NAMD-L: By Thread
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About this archive
Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Aug 29 2008 - 23:11:11 CDT
- Trouble with params file when trying to perform basic dynamics with alanine. Diego Alejandro Vargas (Fri Aug 29 2008 - 23:11:03 CDT)
- nvidia and namd Jorgen Simonsen (Fri Aug 29 2008 - 10:21:17 CDT)
- NPT enzemble and ABF Jorgen Simonsen (Fri Aug 29 2008 - 07:07:39 CDT)
- TXT program editor Alejandro Ortega (Thu Aug 28 2008 - 14:43:14 CDT)
- Re: vmd-l: TXT program editor Peter Freddolino (Thu Aug 28 2008 - 15:06:53 CDT)
- Re: vmd-l: TXT program editor Axel Kohlmeyer (Thu Aug 28 2008 - 15:50:21 CDT)
- Re: TXT program editor Giovanni Bellesia (Thu Aug 28 2008 - 16:21:03 CDT)
- Re: vmd-l: TXT program editor Sabuj Pattanayek (Thu Aug 28 2008 - 17:03:11 CDT)
- NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
- PME questions Lam T Nguyen (Thu Aug 28 2008 - 10:58:54 CDT)
- diffusion coefficient from rmsd Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
- corrupt DCD file Forbes, Jeff (NIH/NIAMS) [E] (Wed Aug 27 2008 - 16:54:07 CDT)
- Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Wed Aug 27 2008 - 11:41:08 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Wed Aug 27 2008 - 12:12:00 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Thu Aug 28 2008 - 12:21:56 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Thu Aug 28 2008 - 14:16:18 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Fri Aug 29 2008 - 11:59:54 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Fri Aug 29 2008 - 13:55:27 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Thu Aug 28 2008 - 12:21:56 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Christopher Gillespie (Wed Aug 27 2008 - 12:49:31 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Wed Aug 27 2008 - 12:12:00 CDT)
- Fe-S cluster topology parameters jose correa (Wed Aug 27 2008 - 09:20:58 CDT)
- change in box geometry for simulation of pure water maria goranovic (Wed Aug 27 2008 - 07:48:12 CDT)
- error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 10:37:25 CDT)
- van der walls-understanding problem Rudra Banerjee (Tue Aug 26 2008 - 09:50:31 CDT)
- running precompiled NAMD with multiple processors Neelanjana Sengupta (Tue Aug 26 2008 - 01:04:57 CDT)
- Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
- How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 17:41:59 CDT)
- NAMD COMPILATION ERROR Semorale (Mon Aug 25 2008 - 08:43:13 CDT)
- Why turning on 'pressureProfile' make NAMD get into sleep? loligo huang (Sun Aug 24 2008 - 21:49:55 CDT)
- How does NAMD count atoms in PDB files? Corenflos, Steven Charles (Thu Aug 21 2008 - 16:15:18 CDT)
- parallel execution speedup Roman Petrenko (Thu Aug 21 2008 - 15:51:57 CDT)
- storing velocity data of a NVE simulation sudipta sinha (Thu Aug 21 2008 - 11:32:37 CDT)
- SMD more than once JARROD EDWARD CHARLES NICKEL (Wed Aug 20 2008 - 14:24:17 CDT)
- about force fields oguz gurbulak (Tue Aug 19 2008 - 09:54:14 CDT)
- bad exclusion error - searching remedies Arturas Ziemys (Mon Aug 18 2008 - 18:12:48 CDT)
- Benchmark calculation rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 12:36:55 CDT)
- Problem in energy conservation in NVE ensemble with 1fs timestep tinni sona (Thu Aug 14 2008 - 11:34:43 CDT)
- Problem in energy conservation in NVE ensemble with 1fs timestep tinni sona (Thu Aug 14 2008 - 11:27:18 CDT)
- Problems with TMD could not be solved with the CVS version Robert Schulz (Thu Aug 14 2008 - 10:06:44 CDT)
- Re: Problems with TMD could not be solved with the CVS version Peter Freddolino (Thu Aug 14 2008 - 11:41:26 CDT)
- TMD and TclForces Gianluca Interlandi (Thu Aug 14 2008 - 01:35:21 CDT)
- FATAL ERROR: Patch needed for tuple is missing rebeca_at_mmb.pcb.ub.es (Wed Aug 13 2008 - 17:31:27 CDT)
- Dihedral angle calculation over the trajectories sunita gupta (Wed Aug 13 2008 - 10:17:14 CDT)
- TclForces and wrapping Gianluca Interlandi (Wed Aug 13 2008 - 03:05:43 CDT)
- namd: 64 p job runs; 128 p job fails why? Sangamesh B (Tue Aug 12 2008 - 12:27:18 CDT)
- 128 core namd job fails to run Sangamesh B (Tue Aug 12 2008 - 10:14:03 CDT)
- SMD forces Roman Petrenko (Mon Aug 11 2008 - 17:38:18 CDT)
- SMD force units Roman Petrenko (Mon Aug 11 2008 - 17:33:25 CDT)
- namd mpi version with smp Vlad Cojocaru (Mon Aug 11 2008 - 05:22:18 CDT)
- torsion potentials for phi/psi angles in CHARMM force field? Roman Petrenko (Sat Aug 09 2008 - 14:52:55 CDT)
- Rv: Value 99999999.9999 during minimization Eduardo Tejera (Fri Aug 08 2008 - 14:50:45 CDT)
- Turn off H-bonding on select residues dora guzman (Fri Aug 08 2008 - 13:21:35 CDT)
- Value 99999999.9999 during minimization rebeca_at_mmb.pcb.ub.es (Fri Aug 08 2008 - 03:16:57 CDT)
- restartfreq question.... Dr. Luis Rosales León (Thu Aug 07 2008 - 16:31:54 CDT)
- Average Velocity and How to choose Right Alias abhijit ramachandran (Thu Aug 07 2008 - 16:13:06 CDT)
- build smp version of namd with intel 10.1 Vlad Cojocaru (Thu Aug 07 2008 - 10:44:02 CDT)
- Abnormal EOF found - buffer Rene Prieto (Thu Aug 07 2008 - 00:46:37 CDT)
- NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 06 2008 - 16:10:01 CDT)
- Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Wed Aug 06 2008 - 17:20:55 CDT)
- Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Thu Aug 07 2008 - 11:17:16 CDT)
- RE: NAMD crashed with TclForce turned on Cojocaru,Vlad (Thu Aug 07 2008 - 14:43:02 CDT)
- RE: NAMD crashed with TclForce turned on Cojocaru,Vlad (Thu Aug 07 2008 - 14:48:11 CDT)
- Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Sat Aug 09 2008 - 17:14:26 CDT)
- RE: NAMD crashed with TclForce turned on Cojocaru,Vlad (Sun Aug 10 2008 - 11:32:57 CDT)
- RE: NAMD crashed with TclForce turned on Axel Kohlmeyer (Sun Aug 10 2008 - 15:35:28 CDT)
- Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Mon Aug 11 2008 - 01:50:09 CDT)
- Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Wed Aug 13 2008 - 07:31:03 CDT)
- Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 13 2008 - 10:33:36 CDT)
- Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Thu Aug 07 2008 - 11:17:16 CDT)
- Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Thu Aug 07 2008 - 03:05:30 CDT)
- Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Wed Aug 06 2008 - 17:20:55 CDT)
- Problems with the charge (membrane simulation) rebeca_at_mmb.pcb.ub.es (Wed Aug 06 2008 - 13:18:34 CDT)
- Warning in log file tinni sona (Wed Aug 06 2008 - 06:23:50 CDT)
- [Fwd: Notice:Re: Re: segmentation fault when running ABF] Vlad Cojocaru (Wed Aug 06 2008 - 05:15:19 CDT)
- Error with Shape Based CG Model Anirban Ghosh (Wed Aug 06 2008 - 05:04:27 CDT)
- membrane using OPLS force field rebeca_at_mmb.pcb.ub.es (Tue Aug 05 2008 - 07:48:45 CDT)
- Some question about Target MD Yang Gao (Tue Aug 05 2008 - 10:40:10 CDT)
- segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:20:32 CDT)
- Re: segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:34:48 CDT)
- Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Tue Aug 05 2008 - 12:13:56 CDT)
- Re: Re: segmentation fault when running ABF Vlad Cojocaru (Wed Aug 06 2008 - 04:13:05 CDT)
- Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Wed Aug 06 2008 - 11:10:48 CDT)
- Re: Re: segmentation fault when running ABF Vlad Cojocaru (Wed Aug 06 2008 - 11:23:45 CDT)
- Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Wed Aug 06 2008 - 11:31:42 CDT)
- Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Tue Aug 05 2008 - 12:13:56 CDT)
- Re: segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:34:48 CDT)
- Zinc-NAMD parameters jose correa (Mon Aug 04 2008 - 14:14:13 CDT)
- how do you debug tcl scripts in vmd ? Andriy Volynets (Mon Aug 04 2008 - 12:12:18 CDT)
- compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:46:11 CDT)
- TMD + temperature/pressure coupling Gianluca Interlandi (Sat Aug 02 2008 - 17:04:31 CDT)
- Impropers in histidine residues Marc Baaden (Sat Aug 02 2008 - 03:56:17 CDT)
- psf-generation. yambem soniya (Thu Jul 31 2008 - 16:57:08 CDT)
- coord file output minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:21:18 CDT)
- SMD in water Roman Petrenko (Thu Jul 31 2008 - 06:22:43 CDT)
- build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 05:06:44 CDT)
- g(r) Rudra Banerjee (Thu Jul 31 2008 - 00:39:47 CDT)
- output .coor minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:27:01 CDT)
- phosphate (PO4) topology Dr. Luis Rosales León (Wed Jul 30 2008 - 17:37:19 CDT)
- namdenergy and amber trajectory Alessandro Nascimento (Wed Jul 30 2008 - 10:06:27 CDT)
- namd linked to tcl8.5 Vlad Cojocaru (Wed Jul 30 2008 - 09:58:23 CDT)
- Does anyone have a sample tcl file for counting H-bonds Yang Gao (Wed Jul 30 2008 - 09:33:18 CDT)
- namdenergy and amber trajectory Alessandro Nascimento (Tue Jul 29 2008 - 14:58:56 CDT)
- DNA pdb file xing jing (Tue Jul 29 2008 - 15:16:16 CDT)
- recenter atom and remove rotation (translation) Lam T Nguyen (Tue Jul 29 2008 - 12:28:11 CDT)
- Running CGMD using NAMD Anirban Ghosh (Mon Jul 28 2008 - 23:46:54 CDT)
- PME fails no matter what Roman Petrenko (Mon Jul 28 2008 - 23:29:54 CDT)
- Re: PME fails no matter what Joshua Adelman (Mon Jul 28 2008 - 23:50:19 CDT)
- Re: PME fails no matter what Peter Freddolino (Tue Jul 29 2008 - 11:38:20 CDT)
- fixed residue Rudra Banerjee (Mon Jul 28 2008 - 22:49:36 CDT)
- ABF simulations Raul Araya (Mon Jul 28 2008 - 14:45:46 CDT)
- ubuntu reads my psf as an audio file patrick wintrode (Mon Jul 28 2008 - 13:29:17 CDT)
- how to run namd in cluster Anupam Nath Jha (Sun Jul 27 2008 - 13:23:22 CDT)
- TMD + harmonic restraints Gianluca Interlandi (Sat Jul 26 2008 - 16:17:42 CDT)
- Different dcd files for minimize and MD Lam T Nguyen (Fri Jul 25 2008 - 07:50:38 CDT)
- Different dcd files for minimize and MD Lam T Nguyen (Thu Jul 24 2008 - 15:20:17 CDT)
- NAMD + TMD on Abe Gianluca Interlandi (Thu Jul 24 2008 - 23:05:38 CDT)
- Appending dcd when restarting a simulation pellegrini (Thu Jul 24 2008 - 03:17:02 CDT)
- virtual and heavy hydrogens in NAMD rebeca_at_mmb.pcb.ub.es (Wed Jul 23 2008 - 09:22:12 CDT)
- Protonation of nucleic acid phosphates in CHARMM for use in NAMD Hughtendo Martin (Tue Jul 22 2008 - 08:43:09 CDT)
- MD problems jose correa (Sun Jul 20 2008 - 21:37:13 CDT)
- CHARMM parameters for H2S Raul Araya (Fri Jul 18 2008 - 17:51:50 CDT)
- ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Lam T Nguyen (Fri Jul 18 2008 - 13:32:14 CDT)
- how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:38:45 CDT)
- Problem while installing NAMD Karan Maroo (Thu Jul 17 2008 - 04:06:17 CDT)
- Re: vmd-l: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...) Peter Freddolino (Wed Jul 16 2008 - 07:20:26 CDT)
- memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
- LangevinTemp and KE calculation E. Prabhu Raman (Tue Jul 15 2008 - 18:25:49 CDT)
- Error in NAMD Time Steps Hsing Pao (Tue Jul 15 2008 - 14:29:36 CDT)
- NAMD Timestep Hsing Pao (Mon Jul 14 2008 - 19:11:59 CDT)
- trajectories jfgaff_at_ncsu.edu (Mon Jul 14 2008 - 13:38:39 CDT)
- NAMD OUTPUT Semorale (Sun Jul 13 2008 - 15:37:14 CDT)
- cannot find -lsrfftw... collect2: ld returned 1 exit status Anupam Nath Jha (Sun Jul 13 2008 - 12:59:09 CDT)
- DNA simulation by NAMD sudipta sinha (Sun Jul 13 2008 - 06:07:20 CDT)
- minimization and MD in one configuration file? NGUYEN LAM (Sat Jul 12 2008 - 10:46:38 CDT)
- installation of charm-6.0 in ia-64 cluster machine Anupam Nath Jha (Fri Jul 11 2008 - 06:49:34 CDT)
- Hi,Thank you! Peter Murphy (Fri Jul 11 2008 - 03:46:57 CDT)
- Hi,Thank you! Peter Murphy (Fri Jul 11 2008 - 03:35:29 CDT)
- use of charmm27 & NPT ensemble for lipid bilayer simulation Ruchi Sachdeva (Fri Jul 11 2008 - 00:26:17 CDT)
- NAMD on blue gene BG/P Andrew Emerson (Thu Jul 10 2008 - 05:46:36 CDT)
- alkane-silicon_dioxide simulation Raul Araya Secchi (Thu Jul 10 2008 - 15:18:06 CDT)
- WCA Particle Dave Rogers (Wed Jul 09 2008 - 21:45:48 CDT)
- TMD SIMULATION - RMSD DOUBT Semorale (Tue Jul 08 2008 - 20:05:37 CDT)
- Interaction energy abhijit ramachandran (Tue Jul 08 2008 - 15:57:47 CDT)
- Maximum Velocities Alejandro Ortega (Tue Jul 08 2008 - 13:20:33 CDT)
- Re: NAMD 2.7 Claw Isthelaw (Tue Jul 08 2008 - 00:30:52 CDT)
- unsubscribe namd-l Richard Swenson (Mon Jul 07 2008 - 14:36:39 CDT)
- relating to NAMD Energy Plugin scripting bo liu (Sun Jul 06 2008 - 23:19:44 CDT)
- Implementation of TCL script in NAMD .conf file sudipta sinha (Sat Jul 05 2008 - 00:18:25 CDT)
- won't launch on linux ubuntu cluster for a parallel run LinJia Qi (Fri Jul 04 2008 - 21:23:45 CDT)
- won't launch on linux ubuntu cluster for a parallel run accomp lin (Fri Jul 04 2008 - 12:21:18 CDT)
- ABF Method Bonnie A Merchant (Wed Jul 02 2008 - 09:19:39 CDT)
- Topology cartoon of proteins DEEPESH AGARWAL (Wed Jul 02 2008 - 06:13:59 CDT)
- Avoiding alpha-helix distortions Valeria Losasso (Wed Jul 02 2008 - 03:38:20 CDT)
- Heat flux along CNT Andy Shelley (Tue Jul 01 2008 - 14:13:36 CDT)
- 2 dimension PBC politr_at_huji.ac.il (Tue Jul 01 2008 - 07:15:29 CDT)
- palmytoilated Balazs JOJART (Mon Jun 30 2008 - 07:09:03 CDT)
- NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 06:42:59 CDT)
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- carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 17:16:26 CDT)
- carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 14:16:08 CDT)
- Problem in making cyclic peptide Narang, Pooja, Ph.D. (Fri Jun 27 2008 - 15:24:38 CDT)
- Re: Running minimization, heating and FEP simulation within the same configuration file. Floris Buelens (Thu Jun 26 2008 - 02:46:41 CDT)
- Cannot spot error in namd config file Claw Isthelaw (Thu Jun 26 2008 - 10:41:53 CDT)
- Re: Output of forces. Osman Yogurtcu (Thu Jun 26 2008 - 02:30:25 CDT)
- Output of forces. Hidekazu WATANABE (Thu Jun 26 2008 - 00:26:51 CDT)
- , Build your vocab (word power)-Get emails daily Fr.ee Deepesh (Thu Jun 26 2008 - 00:02:52 CDT)
- MD for phospho-aspartate using NAMD sunita gupta (Wed Jun 25 2008 - 03:37:51 CDT)
- Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Tue Jun 24 2008 - 20:28:21 CDT)
- charmrun not found Diego Alejandro Vargas (Tue Jun 24 2008 - 21:59:24 CDT)
- Problem regarding psfgen haosheng_at_hec.utah.edu (Tue Jun 24 2008 - 18:03:08 CDT)
- problem with executing MPI program in NAMD simulation Yinglong Miao (Mon Jun 23 2008 - 17:12:56 CDT)
- Incorrect PSF file for min.pme Eva Nong (Mon Jun 23 2008 - 15:32:58 CDT)
- Dihedral scan in NAMD? Kamilla Kopec (Mon Jun 23 2008 - 10:06:30 CDT)
- psf file Christine Horejs DI (Mon Jun 23 2008 - 06:22:48 CDT)
- Impressive Glashutte timepieces Becky Peoples (Sat Jun 21 2008 - 22:17:24 CDT)
- creation and equilibration of a monolayer creston . (Fri Jun 20 2008 - 16:01:06 CDT)
- Typical maximization steps S.K. Ghosh (Fri Jun 20 2008 - 14:05:36 CDT)
- error messages with "reinitvels" Yinglong Miao (Fri Jun 20 2008 - 13:56:25 CDT)
- mutate G->U? paco ty (Fri Jun 20 2008 - 11:16:13 CDT)
- Large MD simulations and atom number limits with NAMD Andrew Thomas (Fri Jun 20 2008 - 09:53:50 CDT)
- (no subject) Ariovaldo de Souza Junior (Fri Jun 20 2008 - 05:27:36 CDT)
- problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 10:15:27 CDT)
- Force Calibration Interaction abhijit ramachandran (Thu Jun 19 2008 - 17:31:57 CDT)
- problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 16:30:57 CDT)
- Simulation with non-periodic boundary condition S.K. Ghosh (Thu Jun 19 2008 - 13:36:50 CDT)
- NVT simulation by NAMD sudipta sinha (Thu Jun 19 2008 - 08:06:50 CDT)
- Time step is incompatible in the NAMD DCD file analyzed with CHARMM twshen (Wed Jun 18 2008 - 14:07:02 CDT)
- amber parameters for congo red Shaheen Ahmed (Wed Jun 18 2008 - 15:29:22 CDT)
- Time step is incompatible in the NAMD DCD file analyzed with CHARMM tw shen (Wed Jun 18 2008 - 14:42:32 CDT)
- Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM twshen (Wed Jun 18 2008 - 12:28:22 CDT)
- Trouble in energy minimization with warning to increase cutoff Eva Nong (Tue Jun 17 2008 - 18:57:49 CDT)
- 2D periodic boundary condn & PME Harindar Keer (Tue Jun 17 2008 - 14:12:28 CDT)
- Simulation stalled at startup Sean Law (Mon Jun 16 2008 - 11:01:06 CDT)
- Problem with .conf file of NAMD sudipta sinha (Mon Jun 16 2008 - 06:30:57 CDT)
- NAMD & CUDA, still in development ? Michael Heymann (Mon Jun 16 2008 - 06:40:24 CDT)
- NAMD log file analysis script problem (namdstats.tcl) sudipta sinha (Sat Jun 14 2008 - 13:39:32 CDT)
- Charmm is not free so how to learn it abhijit ramachandran (Fri Jun 13 2008 - 15:01:50 CDT)
- use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 23:54:34 CDT)
- Seeking suggestions to decide on realistic configuration values S.K. Ghosh (Thu Jun 12 2008 - 14:40:27 CDT)
- Language Used and Elementary doubts abhijit ramachandran (Thu Jun 12 2008 - 00:08:27 CDT)
- use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 06:03:06 CDT)
- ApoB structure Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
- paramter snoze pa (Wed Jun 11 2008 - 17:44:10 CDT)
- Velocity scaling and thermostatting both at a time sudipta sinha (Wed Jun 11 2008 - 13:36:46 CDT)
- April promo on watches Priscilla Dahl (Tue Jun 10 2008 - 16:41:36 CDT)
- Replica or Original? Terrence Hare (Tue Jun 10 2008 - 07:43:09 CDT)
- Classic timepieces replicas Cole Cox (Mon Jun 09 2008 - 19:10:25 CDT)
- capping of end residues sudipta sinha (Mon Jun 09 2008 - 23:55:56 CDT)
- psgfen patch Hatley, Jade M (Mon Jun 09 2008 - 12:05:15 CDT)
- Re: Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 13:21:57 CDT)
- Inexpensive IWC watches Janie Sweeney (Mon Jun 09 2008 - 12:47:28 CDT)
- Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 11:43:56 CDT)
- FW: Hydroxylysine parameters Elham Hamed (Mon Jun 09 2008 - 10:53:08 CDT)
- Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 10:04:24 CDT)
- Correctness of Simulation Results Rahul (Mon Jun 09 2008 - 09:16:13 CDT)
- Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 05:14:59 CDT)
- Different Hbonds values on different machines using same script for same trajectories sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
- NAMD compilation on linux cluster sudipta sinha (Sun Jun 08 2008 - 10:55:36 CDT)
- PME and r-RESPA issue in NAMD sudipta sinha (Sat Jun 07 2008 - 07:05:37 CDT)
- output area JARROD EDWARD CHARLES NICKEL (Thu Jun 05 2008 - 15:26:49 CDT)
- free enrgy calculations - an additional information politr_at_huji.ac.il (Wed Jun 04 2008 - 07:07:01 CDT)
- Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 08:18:16 CDT)
- NAMD in water vs in vacuum Yang Gao (Thu Jun 05 2008 - 09:54:48 CDT)
- Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
- steepest descent technique DEEPESH AGARWAL (Thu Jun 05 2008 - 00:53:30 CDT)
- free energy calculations politr_at_huji.ac.il (Wed Jun 04 2008 - 05:34:01 CDT)
- Thank you for your advices feng jack (Tue Jun 03 2008 - 11:15:41 CDT)
- Postdoctoral Position in Scientific Computing David Brandon (Mon Jun 02 2008 - 15:08:45 CDT)
- Average energy in NAMD feng jack (Sun Jun 01 2008 - 16:31:16 CDT)
- Mindboggling Problem Related To NAMD2 Code Rahul (Sun Jun 01 2008 - 04:19:13 CDT)
- (no subject) feng jack (Fri May 30 2008 - 16:04:44 CDT)
- Building Namd on a linux cluster. Khaled Barakat (Thu May 29 2008 - 21:39:53 CDT)
- Re: Building Namd on a linux cluster. Alexandre A. Vakhrouchev (Fri May 30 2008 - 00:38:25 CDT)
- Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 07:38:12 CDT)
- aromatic-aromatic interaction ramya narasimhan (Thu May 29 2008 - 00:20:43 CDT)
- benchmarking of NAMD: sustained performance (TF) satya work (Wed May 28 2008 - 22:47:30 CDT)
- constraintScaling - FOR LOOP Semorale (Wed May 28 2008 - 20:29:23 CDT)
- dihedral force constant jfgaff_at_ncsu.edu (Tue May 27 2008 - 18:38:06 CDT)
- charmm parameter and topology files me00109_at_cc.uoi.gr (Tue May 27 2008 - 10:17:52 CDT)
- NAMD trajectory format Konrad Hinsen (Tue May 27 2008 - 02:41:29 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Tue May 27 2008 - 05:27:04 CDT)
- Re: NAMD trajectory format Konrad Hinsen (Wed May 28 2008 - 07:35:17 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Wed May 28 2008 - 09:05:46 CDT)
- Re: NAMD trajectory format John Stone (Wed May 28 2008 - 11:18:26 CDT)
- Re: NAMD trajectory format Konrad Hinsen (Thu May 29 2008 - 11:43:13 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Fri May 30 2008 - 07:34:52 CDT)
- Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 08:28:08 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Fri May 30 2008 - 08:29:26 CDT)
- Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 09:15:48 CDT)
- Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 09:24:17 CDT)
- Re: NAMD trajectory format Konrad Hinsen (Fri May 30 2008 - 15:33:40 CDT)
- Re: NAMD trajectory format Konrad Hinsen (Wed May 28 2008 - 07:35:17 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Tue May 27 2008 - 05:27:04 CDT)
- Charm++ compilation sudipta sinha (Tue May 27 2008 - 01:51:12 CDT)
- dihedral restraints "on-the-fly"? Sebastian Stolzenberg (Mon May 26 2008 - 19:40:32 CDT)
- harmonic restraint between two atoms Esben A. Gad (Mon May 26 2008 - 03:55:16 CDT)
- PROTEIN VACUUM MINIMIZATION ERROR Semorale (Sat May 24 2008 - 10:24:47 CDT)
- REMD Khaled Barakat (Sat May 24 2008 - 02:58:54 CDT)
- Error Parsing Config File MIke S (Sat May 24 2008 - 00:01:43 CDT)
- Acceptable pressure values Fabio Zegarra (Fri May 23 2008 - 17:24:22 CDT)
- ABF:reversibility and number of samples Luca Bellucci (Fri May 23 2008 - 07:33:27 CDT)
- a question about equilibrium taojinwuhan_at_sohu.com (Wed May 21 2008 - 20:32:14 CDT)
- Applying weak harmonic force between two proteins greddy1_at_umd.edu (Wed May 21 2008 - 11:12:18 CDT)
- scaling the interaction energy Krishnan, Marimuthu (Wed May 21 2008 - 07:21:20 CDT)
- Unable to edit files in NAMD folder. Alexandre A. Vakhrouchev (Wed May 21 2008 - 03:37:52 CDT)
- Unable to edit files in NAMD folder. Diego Alejandro Vargas (Tue May 20 2008 - 23:39:51 CDT)
- running namd with condor emir mahmut bahsi (Mon May 19 2008 - 15:42:38 CDT)
- CFP: 3rd Annual CMM Workshop on QM/MM Simulations CMM QM/MM Workshop (Mon May 19 2008 - 13:43:55 CDT)
- minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 01:53:05 CDT)
- scaling the interaction energy Krishnan, Marimuthu (Mon May 19 2008 - 01:41:53 CDT)
- pair interaction Osman Yogurtcu (Fri May 16 2008 - 13:34:21 CDT)
- Re: vmd-l: Re: Truncated Octahedron for VMD and NAMD simulation Vlad Cojocaru (Fri May 16 2008 - 09:51:44 CDT)
- Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Thu May 15 2008 - 14:31:48 CDT)
- Error: transport retry exceeded error Alexandre A. Vakhrouchev (Thu May 15 2008 - 13:41:21 CDT)
- NVE ENSEMBLE Semorale (Thu May 15 2008 - 10:24:21 CDT)
- Re: NVE ENSEMBLE Vlad Cojocaru (Fri May 16 2008 - 03:36:38 CDT)
- Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Tue May 20 2008 - 07:11:36 CDT)
- Re: Simulation of Thiolated Biotin-Streptavidin on Gold Axel Kohlmeyer (Tue May 20 2008 - 08:27:50 CDT)
- Re: Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Wed May 21 2008 - 08:16:24 CDT)
- Re: Simulation of Thiolated Biotin-Streptavidin on Gold Jerome Henin (Wed May 21 2008 - 11:29:42 CDT)
- The correct topology/parameter file and pgn S.K. Ghosh (Mon Jun 02 2008 - 15:55:06 CDT)
- Re: The correct topology/parameter file and pgn Peter Freddolino (Tue Jun 03 2008 - 15:11:55 CDT)
- Re: The correct topology/parameter file and pgn S.K. Ghosh (Tue Jun 03 2008 - 18:15:44 CDT)
- Re: The correct topology/parameter file and pgn Peter Freddolino (Tue Jun 03 2008 - 21:56:24 CDT)
- Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 03:51:24 CDT)
- Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 13:48:41 CDT)
- Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Tue May 20 2008 - 07:11:36 CDT)
- Re: NVE ENSEMBLE Vlad Cojocaru (Fri May 16 2008 - 03:36:38 CDT)
- Re: Energy plot script Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
- Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
- how to prepare *.paramas file Kalyan chaitanya (Tue May 13 2008 - 17:48:54 CDT)
- S-OXY CYSTEINE parameter snoze pa (Tue May 13 2008 - 13:53:57 CDT)
- NAMD electrostatics no cutoff or switching Alvaro Foletti (Tue May 13 2008 - 12:44:01 CDT)
- ZINC parameter surendra negi (Tue May 13 2008 - 12:22:47 CDT)
- DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 14:19:57 CDT)
- puase MD integration to communicate between jobs Floris Buelens (Sun May 11 2008 - 12:31:50 CDT)
- Run NPT ensemble simulation with sphericalBC? Yinglong Miao (Fri May 09 2008 - 13:37:04 CDT)
- 2 pdb files Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
- spermine force field bqluan (Thu May 08 2008 - 18:47:54 CDT)
- spermine force field bqluan (Thu May 08 2008 - 17:24:01 CDT)
- Trajectory file formats & structural alignment Wei Huang (Thu May 08 2008 - 15:46:13 CDT)
- running NAMD with ranger@tacc Lei Shi (Wed May 07 2008 - 13:08:50 CDT)
- recalculating energy using dcd file gurvisha_at_leadinvent.com (Wed May 07 2008 - 09:19:14 CDT)
- pbc Ahlam Al-Rawi (Tue May 06 2008 - 18:41:33 CDT)
- Negative Pressure Fabio Zegarra (Tue May 06 2008 - 15:44:53 CDT)
- Question about a shift in rmsd using fixedatom off snoze pa (Tue May 06 2008 - 11:47:45 CDT)
- NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
- Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Mon May 05 2008 - 16:49:43 CDT)
- question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
- help with calcforces Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
- error on installing ImageMagick Hero (Thu May 01 2008 - 13:54:57 CDT)
- electrostatics NAMD vs CHARMM Arturas Ziemys (Thu May 01 2008 - 11:29:49 CDT)
- langevin dynamics and random seeds Peter Freddolino (Thu May 01 2008 - 11:44:40 CDT)
- How to save the animation movie into files? Hero (Thu May 01 2008 - 01:48:35 CDT)
- compilaton error Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
- Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
- Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
- Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 23:47:06 CDT)
- Re: compilaton error Swarna Patra (Fri May 02 2008 - 01:06:48 CDT)
- Re: compilaton error Leonardo Trabuco (Fri May 02 2008 - 01:25:35 CDT)
- Re: molefacture in vmd Subhashis Biswas (Wed Jun 04 2008 - 17:03:29 CDT)
- Re: molefacture in vmd Peter Freddolino (Wed Jun 04 2008 - 17:27:06 CDT)
- Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
- Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
- Running NAMD on cluster sudipta sinha (Wed Apr 30 2008 - 04:41:53 CDT)
- Neutral arginine patch in topology file. Alexandre F. G. (Tue Apr 29 2008 - 16:45:29 CDT)
- NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:40:29 CDT)
- NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:31:34 CDT)
- velocity units in .vel file Neelanjana Sengupta (Mon Apr 28 2008 - 15:21:06 CDT)
- How to save the animation movie into files? Hero (Mon Apr 28 2008 - 00:23:49 CDT)
- A question about restaints force. Yang Gao (Fri Apr 25 2008 - 11:28:20 CDT)
- q=D8=B8=B4=A3=BA=20Re:=20=20nodelist=20being=20ignore?= d during paralleling cong chen (Sun Apr 27 2008 - 21:50:34 CDT)
- How to save vmd figures to jpg or tiff? Hero (Sun Apr 27 2008 - 16:18:35 CDT)
- help with TCL forces script Jim Pfaendtner (Sun Apr 27 2008 - 05:47:30 CDT)
- nodelist being ignored during paralleling cong chen (Sat Apr 26 2008 - 22:24:17 CDT)
- How to play molecule trajectory with VMD? Hero (Sat Apr 26 2008 - 20:00:52 CDT)
- tracing not available with CMK_OPTIMIZE! Semorale (Sat Apr 26 2008 - 16:26:13 CDT)
- How to run namd2 on ubuntu linux? Hero (Sat Apr 26 2008 - 14:45:01 CDT)
- Re: install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:38:19 CDT)
- install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:09:39 CDT)
- Configurations-Statistical Mechanics Mert Gür (Sat Apr 26 2008 - 13:00:08 CDT)
- How to install VMD and NAMD on Ubuntu? Hero (Sat Apr 26 2008 - 12:55:17 CDT)
- FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
- install NAMD on Ubuntu Hero (Fri Apr 25 2008 - 23:46:07 CDT)
- A question about restaints force. Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
- Time factor Alexandre A. Vakhrouchev (Thu Apr 24 2008 - 23:16:04 CDT)
- TMD AND RIGIDBONDS Samuel Morales (Wed Apr 23 2008 - 20:50:43 CDT)
- compiling namd: cannot find -lmodulecommlib Corenflos, Steven Charles (Wed Apr 23 2008 - 14:42:18 CDT)
- reversing constant velocity SMD Jeff Forbes (Wed Apr 23 2008 - 14:36:16 CDT)
- VMD-NAMD-commands Vivek Sharma (Fri Apr 18 2008 - 23:06:12 CDT)
- Format of Binary Restart and Output Coordinate and Velocity Files Joshua D. Moore (Fri Apr 18 2008 - 19:34:20 CDT)
- RE: Reading and writing Binary Restart or Output files with Fortran Joshua D. Moore (Fri Apr 18 2008 - 19:25:55 CDT)
- question on ABF L. Michel Espinoza-Fonseca (Fri Apr 18 2008 - 18:40:08 CDT)
- What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
- Multiple Different Harmonic Restraint Defitions Joshua Adelman (Thu Apr 17 2008 - 20:13:23 CDT)
- 2 molecule pair interactions Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
- Which namd on amd64? Corenflos, Steven Charles (Tue Apr 15 2008 - 15:26:25 CDT)
- binary install question winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
- How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 13:55:14 CDT)
- Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 14:07:03 CDT)
- Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:14:20 CDT)
- Electrostatics cutoff with PME Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
- temperature stepping during heating Low Soo Mei (Tue Apr 15 2008 - 05:21:43 CDT)
- Problem with NAMD crashing without warning or error messages Jacob Durrant (Mon Apr 14 2008 - 20:36:25 CDT)
- help regarding NAMD equilibration snoze pa (Mon Apr 14 2008 - 18:11:46 CDT)
- NAMD CVS RUN ERROR Samuel Morales (Mon Apr 14 2008 - 16:13:31 CDT)
- rmsd_RNA_DNA sripad chandan (Mon Apr 14 2008 - 05:27:45 CDT)
- restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 04:14:19 CDT)
- Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 06:43:40 CDT)
- problem with VMD installation- libstdc++.so.5 => not found steve_at_phas.ubc.ca (Sat Apr 12 2008 - 22:03:05 CDT)
