wed Mar 15 2006 - 19:34:22 CST)
- compile error on amd64 in src/ComputeTclBC.C Sabuj Pattanayek (Wed Mar 15 2006 - 14:27:53 CST)
- difference in total energy values Osman Yogurtcu (Wed Mar 15 2006 - 13:59:44 CST)
- Equilibration with constant temperature and pressure santanu chatterjee (Tue Mar 14 2006 - 19:07:09 CST)
- command line arguments in NAMD ? Himanshu Khandelia (Tue Mar 14 2006 - 17:49:31 CST)
- MD in a loop with different names for dcd files Himanshu Khandelia (Tue Mar 14 2006 - 10:56:21 CST)
- during namd build / compile -ltcl8.4 linking error Sabuj Pattanayek (Mon Mar 13 2006 - 15:41:29 CST)
- Continue a run ? Georgios Papadopoulos (Mon Mar 13 2006 - 11:27:52 CST)
- possible error warning lily jin (Mon Mar 13 2006 - 12:48:58 CST)
- build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Sabuj Pattanayek (Mon Mar 13 2006 - 12:31:56 CST)
- Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Sabuj Pattanayek (Mon Mar 13 2006 - 14:09:45 CST)
- Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Brian Bennion (Mon Mar 13 2006 - 14:18:15 CST)
- Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Gengbin Zheng (Tue Mar 14 2006 - 00:02:33 CST)
- Dumy atoms in FEP Raul Araya Secchi (Mon Mar 13 2006 - 09:13:22 CST)
- Question on simulation energy output Jason Lee (Sun Mar 12 2006 - 21:33:28 CST)
- area per lipid for a protein embedded membrane system M. Madhu (Fri Mar 10 2006 - 11:08:41 CST)
- FEP in vacuum Raul Araya Secchi (Fri Mar 10 2006 - 08:48:52 CST)
- RE: Aligning structures EPF \(Esben Peter Friis\) (Fri Mar 10 2006 - 01:34:40 CST)
- RE: is possible to remove the waterbox before running VMD Wolbach, Jeffrey P \(WOLBACH\) (Thu Mar 09 2006 - 13:45:20 CST)
- LES with PME and neutralizing charges curcio (Thu Mar 09 2006 - 11:48:41 CST)
- is possible to remove the waterbox before running VMD lily jin (Thu Mar 09 2006 - 10:34:02 CST)
- Re: is possible to remove the waterbox before running VMD Sterling Paramore (Thu Mar 09 2006 - 11:50:08 CST)
- Re: is possible to remove the waterbox before running VMD griadi_at_utalca.cl (Thu Mar 09 2006 - 12:56:38 CST)
- Re: vmd-l: is possible to remove the waterbox before running VMD John Stone (Thu Mar 09 2006 - 10:39:27 CST)
- Parameter resetting in NAMD Himanshu Khandelia (Thu Mar 09 2006 - 10:26:55 CST)
- a display problem lily jin (Thu Mar 09 2006 - 10:22:57 CST)
- volume exclusion Kyle Gustafson (Thu Mar 09 2006 - 09:51:30 CST)
- NAMD octahedron matteo filandri (Thu Mar 09 2006 - 07:57:54 CST)
- Pressure -ve Tamal Banerjee (Wed Mar 08 2006 - 08:49:57 CST)
- NAMD Linux LAM/MPI 7.1 execution error Christophe Combet [PBIL/IBCP/CNRS] (Tue Mar 07 2006 - 07:45:35 CST)
- RE: starting simulation in charmm, continuing in NAMD ? EPF \(Esben Peter Friis\) (Sun Mar 05 2006 - 14:35:18 CST)
- starting simulation in charmm, continuing in NAMD ? Himanshu Khandelia (Sun Mar 05 2006 - 11:23:15 CST)
- autocorrelation function ! Subhasish Chatterjee (Fri Mar 03 2006 - 20:17:56 CST)
- A question on simulation with NPT ensemble santanu chatterjee (Fri Mar 03 2006 - 13:18:34 CST)
- system rotates after equilibration Gordon Wells (Fri Mar 03 2006 - 03:21:30 CST)
- where to find the program DOWSER for setting water ? lily jin (Thu Mar 02 2006 - 15:33:03 CST)
- gradient for minimization Shirley Li (Thu Mar 02 2006 - 12:59:40 CST)
- Spherical harmonic restraint Morad Alawneh (Thu Mar 02 2006 - 11:39:48 CST)
- question about total charge change in FEP calculation jz7_at_duke.edu (Thu Mar 02 2006 - 10:01:23 CST)
- Re: question about total charge change in FEP calculation Chris Chipot (Sun Mar 05 2006 - 05:04:43 CST)
- Re: question about total charge change in FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 10:16:23 CDT)
- please help-large energy change during FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 12:13:31 CDT)
- Re: question about total charge change in FEP calculation Chris Chipot (Thu Jun 08 2006 - 14:47:27 CDT)
- Re: question about total charge change in FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 15:28:21 CDT)
- Re: question about total charge change in FEP calculation Chris Chipot (Fri Jun 09 2006 - 02:05:46 CDT)
- Re: question about total charge change in FEP calculation Jerome Henin (Fri Jun 09 2006 - 10:20:01 CDT)
- unsubscribe Lin (Mon Jun 12 2006 - 09:45:23 CDT)
- Re: question about total charge change in FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 10:16:23 CDT)
- Re: question about total charge change in FEP calculation Chris Chipot (Sun Mar 05 2006 - 05:04:43 CST)
- Re: question on membrane crushing Peter Freddolino (Thu Mar 02 2006 - 08:54:05 CST)
- Re: question on membrane crushing Marcos Sotomayor (Thu Mar 02 2006 - 08:32:34 CST)
- Re: question on membrane crushing Himanshu Khandelia (Thu Mar 02 2006 - 08:57:12 CST)
- Re: question on membrane crushing Arneh Babakhani (Fri Mar 03 2006 - 14:49:42 CST)
- Re: question on membrane crushing Arneh Babakhani (Mon Mar 13 2006 - 16:52:04 CST)
- question on membrane crushing Longzhu Shen (Thu Mar 02 2006 - 15:18:09 CST)
- radial distribution function Subhasish Chatterjee (Wed Mar 01 2006 - 16:01:44 CST)
- About Langevin Dynamics. Boyang Wang (Wed Mar 01 2006 - 12:18:30 CST)
- System after pressure change - confirmation needed ARTURAS ZIEMYS (Wed Mar 01 2006 - 09:30:20 CST)
- question about FEP calculation jz7_at_duke.edu (Wed Mar 01 2006 - 11:11:37 CST)
- namdstats gives nan's in tutorial output Jake Michaelson (Wed Mar 01 2006 - 10:40:48 CST)
- radial distribution function Leo.Ghemtio_at_sanofi-aventis.com (Wed Mar 01 2006 - 04:15:15 CST)
- (no subject) Michael Grabe (Tue Feb 28 2006 - 20:37:42 CST)
- NAMD2.6b1 on MAC cluster problems Michael Grabe (Tue Feb 28 2006 - 01:32:22 CST)
- NAMD2.6b1 on MACOSX Michael Grabe (Tue Feb 28 2006 - 12:04:12 CST)
- gradually pressure change (increase/decrease) ARTURAS ZIEMYS (Tue Feb 28 2006 - 11:44:08 CST)
- how gradually change (increase/decrease) pressure ? ARTURAS ZIEMYS (Mon Feb 27 2006 - 11:59:15 CST)
- Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 00:40:02 CST)
- radial distribution function Leo.Ghemtio_at_sanofi-aventis.com (Mon Feb 27 2006 - 08:23:42 CST)
- Re: question on pairinteraction Peter Freddolino (Sun Feb 26 2006 - 11:25:50 CST)
- question on pairinteraction Longzhu Shen (Sun Feb 26 2006 - 12:03:52 CST)
- Still problems with heating patrick wintrode (Sat Feb 25 2006 - 11:15:01 CST)
- tutorial address Georgios Papadopoulos (Sat Feb 25 2006 - 03:16:25 CST)
- Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 01:36:29 CST)
- About Langevin Damping Coefficient. Boyang Wang (Fri Feb 24 2006 - 17:57:24 CST)
- compile NAMD/CHARM on infiniband cluster Rene Salmon (Fri Feb 24 2006 - 16:20:16 CST)
- only minimization lily jin (Thu Feb 23 2006 - 18:11:22 CST)
- Unit of harmonic restraint force constant Leyla Celik (Fri Feb 24 2006 - 07:21:39 CST)
- Problem to run IMD simulation Laurent Leger (Fri Feb 24 2006 - 04:29:29 CST)
- namd and amber force field Fabien Cailliez (Thu Feb 23 2006 - 11:38:01 CST)
- (no subject) Michael Grabe (Wed Feb 22 2006 - 19:47:43 CST)
- waterbox snoze pa (Wed Feb 22 2006 - 10:57:12 CST)
- Electric Field jcm203_at_soton.ac.uk (Wed Feb 22 2006 - 10:17:39 CST)
- LES and minimalization Sławek Orłowski (Tue Feb 21 2006 - 02:42:06 CST)
- (no subject) Xiuping Tao (Thu Feb 16 2006 - 15:49:52 CST)
- NAMD not starting calculations... Jimmy Tang (Thu Feb 16 2006 - 08:00:34 CST)
- useGroupPressure snoze pa (Wed Feb 15 2006 - 15:48:55 CST)
- Re: question on mutate command in NAMD surendra negi (Wed Feb 15 2006 - 10:58:53 CST)
- question on mutate command in NAMD Longzhu Shen (Wed Feb 15 2006 - 16:49:19 CST)
- Problem heating the system patrick wintrode (Wed Feb 15 2006 - 08:37:16 CST)
- Re: HIS to HSD, HSE, and HSP John Eargle (Tue Feb 14 2006 - 17:05:33 CST)
- Pressure Driven flow of Water Wang, Boyang (Tue Feb 14 2006 - 15:14:02 CST)
- HIS to HSD, HSE, and HSP John Eargle (Tue Feb 14 2006 - 14:48:05 CST)
- charm++ over MPI Bogdan Costescu (Tue Feb 14 2006 - 11:07:19 CST)
- Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 14:41:24 CST)
- computer network snoze pa (Mon Feb 13 2006 - 11:26:51 CST)
- how to make dual-hybrid topology? Indrajaya (Mon Feb 13 2006 - 06:47:21 CST)
- Problem with VMD 'animate' command Chandra Ramananjara (Sun Feb 12 2006 - 10:12:36 CST)
- Rattle Error During Equilibration of Lipid Bilayer Membrane Arneh Babakhani (Fri Feb 10 2006 - 22:32:51 CST)
- Re: Rattle Error During Equilibration of Lipid Bilayer Membrane Morad Alawneh (Sat Feb 11 2006 - 09:49:07 CST)
- Re: Rattle Error During Equilibration of Lipid Bilayer Membrane Arneh Babakhani (Wed Feb 22 2006 - 14:09:23 CST)
- Jump in Electrostatic Energy between two values M. Madhu (Fri Feb 10 2006 - 14:33:17 CST)
- extra lines in PSF !!! Georgios Papadopoulos (Fri Feb 10 2006 - 11:47:10 CST)
- Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 10:58:27 CST)
- Re: Fwd: Water Box size Marc Q. Ma (Fri Feb 10 2006 - 12:40:50 CST)
- Re: Fwd: Water Box size Philip Blood (Fri Feb 10 2006 - 13:37:54 CST)
- Re: Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 13:49:07 CST)
- Fwd: Fwd: Water Box size snoze pa (Wed Feb 15 2006 - 11:29:19 CST)
- Re: Fwd: Water Box size snoze pa (Wed Feb 15 2006 - 11:58:33 CST)
- Re: Fwd: Water Box size L. Michel Espinoza-Fonseca (Wed Feb 15 2006 - 12:23:26 CST)
- Re: Fwd: Water Box size L. Michel Espinoza-Fonseca (Wed Feb 15 2006 - 12:00:51 CST)
- Re: Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 13:49:07 CST)
- pairInteractionSelf Yu Wang (Fri Feb 10 2006 - 03:19:34 CST)
- Buffering problems while attempting to read log file Zach Hensel (Fri Feb 10 2006 - 11:08:29 CST)
- I want to know how to make pdb file with 2d structrure file. Taeho Kim (Fri Feb 10 2006 - 02:14:31 CST)
- Re: unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD Dan Strahs (Thu Feb 09 2006 - 18:41:29 CST)
- unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD Dan Strahs (Thu Feb 09 2006 - 17:01:30 CST)
- RE: [Fwd: SMD of titin domain] Mu Gao (Wed Feb 08 2006 - 19:23:29 CST)
- Modeling HCN. Boyang Wang (Wed Feb 08 2006 - 18:47:14 CST)
- How to model HCN gas molecule by NAMD? Boyang Wang (Wed Feb 08 2006 - 18:44:42 CST)
- Amber Parameter in NAMD snoze pa (Wed Feb 08 2006 - 18:42:00 CST)
- [Fwd: increasing RMSD after 2 ns minimization-equilibration] dora guzman (Wed Feb 08 2006 - 17:05:51 CST)
- [Fwd: SMD of titin domain] dora guzman (Wed Feb 08 2006 - 17:05:34 CST)
- Topology file for Building Gramicidin A (tutorial) M. Madhu (Tue Feb 07 2006 - 11:37:13 CST)
- Socket closed before recv. Leandro Martínez (Tue Feb 07 2006 - 05:18:05 CST)
- question on membrane simulation Longzhu Shen (Tue Feb 07 2006 - 11:03:43 CST)
- Question on the bond energy of NAMD tutorial Jason Lee (Mon Feb 06 2006 - 15:51:22 CST)
- Problem with center of mass movement in simulation rwiese_at_unr.edu (Mon Feb 06 2006 - 12:01:21 CST)
- patch in psfgen... Navratna Vajpai (Mon Feb 06 2006 - 11:37:14 CST)
- DNA protonation mustapha.hamdi_at_ensi-bourges.fr (Mon Feb 06 2006 - 05:04:53 CST)
- About "mutate" command in psfgen package. Boyang Wang (Thu Feb 02 2006 - 17:24:42 CST)
- dublicated residue numbers in PDB/PSF ARTURAS ZIEMYS (Wed Feb 01 2006 - 09:14:53 CST)
- Tools to "open" domains ARTURAS ZIEMYS (Tue Jan 31 2006 - 10:12:03 CST)
- How to get different kinds of harmonic constraints in one script? Morad Alawneh (Tue Jan 31 2006 - 09:48:21 CST)
- Can any one help me with this parallel issue Morad Alawneh (Sun Jan 29 2006 - 18:17:06 CST)
- NAMD hangs in parallel on OSX Michael Grabe (Fri Jan 27 2006 - 12:37:38 CST)
- NAMD with Myrinet MX on MacOS X Goran Krilov (Fri Jan 27 2006 - 11:35:54 CST)
- Trying to profile namd to look for memory leaks Scott Atchley (Fri Jan 27 2006 - 10:33:04 CST)
- IMD-host name-port number-connection problem. rakesh... (Thu Jan 26 2006 - 15:54:43 CST)
- Berendsen pressure control problem Jason Lee (Thu Jan 26 2006 - 14:15:29 CST)
- NBFix not working with charmm par file Giovanni Bellesia (Wed Jan 25 2006 - 17:36:03 CST)
- dihedrals multiplicity in xplor psf file Giovanni Bellesia (Wed Jan 25 2006 - 15:12:16 CST)
- hybrid qm/mm Jake Michaelson (Wed Jan 25 2006 - 15:14:47 CST)
- namd2.6b1 has bad scaling Morad Alawneh (Wed Jan 25 2006 - 11:17:53 CST)
- How to create psf for carbohydrate jas theway (Mon Jan 23 2006 - 19:02:13 CST)
- NAMD at NCSA snoze pa (Tue Jan 24 2006 - 11:09:31 CST)
- Problem with biotin autopsf Lin (Tue Jan 24 2006 - 08:14:15 CST)
- question on 1-4scaling factor Hyonseok Hwang (Sun Jan 22 2006 - 22:58:24 CST)
- margin error message surendra negi (Sat Jan 21 2006 - 12:23:01 CST)
- Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. Boyang Wang (Fri Jan 20 2006 - 10:44:36 CST)
- question on the format of adding Lennard-Jones parameters Hyonseok Hwang (Thu Jan 19 2006 - 19:06:54 CST)
- Problem with NAMD and constraint failures rwiese_at_unr.edu (Thu Jan 19 2006 - 18:27:11 CST)
- NAMD memory problems on ASC's SGI Altix machine Sterling Paramore (Thu Jan 19 2006 - 10:46:33 CST)
- peptides confined in a water sphere Giovanni Bellesia (Thu Jan 19 2006 - 09:37:01 CST)
- Configurational temperature - coordinates Alexe Bojovschi (Wed Jan 18 2006 - 21:11:32 CST)
- wrong simulation times or misleading time counting? Carlos Simoes (Wed Jan 18 2006 - 17:48:59 CST)
- atom restraints jsachs_at_mail.csb.yale.edu (Wed Jan 18 2006 - 15:02:26 CST)
- MMTools/PCA Richard Wood (Wed Jan 18 2006 - 12:13:00 CST)
- question on membrane protein simulation Longzhu Shen (Wed Jan 18 2006 - 04:56:44 CST)
- PSF file Jindal Shah (Tue Jan 17 2006 - 13:21:49 CST)
- how to install rmsdtt in Windows... seonah kim (Tue Jan 17 2006 - 09:52:00 CST)
- Compiled NAMD on SGI Altix Sterling Paramore (Mon Jan 16 2006 - 18:51:18 CST)
- Multi Harmonic constrains Morad Alawneh (Mon Jan 16 2006 - 11:01:00 CST)
- which force field to choose Wei Zhuang (Sat Jan 14 2006 - 14:02:25 CST)
- help-minimization and equilibration of Ubiquitin in a water box Zhi Qi (Thu Jan 12 2006 - 18:38:00 CST)
- NAMD fails on Altix Margaret Kahn (Wed Jan 11 2006 - 19:50:44 CST)
- help-minimization and equilibration of Ubiquitin in a water box Zhi Qi (Wed Jan 11 2006 - 14:13:45 CST)
- variable cellOrigin Hugo Azurmendi (Wed Jan 11 2006 - 15:49:30 CST)
- generation of non-standart charmm topology ziemys_at_ecr6.ohio-state.edu (Wed Jan 11 2006 - 12:08:12 CST)
- simulation and equilibration bo baker (Tue Jan 10 2006 - 16:00:19 CST)
- Re: reading a binary restart file Leandro Martínez (Tue Jan 10 2006 - 16:10:31 CST)
- velocity error, still bo baker (Tue Jan 10 2006 - 15:20:58 CST)
- reading a binary restart file Leandro Martínez (Tue Jan 10 2006 - 13:09:18 CST)
- Re: updating TCL version for NAMD? Dan Strahs (Mon Jan 09 2006 - 11:18:16 CST)
- About "get z" command in MD script language. Boyang Wang (Sat Jan 07 2006 - 20:57:08 CST)
- Re: Turning off forces in VMD Richard Wood (Sun Jan 08 2006 - 17:03:28 CST)
- Re: Simulation in vaccum bo baker (Fri Jan 06 2006 - 22:12:40 CST)
- Simulation in vaccum bo baker (Fri Jan 06 2006 - 19:17:03 CST)
- updating TCL version for NAMD? Dan Strahs (Fri Jan 06 2006 - 17:42:35 CST)
- same random numbers?? Shahid Qamar (Fri Jan 06 2006 - 15:49:01 CST)
- problems reading large dcd file Jorge Pikunic (Fri Jan 06 2006 - 10:45:54 CST)
- AutoIMD Richard Wood (Fri Jan 06 2006 - 12:36:03 CST)
- Re: problems reading large dcd file Joshua D. Moore (Fri Jan 06 2006 - 23:22:43 CST)
- RE: problems reading large dcd file Jorge Pikunic (Tue Jan 10 2006 - 10:20:35 CST)
- RE: problems reading large dcd file Michel Espinoza-Fonseca (Tue Jan 10 2006 - 10:59:14 CST)
- RE: problems reading large dcd file Joshua D. Moore (Tue Jan 10 2006 - 19:35:55 CST)
- RE: problems reading large dcd file Jorge Pikunic (Wed Jan 11 2006 - 09:06:59 CST)
- RE: problems reading large dcd file Joshua D. Moore (Fri Jan 13 2006 - 21:32:42 CST)
- 64 bit NAMD on AIX and CatDCD Joshua D. Moore (Sat Jan 21 2006 - 13:22:11 CST)
- Re: vmd-l: 64 bit NAMD on AIX and CatDCD John Stone (Mon Jan 23 2006 - 13:21:14 CST)
- RE: problems reading large dcd file Jorge Pikunic (Tue Jan 10 2006 - 10:20:35 CST)
- Re: problems reading large dcd file Alessandro Pedretti (Sat Jan 07 2006 - 04:14:55 CST)
- What's the highest temperature I can go? Dong Luo (Thu Jan 05 2006 - 13:11:19 CST)
- Atom distance & ptraj bo baker (Thu Jan 05 2006 - 11:47:46 CST)
- PSFGEN for protein containing GTP Shirley Li (Wed Jan 04 2006 - 21:55:13 CST)
- psfgen problem Morad Alawneh (Wed Jan 04 2006 - 17:34:46 CST)
- atom distances bo baker (Wed Jan 04 2006 - 14:17:29 CST)
- velocity error bo baker (Wed Jan 04 2006 - 13:12:45 CST)
- CMAP problem Morad Alawneh (Tue Jan 03 2006 - 13:45:41 CST)
- Energy Plugin bo baker (Mon Jan 02 2006 - 18:54:12 CST)
Last message date: Thu Dec 27 2007 - 12:55:11 CST
Archived on: Wed Feb 29 2012 - 15:45:43 CST
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