NAMD-L: By Thread
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About this archive
Starting: Sat Jan 01 2011 - 12:21:40 CST
Ending: Mon Dec 31 2012 - 14:36:03 CST
- WHAM in the NPT ensemble Shaon Chakrabarti (Mon Dec 31 2012 - 14:35:50 CST)
- loop-to-helix change during SMD yp sun (Mon Dec 31 2012 - 05:17:53 CST)
- Compiling NAMD 2.9 on BlueGene/Q Vasudevan V (Wed Dec 26 2012 - 17:11:17 CST)
- Namd 2.9 on a BlueGene/Q machine Vasudevan V (Wed Dec 26 2012 - 17:29:34 CST)
- smd-tclForce intrerface Jacqueline Schmidt (Wed Dec 26 2012 - 12:04:23 CST)
- discrepancy in results from different machines! Jacqueline Schmidt (Tue Dec 25 2012 - 17:29:05 CST)
- How to improve the GPU utility in NAMD Íõ¾ü (Tue Dec 25 2012 - 02:35:06 CST)
- Namd: nohup: ignoring input and redirecting stderr to stdout Maria Saeed (Mon Dec 24 2012 - 00:30:32 CST)
- First impressions from AMBER ff12SB ? Nicholas M Glykos (Sun Dec 23 2012 - 10:58:36 CST)
- reassigning temperatures Martin, Erik W (Thu Dec 20 2012 - 11:40:36 CST)
- Behavior of explicit water beyond periodic boundaries Dr. Eddie (Thu Dec 20 2012 - 11:03:02 CST)
- Switching function while using AMBER force field Sneha Menon (Thu Dec 20 2012 - 00:06:25 CST)
- charging free energies with alchdecouple Harris, Robert C. (Wed Dec 19 2012 - 11:29:08 CST)
- cylinder constraint with colvar Wang (Tue Dec 18 2012 - 11:42:28 CST)
- How to parameterize Protein ligand complex in membrane? Maria Saeed (Mon Dec 17 2012 - 22:54:06 CST)
- Re: namd-l digest V1 #949 Nicholas M Glykos (Mon Dec 17 2012 - 04:06:22 CST)
- Adaptive Tempering "OPENING EXTENDED SYSTEM TRAJECTORY FILE" error Siri Søndergaard (Sun Dec 16 2012 - 22:53:31 CST)
- GPU acceleration by using ATI video card dongsheng lei (Fri Dec 14 2012 - 02:28:13 CST)
- Re: GPU acceleration by using ATI video card Aron Broom (Fri Dec 14 2012 - 02:49:04 CST)
- Re: GPU acceleration by using ATI video card Axel Kohlmeyer (Fri Dec 14 2012 - 03:11:06 CST)
- understanding the energy term in NAMD log file ç¿æž—å²½ (Wed Dec 12 2012 - 20:46:31 CST)
- checkpoint and revert Dr. Eddie (Wed Dec 12 2012 - 15:04:14 CST)
- Alchemical transformations and DDG of point mutations Gianluca Interlandi (Wed Dec 12 2012 - 14:22:55 CST)
- Re: Alchemical transformations and DDG of point mutations Chris Chipot (Wed Dec 12 2012 - 15:02:02 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Wed Dec 12 2012 - 16:24:09 CST)
- Re: Alchemical transformations and DDG of point mutations Chris Chipot (Thu Dec 13 2012 - 12:47:46 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Thu Dec 13 2012 - 13:22:47 CST)
- Re: Alchemical transformations and DDG of point mutations JC Gumbart (Thu Dec 13 2012 - 15:47:14 CST)
- Re: Alchemical transformations and DDG of point mutations Jérôme Hénin (Fri Dec 14 2012 - 02:38:45 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Fri Dec 14 2012 - 19:07:00 CST)
- Re: Alchemical transformations and DDG of point mutations JC Gumbart (Sun Dec 16 2012 - 19:24:25 CST)
- Re: Alchemical transformations and DDG of point mutations Jérôme Hénin (Mon Dec 17 2012 - 03:06:19 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Thu Dec 13 2012 - 16:10:45 CST)
- Re: Alchemical transformations and DDG of point mutations JC Gumbart (Mon Dec 17 2012 - 17:18:44 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Mon Dec 17 2012 - 18:11:01 CST)
- Re: Alchemical transformations and DDG of point mutations Jérôme Hénin (Tue Dec 18 2012 - 07:57:33 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Tue Dec 18 2012 - 12:53:21 CST)
- Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Wed Dec 12 2012 - 16:24:09 CST)
- Re: Alchemical transformations and DDG of point mutations Chris Chipot (Wed Dec 12 2012 - 15:02:02 CST)
- Multicore executable error with hydrogens Caitlin Scott (Tue Dec 11 2012 - 20:55:36 CST)
- weird energy values of LJ fluids Lindong Weng (Tue Dec 11 2012 - 16:15:55 CST)
- Alchemical transformations and DDG of point mutations Gianluca Interlandi (Tue Dec 11 2012 - 15:22:37 CST)
- Weird energy values of LJ fluids simulation Lindong Weng (Tue Dec 11 2012 - 13:43:16 CST)
- REST or RESTMD in NAMD? Gareth Shannon (Tue Dec 11 2012 - 12:08:21 CST)
- TAU profiler with NAMD2.9 smp mode Takuro Udagawa (Tue Dec 11 2012 - 07:44:44 CST)
- convergence of FEP calculation. dbaogen (Mon Dec 10 2012 - 21:16:09 CST)
- Colvars value is out of boundary DAI, JIAN (Mon Dec 10 2012 - 16:15:45 CST)
- error in psf file farzad kiani (Mon Dec 10 2012 - 09:47:00 CST)
- FEP simulation using AmberFF Jiyong Park (Mon Dec 10 2012 - 01:41:28 CST)
- minimization, slow heating and then Langevin free runs Dr. Eddie (Sun Dec 09 2012 - 10:16:21 CST)
- Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Sun Dec 09 2012 - 17:02:10 CST)
- Re: minimization, slow heating and then Langevin free runs Dr. Eddie (Mon Dec 10 2012 - 09:08:05 CST)
- Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Mon Dec 10 2012 - 11:00:40 CST)
- Re: minimization, slow heating and then Langevin free runs Dr. Eddie (Mon Dec 10 2012 - 12:20:07 CST)
- Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Mon Dec 10 2012 - 13:33:08 CST)
- Re: minimization, slow heating and then Langevin free runs Dr. Eddie (Mon Dec 10 2012 - 15:00:56 CST)
- Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Fri Dec 14 2012 - 13:38:02 CST)
- Re: minimization, slow heating and then Langevin free runs Dr. Eddie (Mon Dec 10 2012 - 09:08:05 CST)
- Re: minimization, slow heating and then Langevin free runs Rajan Vatassery (Sun Dec 09 2012 - 17:02:10 CST)
- Getting "nan" at ELEC energy value jesmin jahan (Fri Dec 07 2012 - 22:48:46 CST)
- NAMD CUDA 2.9 Performance drop compared to 2.8 Norman Geist (Fri Dec 07 2012 - 05:37:20 CST)
- ask for new toppar files for drude in NAMD2.9 Huihui Liu (Thu Dec 06 2012 - 05:30:25 CST)
- aMD with implicit solvent - Segmentation fault Thomas Evangelidis (Wed Dec 05 2012 - 10:43:57 CST)
- Simulation Box Deformation John Doe (Mon Dec 03 2012 - 20:19:47 CST)
- how to find cellorigin for periodic boundary condition Maria Saeed (Tue Dec 04 2012 - 10:34:09 CST)
- NAMD parameters +mergegrids +ignoresharing Norman Geist (Tue Dec 04 2012 - 01:04:09 CST)
- How to compute "only the GB Energy" using NAMD? jesmin jahan (Mon Dec 03 2012 - 20:34:02 CST)
- What's the difference between upperboundary and upperwall? DAI, JIAN (Mon Dec 03 2012 - 16:34:32 CST)
- Simulation Box Deformation John Doe (Mon Dec 03 2012 - 15:51:57 CST)
- problems with simulation of LJ fluid ç¿æž—å²½ (Sat Dec 01 2012 - 17:30:28 CST)
- about long namd trajectory and pbc effect Liqun Zhang (Sun Dec 02 2012 - 14:53:24 CST)
- namd runs on compute nodes but not update files in the head node Ada Zhan (Fri Nov 30 2012 - 16:34:01 CST)
- Re: NAMD parameters +mergegrids +ignoresharing Aron Broom (Fri Nov 30 2012 - 09:41:04 CST)
- Force field Parametrization Dr. Eddie (Fri Nov 30 2012 - 09:09:34 CST)
- NAMD parameters +mergegrids +ignoresharing Norman Geist (Fri Nov 30 2012 - 00:49:17 CST)
- AccelMD + GBIS Felipe Merino (Thu Nov 29 2012 - 09:39:18 CST)
- Re: AccelMD + GBIS Jeff Wereszczynski (Thu Nov 29 2012 - 16:57:24 CST)
- Re: AccelMD + GBIS Felipe Merino (Fri Nov 30 2012 - 04:26:21 CST)
- Re: AccelMD + GBIS Thomas Evangelidis (Sat Dec 01 2012 - 08:39:09 CST)
- Re: AccelMD + GBIS Thomas Evangelidis (Sat Dec 01 2012 - 12:00:44 CST)
- Re: AccelMD + GBIS Thomas Evangelidis (Sat Dec 01 2012 - 12:03:53 CST)
- Re: AccelMD + GBIS Thomas Evangelidis (Sat Dec 01 2012 - 12:06:55 CST)
- Re: AccelMD + GBIS Thomas Evangelidis (Sat Dec 01 2012 - 12:09:03 CST)
- Re: AccelMD + GBIS Felipe Merino (Fri Nov 30 2012 - 04:26:21 CST)
- Re: AccelMD + GBIS Jeff Wereszczynski (Thu Nov 29 2012 - 16:57:24 CST)
- Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS Tristan Croll (Wed Nov 28 2012 - 05:40:18 CST)
- performance variation during run time Thomas C. Bishop (Wed Nov 28 2012 - 18:53:10 CST)
- error Maria Saeed (Wed Nov 28 2012 - 03:24:50 CST)
- error regarding membrane embedded protein Maria Saeed (Wed Nov 28 2012 - 01:58:31 CST)
- performance loss on GPUs Thomas Evangelidis (Wed Nov 28 2012 - 01:13:53 CST)
- Re: performance loss on GPUs Aron Broom (Wed Nov 28 2012 - 01:31:12 CST)
- Re: performance loss on GPUs Axel Kohlmeyer (Wed Nov 28 2012 - 02:21:14 CST)
- Re: performance loss on GPUs Aron Broom (Wed Nov 28 2012 - 09:57:06 CST)
- Re: performance loss on GPUs Axel Kohlmeyer (Wed Nov 28 2012 - 10:07:02 CST)
- Re: performance loss on GPUs Aron Broom (Wed Nov 28 2012 - 10:40:11 CST)
- Re: performance loss on GPUs Thomas Evangelidis (Wed Nov 28 2012 - 16:09:10 CST)
- Re: performance loss on GPUs Thomas Evangelidis (Wed Nov 28 2012 - 16:44:36 CST)
- Re: performance loss on GPUs Aron Broom (Wed Nov 28 2012 - 09:57:06 CST)
- Should the windows for ABF calculations be overlapped or not? DAI, JIAN (Tue Nov 27 2012 - 08:38:17 CST)
- Re: how to run NAMD-CUDA on multiple nodes Thomas Evangelidis (Tue Nov 27 2012 - 03:20:16 CST)
- Functionalizing the nanopore Sridhar Kumar Kannam (Mon Nov 26 2012 - 23:24:19 CST)
- how to run NAMD-CUDA on multiple nodes Thomas Evangelidis (Mon Nov 26 2012 - 07:57:18 CST)
- AW: AW: AW: libcudart.so.4 error Norman Geist (Mon Nov 26 2012 - 00:11:25 CST)
- Replica exchange - Temperatures and number of replicas Siri Søndergaard (Sun Nov 25 2012 - 17:06:44 CST)
- Benchmarks for GTX 690's and 590's Dr. Eddie (Sun Nov 25 2012 - 11:41:46 CST)
- question about relative binding free energy calculation method using FEP dbaogen (Sat Nov 24 2012 - 05:58:55 CST)
- (no subject) Steven W Rick (Fri Nov 23 2012 - 14:29:17 CST)
- libcudart.so.4 error flavio seixas (Thu Nov 22 2012 - 12:42:57 CST)
- Re: libcudart.so.4 error Aron Broom (Thu Nov 22 2012 - 13:25:23 CST)
- Re: libcudart.so.4 error Thomas Evangelidis (Thu Nov 22 2012 - 13:50:18 CST)
- Re: libcudart.so.4 error flavio seixas (Thu Nov 22 2012 - 14:26:30 CST)
- Re: libcudart.so.4 error Aron Broom (Thu Nov 22 2012 - 15:17:45 CST)
- Re: libcudart.so.4 error Thomas Evangelidis (Thu Nov 22 2012 - 15:33:10 CST)
- AW: libcudart.so.4 error Norman Geist (Fri Nov 23 2012 - 00:50:54 CST)
- Re: AW: libcudart.so.4 error flavio seixas (Fri Nov 23 2012 - 04:47:36 CST)
- AW: AW: libcudart.so.4 error Norman Geist (Fri Nov 23 2012 - 07:43:50 CST)
- Re: libcudart.so.4 error flavio seixas (Thu Nov 22 2012 - 13:57:53 CST)
- Re: libcudart.so.4 error Thomas Evangelidis (Thu Nov 22 2012 - 13:50:18 CST)
- Re: libcudart.so.4 error Aron Broom (Thu Nov 22 2012 - 13:25:23 CST)
- NAMD 2.9 not migrating to computing nodes on Windows Server 2008 R2 HPC MPI Alex Smith (Thu Nov 22 2012 - 05:44:28 CST)
- NAMDEnergy: run with XSC file or not? Evgeny Bulat (Wed Nov 21 2012 - 13:27:23 CST)
- src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target Paraskevi Gkeka (Wed Nov 21 2012 - 06:14:09 CST)
- Re: namd-l digest V1 #918 Aaron Cann (Tue Nov 20 2012 - 13:10:24 CST)
- Parametarization and geometry optimization Dhiraj Srivastava (Tue Nov 20 2012 - 07:26:35 CST)
- problem in accelerated MD with NAMD-GPU Thomas Evangelidis (Mon Nov 19 2012 - 11:19:56 CST)
- ABACAVIR parameters Athanassios Stavrakoudis (Mon Nov 19 2012 - 08:38:12 CST)
- where does the second boost in accelMDdual mode refer to Thomas Evangelidis (Sun Nov 18 2012 - 16:25:50 CST)
- Compiling NAMD with CUDA on MacOSX Mountain Lion Maximilian Ebert (Sat Nov 17 2012 - 18:39:25 CST)
- Compiling NAMD with CUDA on MacOSX Mountain Lion Maximilian Ebert (Sat Nov 17 2012 - 18:38:51 CST)
- pressure profile calculations upayan baul (Sat Nov 17 2012 - 04:55:59 CST)
- Re: NAMD failed to read AMBER parm file Sneha Menon (Sat Nov 17 2012 - 03:44:08 CST)
- cross terms Dr. Eddie (Fri Nov 16 2012 - 13:15:59 CST)
- (no subject) saman amiri (Fri Nov 16 2012 - 08:05:21 CST)
- Conflict between CUDA NAMD and PMEMD Martin, Erik W (Thu Nov 15 2012 - 18:38:55 CST)
- Carma v.1.2 released. Nicholas M Glykos (Thu Nov 15 2012 - 04:22:25 CST)
- How to decide whether an ABF curve has been converged? dream (Thu Nov 15 2012 - 03:38:39 CST)
- acylated and amidated parameters. Martin, Erik W (Wed Nov 14 2012 - 11:45:32 CST)
- Force Field Topology and Parameter Files Stephen Holmes (Tue Nov 13 2012 - 09:00:59 CST)
- Replica-exchange metadynamics scripts Robert Elder (Tue Nov 13 2012 - 12:12:39 CST)
- Re: Bond Breaking in Polymer Networks - United Atom Forcefield Axel Kohlmeyer (Tue Nov 13 2012 - 10:53:11 CST)
- Errors compiling namd with CUDA Martin, Erik W (Tue Nov 13 2012 - 10:15:53 CST)
- metadynamics/ABF simulations using collective variables - issues with restarting the calculations Marimuthu Krishnan (Tue Nov 13 2012 - 08:42:43 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Jérôme Hénin (Tue Nov 13 2012 - 10:21:19 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Aron Broom (Tue Nov 13 2012 - 10:47:52 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Marimuthu Krishnan (Tue Nov 13 2012 - 13:47:41 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Aron Broom (Tue Nov 13 2012 - 13:58:29 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Giacomo Fiorin (Tue Nov 13 2012 - 14:11:05 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Marimuthu Krishnan (Wed Nov 14 2012 - 18:22:48 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Giacomo Fiorin (Wed Nov 14 2012 - 18:26:29 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Marimuthu Krishnan (Tue Nov 13 2012 - 13:22:57 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Aron Broom (Tue Nov 13 2012 - 10:47:52 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations Jérôme Hénin (Tue Nov 13 2012 - 10:21:19 CST)
- Bond Breaking in Polymer Networks - United Atom Forcefield Stefanos Anogiannakis (Tue Nov 13 2012 - 04:14:38 CST)
- Replica-exchange MD on a single node / SMP workstation Zachary Ulissi (Fri Nov 09 2012 - 17:57:26 CST)
- Information about error compiling with CUDA Martin, Erik W (Fri Nov 09 2012 - 14:50:44 CST)
- create junction between nanotubes farzad kiani (Fri Nov 09 2012 - 06:13:59 CST)
- NAMD failed to read AMBER parm file Sneha Menon (Thu Nov 08 2012 - 23:19:00 CST)
- Re: CUDA error vs clashes Francesco Pietra (Thu Nov 08 2012 - 11:42:09 CST)
- Moving atoms with bad contacts followed by CUDA error Francesco Pietra (Thu Nov 08 2012 - 09:45:00 CST)
- A bug in replica.namd? Ada Zhan (Wed Nov 07 2012 - 16:37:13 CST)
- Input configuration files for GPU version of NAMD Ganesh Kamath (Wed Nov 07 2012 - 12:56:27 CST)
- Accelerated MD Felipe Merino (Wed Nov 07 2012 - 10:08:15 CST)
- Fwd: CUDA error vs clashes Francesco Pietra (Wed Nov 07 2012 - 09:26:19 CST)
- CUDA error (as a misleding error message) Francesco Pietra (Wed Nov 07 2012 - 05:33:41 CST)
- replica exchange and replica.namd Siri Søndergaard (Tue Nov 06 2012 - 20:57:18 CST)
- no. of CPUs for optimal GTX-690 performance Michael Purdy (Tue Nov 06 2012 - 13:01:41 CST)
- Re: no. of CPUs for optimal GTX-690 performance Ajasja LjubetiÄ (Tue Nov 06 2012 - 13:43:28 CST)
- Re: no. of CPUs for optimal GTX-690 performance Aron Broom (Tue Nov 06 2012 - 13:44:06 CST)
- Re: no. of CPUs for optimal GTX-690 performance Giacomo Fiorin (Tue Nov 06 2012 - 14:46:02 CST)
- AW: no. of CPUs for optimal GTX-690 performance Norman Geist (Wed Nov 07 2012 - 01:56:25 CST)
- Re: no. of CPUs for optimal GTX-690 performance Ajasja LjubetiÄ (Wed Nov 07 2012 - 04:34:10 CST)
- Re: no. of CPUs for optimal GTX-690 performance Ajasja LjubetiÄ (Wed Nov 07 2012 - 04:57:11 CST)
- Re: no. of CPUs for optimal GTX-690 performance Michael Purdy (Wed Nov 07 2012 - 08:45:13 CST)
- Re: no. of CPUs for optimal GTX-690 performance Aron Broom (Wed Nov 07 2012 - 10:23:21 CST)
- Re: no. of CPUs for optimal GTX-690 performance Axel Kohlmeyer (Wed Nov 07 2012 - 11:05:48 CST)
- namd 2.9 Replica Exchange with colvar Ada Zhan (Mon Nov 05 2012 - 13:11:30 CST)
- Re: increment torsion restrain before minimization Tina Stokelj (Mon Nov 05 2012 - 06:38:32 CST)
- Re: NAMD 2.9 Windows CUDA build? Axel Kohlmeyer (Mon Nov 05 2012 - 02:01:30 CST)
- increment torsion restrain before minimization Tina Stokelj (Sat Nov 03 2012 - 09:59:43 CDT)
- NAMD 2.9 Windows CUDA build? Frederik Heurlin Aidt (Fri Nov 02 2012 - 05:30:54 CDT)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG2R Shubhra Ghosh Dastidar (Wed Oct 31 2012 - 21:55:49 CDT)
- malloc memory error using CUDA devices Blake Mertz (Wed Oct 31 2012 - 07:25:11 CDT)
- namd 2.9 and plumed Vlad Cojocaru (Wed Oct 31 2012 - 07:24:07 CDT)
- Metadynamics and Colvar Width Marc Gordon (Mon Oct 29 2012 - 09:19:45 CDT)
- compilation with CUDA error Thomas Evangelidis (Mon Oct 29 2012 - 08:44:23 CDT)
- Colvars Error? David Minh (Fri Oct 26 2012 - 11:13:21 CDT)
- SMD: Compressing a Molecule raghav singh (Thu Oct 25 2012 - 14:57:32 CDT)
- Restarting Multiple Walker/Well Tempered Metadynamics Jeff Wereszczynski (Thu Oct 25 2012 - 13:17:27 CDT)
- NAMD compilation -- compiler issue Dmitry Osolodkin (Thu Oct 25 2012 - 09:02:22 CDT)
- unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 09:55:52 CDT)
- Re: unreasonably high temp/pressure Aron Broom (Wed Oct 24 2012 - 10:26:43 CDT)
- Re: unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 10:34:57 CDT)
- Re: unreasonably high temp/pressure Jesper Sørensen (Wed Oct 24 2012 - 15:00:07 CDT)
- Re: unreasonably high temp/pressure. . Martin, Erik W (Wed Oct 24 2012 - 15:31:58 CDT)
- Re: unreasonably high temp/pressure Aron Broom (Wed Oct 24 2012 - 17:04:54 CDT)
- Re: unreasonably high temp/pressure. . Martin, Erik W (Wed Oct 24 2012 - 17:18:06 CDT)
- Re: unreasonably high temp/pressure. . Jesper Sørensen (Wed Oct 24 2012 - 23:24:42 CDT)
- Re: unreasonably high temp/pressure Aron Broom (Wed Oct 24 2012 - 10:26:43 CDT)
- CUDA - OwnerBox::close failure Vlastimil ZÃma (Wed Oct 24 2012 - 05:21:43 CDT)
- AW: How can I write a log file on my cluster? Norman Geist (Wed Oct 24 2012 - 00:42:06 CDT)
- Hybrid Monte Carlo? David Minh (Tue Oct 23 2012 - 09:58:26 CDT)
- Grid Forces: example code, documentation edit, and requested feature David Minh (Tue Oct 23 2012 - 09:49:26 CDT)
- extract velocities Giulia (Tue Oct 23 2012 - 06:58:38 CDT)
- Pressure problem to equilibrate NPT Mariana Graterol (Mon Oct 22 2012 - 17:28:55 CDT)
- How can I write a log file on my cluster? äÍÉÔÒÉÊ âÅÇÏ×ÁÔÏ× (Mon Oct 22 2012 - 01:39:58 CDT)
- inputPrefix for ABF Branko (Sat Oct 20 2012 - 16:36:16 CDT)
- NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) Jose Borreguero (Sat Oct 20 2012 - 15:55:51 CDT)
- NAMD in parallel on CPUs of different type Thomas Albers (Fri Oct 19 2012 - 21:03:08 CDT)
- REMD and NAMD options Martin, Erik W (Fri Oct 19 2012 - 09:36:38 CDT)
- optimal CPU number for parallel MD of a small system Isaure Chauvot de Beauchêne (Fri Oct 19 2012 - 08:32:57 CDT)
- Re: NAMD SGE Job Script Scale Up issues! Aditya Ranganathan (Fri Oct 19 2012 - 02:29:07 CDT)
- duplicate residue key Katrin Stöbener (Fri Oct 19 2012 - 02:30:19 CDT)
- Pressure in equilibration stage of MD Mariana Graterol (Thu Oct 18 2012 - 16:52:05 CDT)
- NAMD SGE Job Script Scale Up issues! Aditya Ranganathan (Thu Oct 18 2012 - 08:04:53 CDT)
- Invitation to connect on LinkedIn Adebayo Adeleke via LinkedIn (Wed Oct 17 2012 - 03:28:28 CDT)
- the fictitious force or the viscosity of water ishiikai08_at_yahoo.co.jp (Wed Oct 17 2012 - 02:44:04 CDT)
- 1-4 tabulated potentials? Jorge Hernandez Cobos (Tue Oct 16 2012 - 15:04:57 CDT)
- pulling constant verocity ishiikai08_at_yahoo.co.jp (Tue Oct 16 2012 - 02:13:22 CDT)
- postdoc position available JC Gumbart (Tue Oct 16 2012 - 00:47:41 CDT)
- compiling namd-2.9 on bluegeneQ Zhuyi Xue (Mon Oct 15 2012 - 15:46:40 CDT)
- Vacuum simulations mohan maruthi sena (Mon Oct 15 2012 - 14:16:04 CDT)
- Handling torsional potentials other than CHARMM type - regd Ramesh Cheerla (Fri Oct 12 2012 - 14:46:10 CDT)
- question of MMPBSA calculation combined NAMD and APBS software baogen duan (Thu Oct 11 2012 - 20:52:22 CDT)
- help with how pbc are defined. Martin, Erik W (Thu Oct 11 2012 - 12:48:27 CDT)
- Basic question on fixed atom Ganesh Kamath (Thu Oct 11 2012 - 09:08:37 CDT)
- structure changing ishiikai08_at_yahoo.co.jp (Wed Oct 10 2012 - 23:51:12 CDT)
- Tabulated potentials - regd Ramesh Cheerla (Tue Oct 09 2012 - 09:01:52 CDT)
- Warning & error Narasimhan LOGANATHAN (Tue Oct 09 2012 - 08:48:43 CDT)
- velocity distribution Namd Namd (Mon Oct 08 2012 - 06:46:52 CDT)
- units of pmf files Marc Gordon (Mon Oct 08 2012 - 05:42:37 CDT)
- Fixed atoms in SMD khalil ghafarian (Mon Oct 08 2012 - 05:22:25 CDT)
- Running fulldirect in parallel Tom Coles (Sun Oct 07 2012 - 15:08:11 CDT)
- a question on version nightly build flatforms Hyonseok Hwang (Sun Oct 07 2012 - 01:26:26 CDT)
- tcl script for rmsd yp sun (Thu Oct 04 2012 - 04:43:37 CDT)
- release the memory taking by the aotmselects/vars Jacqueline Schmidt (Wed Oct 03 2012 - 10:45:48 CDT)
- box dimension for unwrapped boxes? Jacqueline Schmidt (Wed Oct 03 2012 - 10:14:09 CDT)
- Cuda errors in Ubuntu12amd64 ´ÞÓ×Ìñ (Tue Oct 02 2012 - 22:33:49 CDT)
- Is the TMD equation in the user manual correct? Mert Gür (Tue Oct 02 2012 - 12:43:00 CDT)
- handling buckingham potentials in NAMD - regd Ramesh Cheerla (Tue Oct 02 2012 - 10:17:47 CDT)
- expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 13:52:53 CDT)
- Re: expandBoundaries and multiple walker metadynamics Giacomo Fiorin (Mon Oct 01 2012 - 14:21:11 CDT)
- Re: expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 14:52:08 CDT)
- Re: expandBoundaries and multiple walker metadynamics Aron Broom (Mon Oct 01 2012 - 15:13:41 CDT)
- Re: expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 15:24:46 CDT)
- Re: expandBoundaries and multiple walker metadynamics Aron Broom (Mon Oct 01 2012 - 15:39:41 CDT)
- Re: expandBoundaries and multiple walker metadynamics Giacomo Fiorin (Mon Oct 01 2012 - 15:44:48 CDT)
- Re: expandBoundaries and multiple walker metadynamics Aron Broom (Mon Oct 01 2012 - 15:50:29 CDT)
- Re: expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 15:50:12 CDT)
- Re: expandBoundaries and multiple walker metadynamics Aron Broom (Mon Oct 01 2012 - 15:54:32 CDT)
- Re: expandBoundaries and multiple walker metadynamics Giacomo Fiorin (Mon Oct 01 2012 - 16:15:36 CDT)
- Re: expandBoundaries and multiple walker metadynamics Giacomo Fiorin (Mon Oct 01 2012 - 15:40:18 CDT)
- Re: expandBoundaries and multiple walker metadynamics Jeff Wereszczynski (Mon Oct 01 2012 - 14:52:08 CDT)
- Re: expandBoundaries and multiple walker metadynamics Giacomo Fiorin (Mon Oct 01 2012 - 14:21:11 CDT)
- intergation algoritm of NAMD Namd Namd (Mon Oct 01 2012 - 03:52:30 CDT)
- Convergence of the Gram-Charlier expansion Ali Khanlarkhani (Sun Sep 30 2012 - 10:34:56 CDT)
- Umbrella Sampling after multiple replicas metadynamics Aron Broom (Fri Sep 28 2012 - 16:23:15 CDT)
- Namd list: Problem in equilibration stage Mariana Graterol (Thu Sep 27 2012 - 08:35:31 CDT)
- experimental density value oguz gurbulak (Thu Sep 27 2012 - 07:40:35 CDT)
- Re: compiling charm++ Error: can not find mpi library Thomas Evangelidis (Thu Sep 27 2012 - 02:00:24 CDT)
- compiling charm++ Error: can not find mpi library Thomas Evangelidis (Wed Sep 26 2012 - 17:15:00 CDT)
- Parameters for 3 methyl histidine. amin_at_imtech.res.in (Wed Sep 26 2012 - 09:13:34 CDT)
- namd on nvidia 302.17 Francesco Pietra (Wed Sep 26 2012 - 08:58:45 CDT)
- Re: W and S Axel Kohlmeyer (Tue Sep 25 2012 - 12:45:40 CDT)
- W and S Mikhail Suyetin (Tue Sep 25 2012 - 05:24:34 CDT)
- Printing energy of selected atoms in NAMD Ganesh Kamath (Mon Sep 24 2012 - 13:59:33 CDT)
- questions about accelerated MD Thomas Evangelidis (Mon Sep 24 2012 - 09:46:30 CDT)
- FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Sep 22 2012 - 07:41:25 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Chris Harrison (Sat Sep 22 2012 - 07:56:34 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Sep 22 2012 - 08:19:11 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Chris Harrison (Sat Sep 22 2012 - 09:03:42 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Sep 22 2012 - 10:09:11 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Chris Harrison (Sat Sep 22 2012 - 10:23:16 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Sep 22 2012 - 10:32:11 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Oct 20 2012 - 11:46:53 CDT)
- AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Norman Geist (Mon Oct 22 2012 - 01:01:02 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Aron Broom (Mon Oct 22 2012 - 10:10:54 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version David Hardy (Mon Oct 22 2012 - 12:00:48 CDT)
- AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Norman Geist (Tue Oct 23 2012 - 00:37:16 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Mon Oct 22 2012 - 16:42:57 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sat Sep 22 2012 - 08:19:11 CDT)
- RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Roberts, Jason (Sat Sep 22 2012 - 20:34:50 CDT)
- Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sun Sep 23 2012 - 11:33:31 CDT)
- AW: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Norman Geist (Mon Sep 24 2012 - 00:19:08 CDT)
- Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Thu Sep 27 2012 - 06:08:04 CDT)
- Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Thomas Evangelidis (Sun Sep 23 2012 - 11:33:31 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version Chris Harrison (Sat Sep 22 2012 - 07:56:34 CDT)
- Regarding Delta Delta G in FEP calculation snoze pa (Thu Sep 20 2012 - 13:09:57 CDT)
- using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion nabaneeta mukhopadhyay (Thu Sep 20 2012 - 11:21:33 CDT)
- AMBER in NAMD Shomesankar Bhunia (Thu Sep 20 2012 - 11:12:26 CDT)
- zero mass particles in NAMD Markus Dahlgren (Wed Sep 19 2012 - 08:32:02 CDT)
- AW: periodicity error Norman Geist (Tue Sep 18 2012 - 08:58:27 CDT)
- periodicity error Shomesankar Bhunia (Mon Sep 17 2012 - 04:33:50 CDT)
- VMD_waterbox Shomesankar Bhunia (Mon Sep 17 2012 - 01:47:35 CDT)
- AW: RE: Wrapping Norman Geist (Mon Sep 17 2012 - 01:08:36 CDT)
- Re: outputting atom coordinated Ehsan Ban (Sun Sep 16 2012 - 20:01:45 CDT)
- outputting atom coordinated Jacqueline Schmidt (Sun Sep 16 2012 - 16:17:25 CDT)
- n-terminus in my psfgen created pdb/psf file is missing Jacqueline Schmidt (Sun Sep 16 2012 - 11:15:41 CDT)
- NAMD- molecular dynamics Shomesankar Bhunia (Thu Sep 13 2012 - 14:55:14 CDT)
- GTX-660 Ti benchmark Thomas Albers (Thu Sep 13 2012 - 14:50:43 CDT)
- Re: GTX-660 Ti benchmark Aron Broom (Thu Sep 13 2012 - 18:01:14 CDT)
- Re: GTX-660 Ti benchmark Wenyu Zhong (Thu Sep 13 2012 - 22:02:07 CDT)
- Re: GTX-660 Ti benchmark Wenyu Zhong (Thu Sep 13 2012 - 22:10:23 CDT)
- Re: GTX-660 Ti benchmark Guanglei Cui (Fri Sep 14 2012 - 08:50:41 CDT)
- execute vs. config directory Thomas C. Bishop (Fri Sep 14 2012 - 15:07:24 CDT)
- Re: execute vs. config directory Aron Broom (Fri Sep 14 2012 - 15:51:17 CDT)
- AW: execute vs. config directory Norman Geist (Mon Sep 17 2012 - 01:47:22 CDT)
- AW: execute vs. config directory Norman Geist (Mon Sep 17 2012 - 01:43:57 CDT)
- AW: GTX-660 Ti benchmark Norman Geist (Mon Sep 17 2012 - 01:31:12 CDT)
- Re: GTX-660 Ti benchmark Thomas Albers (Sun Sep 16 2012 - 14:47:35 CDT)
- Re: GTX-660 Ti benchmark Thomas Albers (Sun Sep 16 2012 - 14:54:49 CDT)
- Re: GTX-660 Ti benchmark Roberts, Jason (Sun Sep 16 2012 - 17:08:55 CDT)
- Re: GTX-660 Ti benchmark Guanglei Cui (Tue Sep 18 2012 - 09:38:39 CDT)
- Re: GTX-660 Ti benchmark Guanglei Cui (Wed Sep 19 2012 - 08:32:38 CDT)
- Re: GTX-660 Ti benchmark Wenyu Zhong (Thu Sep 13 2012 - 22:02:07 CDT)
- Re: GTX-660 Ti benchmark Aron Broom (Thu Sep 13 2012 - 18:01:14 CDT)
- Unable to reproduce same results in minimization with GBIS Kasam, Vinod (Thu Sep 13 2012 - 10:52:31 CDT)
- namd 2.9 not going so well Michael Galloway (Thu Sep 13 2012 - 10:30:09 CDT)
- problems with auto-psf gen and autoionize for ligand with atomtypes of more than 4 characters Raul Araya (Wed Sep 12 2012 - 16:34:57 CDT)
- CHARMM parameters and topology for YO-PRO and/or Lucyfer Yellow Raul Araya (Wed Sep 12 2012 - 09:58:18 CDT)
- ReaxFF and REBO Mikhail Suyetin (Wed Sep 12 2012 - 04:46:44 CDT)
- psfgen and CHARMM19 explicit exclusions Andrey (Tue Sep 11 2012 - 21:10:20 CDT)
- Treating Multi Chain Proteins Roy Fernando (Tue Sep 11 2012 - 14:58:14 CDT)
- an error when merge pdb and psf files in vmd for big model farzad kiani (Sun Sep 09 2012 - 08:45:58 CDT)
- Wrapping Buddhadev Maiti (Fri Sep 07 2012 - 22:35:10 CDT)
- namd 2.9 ibverbs issues Michael Galloway (Sat Sep 08 2012 - 12:29:12 CDT)
- CUDA workstation Arturas (Sat Sep 08 2012 - 11:22:49 CDT)
- rmsd calculation in namd Guanglei Cui (Fri Sep 07 2012 - 14:57:59 CDT)
- question about "useflexiblecell' command in NAMD operation Patrick Chiu (Fri Sep 07 2012 - 14:05:32 CDT)
- merge pdb/psf files by psfgen - sets coordinates to zero Jacqueline Schmidt (Fri Sep 07 2012 - 13:44:49 CDT)
- [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Salvatore Mario Cosseddu (Fri Sep 07 2012 - 07:49:36 CDT)
- Re: [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Giacomo Fiorin (Fri Sep 07 2012 - 11:38:08 CDT)
- namd 2.9 run instability (segfaults) Michael Galloway (Thu Sep 06 2012 - 09:19:05 CDT)
- NAMD Run Instabilities Marc Gordon (Thu Sep 06 2012 - 08:15:58 CDT)
- Rückruf: scnb value to prevent VDWs scaling Norman Geist (Thu Sep 06 2012 - 08:10:22 CDT)
- Reflecting boundary z axis in NAMD Ganesh Kamath (Tue Sep 04 2012 - 14:11:22 CDT)
- Question of using deuterated water in NAMD Ganesh Kamath (Tue Sep 04 2012 - 13:13:27 CDT)
- restarting umbrella sampling simulation. ipsita basu (Tue Sep 04 2012 - 00:42:09 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 04 2012 - 02:48:15 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 04 2012 - 04:31:05 CDT)
- Re: restarting umbrella sampling simulation. ipsita basu (Tue Sep 04 2012 - 07:18:02 CDT)
- Re: restarting umbrella sampling simulation. ipsita basu (Wed Sep 05 2012 - 02:34:34 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Wed Sep 05 2012 - 09:00:57 CDT)
- Re: restarting umbrella sampling simulation. ipsita basu (Mon Sep 10 2012 - 01:48:44 CDT)
- Re: restarting umbrella sampling simulation. ipsita basu (Tue Sep 11 2012 - 06:12:22 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 11 2012 - 07:02:02 CDT)
- Re: restarting umbrella sampling simulation. Aron Broom (Tue Sep 11 2012 - 08:54:27 CDT)
- Re: restarting umbrella sampling simulation. ipsita basu (Wed Sep 12 2012 - 04:32:46 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 04 2012 - 04:31:05 CDT)
- Re: restarting umbrella sampling simulation. Jérôme Hénin (Tue Sep 04 2012 - 02:48:15 CDT)
- problem with pdb psf files! Jacqueline Schmidt (Sun Sep 02 2012 - 21:44:59 CDT)
- AW: problem with pdb psf files! Norman Geist (Mon Sep 03 2012 - 02:18:08 CDT)
- Re: AW: problem with pdb psf files! Jacqueline Schmidt (Mon Sep 03 2012 - 11:01:17 CDT)
- Re: AW: problem with pdb psf files! Axel Kohlmeyer (Mon Sep 03 2012 - 11:20:45 CDT)
- AW: AW: problem with pdb psf files! Norman Geist (Tue Sep 04 2012 - 01:59:41 CDT)
- Re: AW: AW: problem with pdb psf files! Jacqueline Schmidt (Tue Sep 04 2012 - 06:06:06 CDT)
- Re: AW: AW: problem with pdb psf files! Axel Kohlmeyer (Tue Sep 04 2012 - 06:15:27 CDT)
- Re: AW: problem with pdb psf files! Jacqueline Schmidt (Mon Sep 03 2012 - 11:01:17 CDT)
- AW: problem with pdb psf files! Norman Geist (Mon Sep 03 2012 - 02:18:08 CDT)
- problem with pdb pdf! Jacqueline Schmidt (Sun Sep 02 2012 - 21:36:17 CDT)
- Error in membrane protein simulation amin_at_imtech.res.in (Sat Sep 01 2012 - 01:59:27 CDT)
- AW: Error in membrane protein simulation Norman Geist (Mon Sep 03 2012 - 01:52:45 CDT)
- Re: AW: Error in membrane protein simulation amin_at_imtech.res.in (Mon Sep 03 2012 - 03:41:25 CDT)
- Re: AW: Error in membrane protein simulation Ajasja LjubetiÄ (Mon Sep 03 2012 - 04:16:11 CDT)
- AW: AW: Error in membrane protein simulation Norman Geist (Mon Sep 03 2012 - 04:45:25 CDT)
- Re: AW: AW: Error in membrane protein simulation amin_at_imtech.res.in (Mon Sep 03 2012 - 06:27:14 CDT)
- AW: AW: AW: Error in membrane protein simulation Norman Geist (Mon Sep 03 2012 - 10:33:31 CDT)
- Re: AW: AW: AW: Error in membrane protein simulation amin_at_imtech.res.in (Mon Sep 03 2012 - 11:50:08 CDT)
- Re: AW: AW: AW: Error in membrane protein simulation Rajan Vatassery (Mon Sep 03 2012 - 15:03:21 CDT)
- Re: AW: AW: AW: Error in membrane protein simulation Axel Kohlmeyer (Mon Sep 03 2012 - 15:13:39 CDT)
- Re: AW: AW: AW: Error in membrane protein simulation Rajan Vatassery (Mon Sep 03 2012 - 15:15:28 CDT)
- Re: AW: AW: AW: Error in membrane protein simulation Axel Kohlmeyer (Mon Sep 03 2012 - 15:28:20 CDT)
- AW: AW: AW: AW: Error in membrane protein simulation Norman Geist (Tue Sep 04 2012 - 01:53:15 CDT)
- Re: AW: AW: AW: AW: Error in membrane protein simulation amin_at_imtech.res.in (Tue Sep 04 2012 - 02:12:37 CDT)
- Re: AW: Error in membrane protein simulation amin_at_imtech.res.in (Mon Sep 03 2012 - 03:41:25 CDT)
- Re: Error in membrane protein simulation JC Gumbart (Mon Sep 03 2012 - 15:51:35 CDT)
- AW: Error in membrane protein simulation Norman Geist (Mon Sep 03 2012 - 01:52:45 CDT)
- The size of a periodic cell in NAMD operation Patrick Chiu (Fri Aug 31 2012 - 18:45:19 CDT)
- NAMD 2.9 with CUDA runs Ashley Chew (Fri Aug 31 2012 - 04:02:48 CDT)
- Oscillating Electric Field Quick, Ross (Fri Aug 31 2012 - 11:26:39 CDT)
- Re: dump specific atom positions into a txt file during the simulation Jacqueline Schmidt (Fri Aug 31 2012 - 03:15:56 CDT)
- dump specific atom positions into a txt file during the simulation Jacqueline Schmidt (Fri Aug 31 2012 - 01:14:09 CDT)
- AW: AW: simulation:protein,ligand,lipid,water and ions Norman Geist (Fri Aug 31 2012 - 00:47:21 CDT)
- NAMD on Peta-Scale Machines Yim, Keun Soo (Thu Aug 30 2012 - 13:19:10 CDT)
- NBTABLE issue Arturas (Thu Aug 30 2012 - 13:45:14 CDT)
- AW: simulation:protein,ligand,lipid,water and ions Norman Geist (Thu Aug 30 2012 - 09:47:47 CDT)
- NAMD 2.8 and PLUMED 1.3 candy deck (Thu Aug 30 2012 - 07:59:41 CDT)
- AW: question regarding simulated annealing Norman Geist (Thu Aug 30 2012 - 02:56:04 CDT)
- question and NAMD operation Patrick Chiu (Wed Aug 29 2012 - 15:19:36 CDT)
- Accelerated MD Thomas Albers (Wed Aug 29 2012 - 15:06:04 CDT)
- Question regarding FEP parameters snoze pa (Wed Aug 29 2012 - 13:05:15 CDT)
- (no subject) Jacqueline Schmidt (Wed Aug 29 2012 - 11:06:10 CDT)
- Run NAMD binaries Monika Madhavi (Wed Aug 29 2012 - 03:58:12 CDT)
- Warning: Not all atoms have unique coordinates Jacqueline Schmidt (Tue Aug 28 2012 - 19:17:54 CDT)
- namd simulation​:protein,l​igand,lipi​d,water and ions Marlet Martinez (Tue Aug 28 2012 - 12:30:04 CDT)
- Namd list: "Size cell" for restart Mariana Graterol (Tue Aug 28 2012 - 08:07:03 CDT)
- simulation of non-rectangular surface Jacqueline Schmidt (Tue Aug 28 2012 - 10:20:02 CDT)
- question regarding simulated annealing Puspita Halder (Tue Aug 28 2012 - 07:03:39 CDT)
- water parameters Mark Abraham (Mon Aug 27 2012 - 18:29:25 CDT)
- need help in using colvars option sudipta (Mon Aug 27 2012 - 17:41:51 CDT)
- NAMD pulling one domain snoze pa (Mon Aug 27 2012 - 14:36:34 CDT)
- The structure files for the second turn of simulation yp sun (Sun Aug 26 2012 - 20:30:04 CDT)
- Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0 Mariana Graterol (Sun Aug 26 2012 - 14:07:17 CDT)
- Water bubbles in NVT equilibration dynamics Mariana Graterol (Fri Aug 24 2012 - 18:52:28 CDT)
- Functional form to apply constraints Mariana Graterol (Fri Aug 24 2012 - 18:28:43 CDT)
- what is fullSamples? ¼¿ëÀÏ (Sun Aug 26 2012 - 22:56:59 CDT)
- (no subject) ¼¿ëÀÏ (Sun Aug 26 2012 - 22:55:40 CDT)
- restraining Christopher Rowley (Thu Aug 23 2012 - 13:55:59 CDT)
- Re: restraining Chris Harrison (Thu Aug 23 2012 - 22:08:49 CDT)
- Re: restraining Christopher Rowley (Thu Aug 23 2012 - 22:20:55 CDT)
- Re: restraining Chris Harrison (Thu Aug 23 2012 - 22:29:54 CDT)
- AW: restraining Norman Geist (Fri Aug 24 2012 - 01:42:27 CDT)
- Re: AW: restraining Christopher Rowley (Fri Aug 24 2012 - 08:08:42 CDT)
- Re: AW: restraining Axel Kohlmeyer (Fri Aug 24 2012 - 08:25:22 CDT)
- Re: AW: restraining Jeffrey Potoff (Fri Aug 24 2012 - 09:37:49 CDT)
- Re: restraining Axel Kohlmeyer (Fri Aug 24 2012 - 03:09:54 CDT)
- Re: restraining Christopher Rowley (Thu Aug 23 2012 - 22:20:55 CDT)
- Re: restraining Chris Harrison (Thu Aug 23 2012 - 22:08:49 CDT)
- equilibrate glycerol molecules Namd Namd (Thu Aug 23 2012 - 03:45:32 CDT)
- shift the molecules oguz gurbulak (Thu Aug 23 2012 - 03:29:53 CDT)
- Sr2+ Maria Bykhovskaia (Wed Aug 22 2012 - 14:54:38 CDT)
- has system reached a steady state condition? farzad kiani (Wed Aug 22 2012 - 06:11:06 CDT)
- NPT at 100 bar Francesco Pietra (Wed Aug 22 2012 - 03:02:03 CDT)
- umbrella sampling ipsita basu (Wed Aug 22 2012 - 01:52:14 CDT)
- AW: GPU workstation build Norman Geist (Tue Aug 21 2012 - 09:33:48 CDT)
- No output after "scheduler running in netpoll mode" amin_at_imtech.res.in (Tue Aug 21 2012 - 08:58:40 CDT)
- Fwd: GPU workstation build Francesco Pietra (Tue Aug 21 2012 - 08:44:09 CDT)
- Displaying the gradient tolerance in the output Webber (Tue Aug 21 2012 - 03:46:25 CDT)
- energy minimization yandong Huang (Mon Aug 20 2012 - 23:24:30 CDT)
- GPU workstation build Blake Mertz (Mon Aug 20 2012 - 10:41:13 CDT)
- Displaying the gradient tolerance in the output as the example output from tutorial 1-2 Water Sphere Webber (Sun Aug 19 2012 - 19:02:29 CDT)
- Calculating Potential Energy for an atom selection Aron Broom (Fri Aug 17 2012 - 15:49:38 CDT)
- multiple dynamic sections in the config file? Jacqueline Schmidt (Thu Aug 16 2012 - 19:03:44 CDT)
- shift the molecules oguz gurbulak (Thu Aug 16 2012 - 03:13:10 CDT)
- equilibrate conf file Namd Namd (Thu Aug 16 2012 - 02:56:30 CDT)
- Evaluate Work for Targeted Molecular Dynamics Simulations Mert Gür (Wed Aug 15 2012 - 16:08:52 CDT)
- Multiple gpu cards Dr. Eddie (Wed Aug 15 2012 - 09:24:46 CDT)
- inputPrefix in ABF Branko (Tue Aug 14 2012 - 12:04:57 CDT)
- pressure profile calculations JC Gumbart (Mon Aug 13 2012 - 21:11:20 CDT)
- scnb value to prevent VDWs scaling Marc Gordon (Mon Aug 13 2012 - 08:40:13 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Thu Sep 06 2012 - 07:26:55 CDT)
- AW: scnb value to prevent VDWs scaling Norman Geist (Thu Sep 06 2012 - 08:09:22 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Sat Sep 08 2012 - 05:21:49 CDT)
- Re: scnb value to prevent VDWs scaling Axel Kohlmeyer (Sat Sep 08 2012 - 06:04:23 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Mon Sep 10 2012 - 07:56:44 CDT)
- Re: scnb value to prevent VDWs scaling Axel Kohlmeyer (Mon Sep 10 2012 - 08:02:18 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Mon Sep 10 2012 - 08:28:25 CDT)
- Re: scnb value to prevent VDWs scaling Axel Kohlmeyer (Mon Sep 10 2012 - 08:33:05 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Mon Sep 10 2012 - 08:45:24 CDT)
- Re: scnb value to prevent VDWs scaling Marc Gordon (Thu Sep 06 2012 - 07:26:55 CDT)
- 1-4 vdw scaling? Jacqueline Schmidt (Sat Aug 11 2012 - 14:41:20 CDT)
- Namd, lammps comparing energies Jacqueline Schmidt (Fri Aug 10 2012 - 12:44:05 CDT)
- RE: openAtom/NAMD2.9 implementation Bennion, Brian (Thu Aug 09 2012 - 12:17:57 CDT)
- residue_rmsd.tcl via Branko (Thu Aug 09 2012 - 07:50:56 CDT)
- win64 namd cuda: compile? Aaron Cann (Tue Aug 07 2012 - 00:09:36 CDT)
- fep/parm7 Francesco Pietra (Mon Aug 06 2012 - 10:57:36 CDT)
- Newbie's question Theresa H (Mon Aug 06 2012 - 09:46:49 CDT)
- Alchemical protein transformation with a group of (non proteic) atoms bound to two amino acids Francesco Pietra (Mon Aug 06 2012 - 02:36:47 CDT)
- connect a spring between all the atoms present in pdb structure SONY kaur (Sat Aug 04 2012 - 04:31:42 CDT)
- Re: vmd-l: connect a spring between all the atoms present in pdb structure Axel Kohlmeyer (Sat Aug 04 2012 - 13:20:05 CDT)
- Re: connect a spring between all the atoms present in pdb structure Axel Kohlmeyer (Sat Aug 04 2012 - 13:21:27 CDT)
- Re: vmd-l: connect a spring between all the atoms present in pdb structure Eduard Schreiner (Sat Aug 04 2012 - 16:36:38 CDT)
- Re: How to create psf for graphene Monika Madhavi (Sat Aug 04 2012 - 01:04:24 CDT)
- How to create psf for graphene Monika Madhavi (Fri Aug 03 2012 - 22:35:28 CDT)
- accelerated MD (aMD) with GPU Jiyong Park (Fri Aug 03 2012 - 17:48:42 CDT)
- how do I pass environmental variables to namd on BlueGene/P? Aaron Oakley (Thu Aug 02 2012 - 23:39:06 CDT)
- no output for corrfunc Rui Zhang (Thu Aug 02 2012 - 19:06:25 CDT)
- RMSD difference on alignment of two states of protein in VMD and NAMD TMD Nikita chopra (Thu Aug 02 2012 - 15:27:36 CDT)
- Drude polarizable models with namd Ana Celia Vila Verde (Thu Aug 02 2012 - 11:11:08 CDT)
- LCPO SASA Calculation on the GPU Aron Broom (Wed Aug 01 2012 - 22:44:09 CDT)
- restarting ABF Branko (Wed Aug 01 2012 - 10:13:29 CDT)
- laptop GPU support Thomas Evangelidis (Wed Aug 01 2012 - 05:27:58 CDT)
- Re: peculiar scaling on the GPU Axel Kohlmeyer (Wed Aug 01 2012 - 01:40:56 CDT)
- (no subject) Sean T Kigerl (Tue Jul 31 2012 - 18:27:12 CDT)
- NAMD 2.9: Segmentation fault? María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 12:44:09 CDT)
- Re: NAMD 2.9: Segmentation fault? Aron Broom (Tue Jul 31 2012 - 12:52:37 CDT)
- Re: NAMD 2.9: Segmentation fault? Branko (Tue Jul 31 2012 - 13:04:59 CDT)
- Re: NAMD 2.9: Segmentation fault? María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 13:13:03 CDT)
- Re: NAMD 2.9: Segmentation fault? Branko (Tue Jul 31 2012 - 13:42:34 CDT)
- Re: NAMD 2.9: Segmentation fault? María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 13:47:05 CDT)
- Re: NAMD 2.9: Segmentation fault? Aron Broom (Tue Jul 31 2012 - 14:14:55 CDT)
- Re: NAMD 2.9: Segmentation fault? Maria Antonieta Sanchez Farran (Tue Jul 31 2012 - 14:52:10 CDT)
- AW: NAMD 2.9: Segmentation fault? Norman Geist (Wed Aug 01 2012 - 01:20:53 CDT)
- Re: AW: NAMD 2.9: Segmentation fault? Maria Antonieta Sanchez Farran (Wed Aug 01 2012 - 15:25:15 CDT)
- Re: NAMD 2.9: Segmentation fault? Aron Broom (Tue Jul 31 2012 - 12:52:37 CDT)
- peculiar scaling on the GPU Ajasja LjubetiÄ (Tue Jul 31 2012 - 09:06:50 CDT)
- Uneven sampling when using ABF DAI, JIAN (Mon Jul 30 2012 - 12:38:12 CDT)
- Re: Uneven sampling when using ABF Aron Broom (Mon Jul 30 2012 - 18:10:03 CDT)
- Re: Uneven sampling when using ABF JC Gumbart (Mon Jul 30 2012 - 20:15:02 CDT)
- Re: Uneven sampling when using ABF Aron Broom (Mon Jul 30 2012 - 20:33:32 CDT)
- RE: Uneven sampling when using ABF DAI, JIAN (Mon Jul 30 2012 - 20:54:15 CDT)
- Re: Uneven sampling when using ABF JC Gumbart (Mon Jul 30 2012 - 21:36:05 CDT)
- Re: Uneven sampling when using ABF Aron Broom (Tue Jul 31 2012 - 07:36:22 CDT)
- Re: Uneven sampling when using ABF JC Gumbart (Mon Jul 30 2012 - 20:15:02 CDT)
- Re: Uneven sampling when using ABF Aron Broom (Mon Jul 30 2012 - 18:10:03 CDT)
- openAtom/NAMD2.9 implementation Bennion, Brian (Mon Jul 30 2012 - 11:59:29 CDT)
- Uneven sampling in using ABF DAI, JIAN (Mon Jul 30 2012 - 08:17:45 CDT)
- Low CPU usage with NAMD running on linux cluster amin_at_imtech.res.in (Sat Jul 28 2012 - 01:33:17 CDT)
- Re: Low CPU usage with NAMD running on linux cluster Branko (Sat Jul 28 2012 - 07:52:17 CDT)
- Re: Low CPU usage with NAMD running on linux cluster amin_at_imtech.res.in (Sat Jul 28 2012 - 10:10:02 CDT)
- Re: Low CPU usage with NAMD running on linux cluster amin_at_imtech.res.in (Sun Jul 29 2012 - 00:09:49 CDT)
- AW: Low CPU usage with NAMD running on linux cluster Norman Geist (Mon Jul 30 2012 - 11:01:37 CDT)
- Re: AW: Low CPU usage with NAMD running on linux cluster amin_at_imtech.res.in (Tue Jul 31 2012 - 00:01:02 CDT)
- AW: AW: Low CPU usage with NAMD running on linux cluster Norman Geist (Tue Jul 31 2012 - 01:06:32 CDT)
- Re: AW: AW: Low CPU usage with NAMD running on linux cluster amin_at_imtech.res.in (Wed Aug 01 2012 - 00:16:30 CDT)
- Re: Low CPU usage with NAMD running on linux cluster Aron Broom (Mon Jul 30 2012 - 18:14:44 CDT)
- Re: Low CPU usage with NAMD running on linux cluster Branko (Sat Jul 28 2012 - 07:52:17 CDT)
- AW: Atoms moving too fast with NAMD/Amber Norman Geist (Fri Jul 27 2012 - 03:39:33 CDT)
- Random seed and equilibrated structure Dr. Eddie (Thu Jul 26 2012 - 15:55:13 CDT)
- startup phase 8: not complete! mj_aghaei_at_aut.ac.ir (Wed Jul 25 2012 - 21:12:31 CDT)
- namd crashes after 300K steps Peter Jones (Thu Jul 26 2012 - 03:06:17 CDT)
- Atoms moving too fast with NAMD/Amber Francesco Pietra (Thu Jul 26 2012 - 00:48:46 CDT)
- problem with NAMD surface area calculation (LCPO) -- fixed Clayton (Mon Jul 23 2012 - 10:08:35 CDT)
- drude water in namd Sandeep Patel (Tue Jul 24 2012 - 16:07:50 CDT)
- secondary structure restraints in coarse grain Eun Kim (Tue Jul 24 2012 - 13:35:00 CDT)
- CNT builder farzad kiani (Tue Jul 24 2012 - 09:25:23 CDT)
- Error: periodicity of dihedral zero Francesco Pietra (Tue Jul 24 2012 - 03:23:19 CDT)
- Tabulated potential Adam Skelton (Mon Jul 23 2012 - 16:17:35 CDT)
- Lenard Jones coefficients for Neon atoms Roy Fernando (Mon Jul 23 2012 - 08:53:39 CDT)
- Keeping water out of the binding pocket with ColVar Wang Yi (Fri Jul 20 2012 - 20:14:41 CDT)
- crossterm error Cristhian Boetsch (Fri Jul 20 2012 - 13:06:04 CDT)
- constant velocity of carbon nanotube through water bond.james (Fri Jul 20 2012 - 00:11:27 CDT)
- different seeds and protein behavior Dr. Eddie (Thu Jul 19 2012 - 18:29:21 CDT)
- Re: different seeds and protein behavior Aron Broom (Thu Jul 19 2012 - 20:21:44 CDT)
- Re: different seeds and protein behavior Nicholas M Glykos (Fri Jul 20 2012 - 03:14:17 CDT)
- Re: different seeds and protein behavior Dr. Eddie (Fri Jul 20 2012 - 07:56:44 CDT)
- Re: different seeds and protein behavior Aron Broom (Fri Jul 20 2012 - 08:50:40 CDT)
- Re: different seeds and protein behavior Ajasja LjubetiÄ (Fri Jul 20 2012 - 09:06:58 CDT)
- Re: different seeds and protein behavior Aron Broom (Fri Jul 20 2012 - 11:58:13 CDT)
- Re: different seeds and protein behavior Nicholas M Glykos (Fri Jul 20 2012 - 03:14:17 CDT)
- Re: different seeds and protein behavior amin_at_imtech.res.in (Thu Jul 19 2012 - 21:36:23 CDT)
- Re: different seeds and protein behavior Aron Broom (Thu Jul 19 2012 - 20:21:44 CDT)
- NAMD2.9 Release and Multi-GPU Minimization Errors c jepson (Thu Jul 19 2012 - 15:15:32 CDT)
- no CUDA-capable device is detected Damián Montaldo (Thu Jul 19 2012 - 14:12:06 CDT)
- Generalized Born Solvent Question Aron Broom (Thu Jul 19 2012 - 13:34:34 CDT)
- Re: Generalized Born Solvent Question Aron Broom (Mon Jul 30 2012 - 17:06:54 CDT)
- Re: Generalized Born Solvent Question Roy Fernando (Fri Aug 03 2012 - 14:07:26 CDT)
- Re: Generalized Born Solvent Question Aron Broom (Fri Aug 03 2012 - 15:21:22 CDT)
- Re: Generalized Born Solvent Question Roy Fernando (Tue Aug 07 2012 - 14:55:57 CDT)
- Re: Generalized Born Solvent Question Gianluca Interlandi (Tue Aug 07 2012 - 15:16:04 CDT)
- Re: Generalized Born Solvent Question Aron Broom (Tue Aug 07 2012 - 16:10:05 CDT)
- Re: Generalized Born Solvent Question Gianluca Interlandi (Tue Aug 07 2012 - 16:20:34 CDT)
- Re: Generalized Born Solvent Question Roy Fernando (Tue Aug 07 2012 - 16:47:01 CDT)
- Re: Generalized Born Solvent Question Roy Fernando (Fri Aug 03 2012 - 14:07:26 CDT)
- Re: Generalized Born Solvent Question Aron Broom (Mon Jul 30 2012 - 17:06:54 CDT)
- NAMD does not exit simulation on satisfying condition in the tclforces script Mithun Biswas (Thu Jul 19 2012 - 10:26:01 CDT)
- Running Parallel Jobs Simultaneously with MPIRUN Rajan Vatassery (Wed Jul 18 2012 - 10:36:04 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Axel Kohlmeyer (Wed Jul 18 2012 - 11:33:46 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Rajan Vatassery (Wed Jul 18 2012 - 14:28:07 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Aron Broom (Wed Jul 18 2012 - 15:30:56 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Axel Kohlmeyer (Wed Jul 18 2012 - 15:47:40 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Hugh Heldenbrand (Wed Jul 18 2012 - 16:29:27 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Rajan Vatassery (Thu Jul 19 2012 - 01:59:55 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Rajan Vatassery (Wed Jul 18 2012 - 14:28:07 CDT)
- Re: Running Parallel Jobs Simultaneously with MPIRUN Axel Kohlmeyer (Wed Jul 18 2012 - 11:33:46 CDT)
- Instabilities in Minimization Sándor Kovács (Tue Jul 17 2012 - 17:14:10 CDT)
- Cuda error Dr. Eddie (Mon Jul 16 2012 - 13:19:19 CDT)
- Re: Cuda error Aron Broom (Mon Jul 16 2012 - 13:30:57 CDT)
- Aspirin charmm ff Ramin Ekhteiari (Tue Jul 17 2012 - 10:21:13 CDT)
- Umbrella Sampling plus restraints felmerino_at_uchile.cl (Wed Jul 18 2012 - 07:18:10 CDT)
- Re: Umbrella Sampling plus restraints Aron Broom (Wed Jul 18 2012 - 08:47:34 CDT)
- Re: Umbrella Sampling plus restraints felmerino_at_uchile.cl (Fri Jul 20 2012 - 04:44:48 CDT)
- Re: Umbrella Sampling plus restraints Aron Broom (Fri Jul 20 2012 - 08:48:00 CDT)
- Aspirin charmm ff Ramin Ekhteiari (Tue Jul 17 2012 - 10:21:13 CDT)
- Re: Cuda error Aron Broom (Mon Jul 16 2012 - 13:30:57 CDT)
- (no subject) ÖÓË´ (Mon Jul 16 2012 - 08:59:14 CDT)
- postdoctoral position available in simulations of ionic liquids at NASA Ames Lawson, John W. (ARC-TSM) (Mon Jul 16 2012 - 00:35:46 CDT)
- Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Roy Fernando (Sun Jul 15 2012 - 17:13:22 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Aron Broom (Sun Jul 15 2012 - 20:31:26 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Ajasja LjubetiÄ (Mon Jul 16 2012 - 01:25:10 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Roy Fernando (Mon Jul 16 2012 - 15:03:53 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Axel Kohlmeyer (Mon Jul 16 2012 - 15:46:51 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Aron Broom (Mon Jul 16 2012 - 16:27:34 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Roy Fernando (Mon Jul 16 2012 - 16:43:04 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Aron Broom (Mon Jul 16 2012 - 16:59:22 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration Aron Broom (Sun Jul 15 2012 - 20:31:26 CDT)
- gentoo ebuild Dr. Eddie (Fri Jul 13 2012 - 16:01:12 CDT)
- Am I doing the Right Thing? Roy Fernando (Thu Jul 12 2012 - 12:02:05 CDT)
- gtx-680: CUDA error in cudaGetDeviceCount lcbllcc_at_gmail.com (Thu Jul 12 2012 - 04:28:08 CDT)
- Re: vmd-l: vmd installation problem oguz gurbulak (Thu Jul 12 2012 - 00:59:23 CDT)
- How does NAMD treat a bond across periodic boundaries mj_aghaei_at_aut.ac.ir (Wed Jul 11 2012 - 23:17:49 CDT)
- umbrella sampling ipsita basu (Wed Jul 11 2012 - 06:48:16 CDT)
- Alchemical with parm7 ff Francesco Pietra (Wed Jul 11 2012 - 03:39:30 CDT)
- What is a good (small) test system for NAMD Roy Fernando (Tue Jul 10 2012 - 14:13:01 CDT)
- Re: What is a good (small) test system for NAMD Giacomo Fiorin (Tue Jul 10 2012 - 14:17:41 CDT)
- Running NAMD on Forge (CUDA) Gianluca Interlandi (Tue Jul 10 2012 - 12:14:52 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Tue Jul 10 2012 - 12:21:45 CDT)
- Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 13:41:16 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Thu Jul 12 2012 - 13:50:59 CDT)
- Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 14:21:38 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Thu Jul 12 2012 - 14:28:33 CDT)
- Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 14:53:44 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Thu Jul 12 2012 - 15:05:59 CDT)
- Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 15:58:42 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Thu Jul 12 2012 - 16:12:39 CDT)
- Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 17:25:52 CDT)
- AW: Running NAMD on Forge (CUDA) Norman Geist (Fri Jul 13 2012 - 01:28:49 CDT)
- Re: AW: Running NAMD on Forge (CUDA) Gianluca Interlandi (Fri Jul 13 2012 - 01:35:49 CDT)
- AW: AW: Running NAMD on Forge (CUDA) Norman Geist (Fri Jul 13 2012 - 02:09:04 CDT)
- Re: AW: AW: Running NAMD on Forge (CUDA) Gianluca Interlandi (Fri Jul 13 2012 - 14:08:57 CDT)
- Re: AW: AW: Running NAMD on Forge (CUDA) Gianluca Interlandi (Sat Jul 14 2012 - 20:59:05 CDT)
- AW: AW: AW: Running NAMD on Forge (CUDA) Norman Geist (Mon Jul 16 2012 - 02:11:45 CDT)
- Re: AW: AW: Running NAMD on Forge (CUDA) Axel Kohlmeyer (Mon Jul 16 2012 - 02:28:25 CDT)
- Re: Running NAMD on Forge (CUDA) Gianluca Interlandi (Thu Jul 12 2012 - 13:41:16 CDT)
- Re: Running NAMD on Forge (CUDA) Aron Broom (Tue Jul 10 2012 - 12:21:45 CDT)
- force field parameters for Silicon farzad kiani (Tue Jul 10 2012 - 07:57:05 CDT)
- Re: Fixing bonds in dihydrogen phosphate to save computation time Axel Kohlmeyer (Tue Jul 10 2012 - 05:21:14 CDT)
- Re: Multi core problem Axel Kohlmeyer (Tue Jul 10 2012 - 05:18:28 CDT)
- pairlist violations Thomas Brian (Mon Jul 09 2012 - 18:44:55 CDT)
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois David Brandon (Mon Jul 09 2012 - 14:29:08 CDT)
- Fixing bonds in dihydrogen phosphate to save computation time Evgeny Bulat (Mon Jul 09 2012 - 13:55:45 CDT)
- Multi core problem flavio seixas (Sun Jul 08 2012 - 14:48:04 CDT)
- periodic boundaries farzad kiani (Sat Jul 07 2012 - 05:51:22 CDT)
- steered molecular dynamics with multiple molecules Koivuniemi Artturi (Wed Jul 04 2012 - 05:19:15 CDT)
- testing digest demime - please ignore #2 Jim Phillips (Tue Jul 03 2012 - 19:59:09 CDT)
- testing digest demime - please ignore Jim Phillips (Tue Jul 03 2012 - 17:50:18 CDT)
- Compiling and running NAMD on multiple nodes of SDSC Trestles Gianluca Interlandi (Tue Jul 03 2012 - 13:28:36 CDT)
- one-sided harmonic restraint potential Sandeep Patel (Mon Jul 02 2012 - 21:51:21 CDT)
- about dcd files Namd Namd (Mon Jul 02 2012 - 08:30:17 CDT)
- Targeted Molecular Dynamics Thomas Albers (Sat Jun 30 2012 - 14:56:53 CDT)
- pbc precision Thomas Brian (Thu Jun 28 2012 - 15:18:10 CDT)
- Re: efield energies incorrect in analysis mode (run 0) ? Mark Triger (Thu Jun 28 2012 - 14:22:18 CDT)
- namd cuda error. kanchi subbarao rao (Thu Jun 28 2012 - 11:13:43 CDT)
- wrap dcd files Namd Namd (Thu Jun 28 2012 - 05:03:10 CDT)
- RE: namd-l digest V1 #787 Hyuntae Na (Wed Jun 27 2012 - 20:22:15 CDT)
- efield energies incorrect in analysis mode (run 0) ? Mark Triger (Wed Jun 27 2012 - 16:25:04 CDT)
- efield energies incorrect in analysis mode (run 0) ? Mark Triger (Wed Jun 27 2012 - 13:19:48 CDT)
- Re: Techinal problems with ABF simulations Jérôme Hénin (Wed Jun 27 2012 - 08:29:09 CDT)
- jobs with Intel i7 Neelanjana Sengupta (Wed Jun 27 2012 - 07:33:09 CDT)
- AW: AW: Atoms moving too fast only with CUDA version. Norman Geist (Wed Jun 27 2012 - 03:28:33 CDT)
- Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 00:37:55 CDT)
- Re: Atoms moving too fast only with CUDA version. Aron Broom (Wed Jun 27 2012 - 00:51:33 CDT)
- Re: Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 01:34:28 CDT)
- AW: Atoms moving too fast only with CUDA version. Norman Geist (Wed Jun 27 2012 - 01:43:14 CDT)
- Re: AW: Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 02:10:04 CDT)
- Re: AW: Atoms moving too fast only with CUDA version. Aron Broom (Wed Jun 27 2012 - 02:12:40 CDT)
- AW: AW: Atoms moving too fast only with CUDA version. Norman Geist (Wed Jun 27 2012 - 03:23:23 CDT)
- Re: Atoms moving too fast only with CUDA version. Aron Broom (Wed Jun 27 2012 - 00:51:33 CDT)
- umbrella sampling ipsita basu (Mon Jun 25 2012 - 02:22:21 CDT)
- Nicolas te ha dejado un mensaje... Badoo (Sun Jun 24 2012 - 16:13:10 CDT)
- Sudden energy drop after minimization Hyuntae Na (Fri Jun 22 2012 - 19:56:14 CDT)
- AW: Sudden energy drop after minimization Norman Geist (Mon Jun 25 2012 - 00:37:43 CDT)
- RE: AW: Sudden energy drop after minimization Hyuntae Na (Mon Jun 25 2012 - 00:59:18 CDT)
- Re: AW: Sudden energy drop after minimization Aron Broom (Mon Jun 25 2012 - 22:05:39 CDT)
- AW: AW: Sudden energy drop after minimization Norman Geist (Tue Jun 26 2012 - 01:40:39 CDT)
- RE: AW: AW: Sudden energy drop after minimization Hyuntae Na (Tue Jun 26 2012 - 01:56:00 CDT)
- RE: AW: AW: Sudden energy drop after minimization tillmann.utesch_at_mail.tu-berlin.de (Tue Jun 26 2012 - 03:03:34 CDT)
- AW: AW: AW: Sudden energy drop after minimization Norman Geist (Tue Jun 26 2012 - 04:31:42 CDT)
- RE: AW: Sudden energy drop after minimization Hyuntae Na (Mon Jun 25 2012 - 00:59:18 CDT)
- AW: Sudden energy drop after minimization Norman Geist (Mon Jun 25 2012 - 00:37:43 CDT)
- NAMD 2.9 CUDA multicore, single machine Brett T. Hannigan (Fri Jun 22 2012 - 13:04:34 CDT)
- AW: GPU cluster Norman Geist (Thu Jun 21 2012 - 05:43:56 CDT)
- lookup tables Thomas Brian (Wed Jun 20 2012 - 23:17:11 CDT)
- Workshop for Computational Chemistry & Physics MARK PLUMMER (Wed Jun 20 2012 - 15:17:27 CDT)
- Fwd: Fwd: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 12:57:06 CDT)
- Re: Fwd: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 09:38:32 CDT)
- Re: Fwd: namd on gtx-680 Francesco Pietra (Wed Jun 20 2012 - 05:08:30 CDT)
- ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Tue Jun 19 2012 - 15:43:26 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Aron Broom (Tue Jun 19 2012 - 16:56:51 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Jérôme Hénin (Wed Jun 20 2012 - 06:25:36 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Wed Jun 20 2012 - 11:30:29 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Jérôme Hénin (Thu Jun 21 2012 - 09:47:28 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Tue Jul 03 2012 - 13:47:38 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Jérôme Hénin (Thu Jul 05 2012 - 05:24:31 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Thu Jul 12 2012 - 14:47:49 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Fri Jul 13 2012 - 13:35:46 CDT)
- Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes Robert Johnson (Wed Jun 20 2012 - 11:30:29 CDT)
- GPU cluster Matthew B. Roark (Tue Jun 19 2012 - 14:07:58 CDT)
- namd simulation​:protein,l​igand,lipi​d,water and ions Marlet Martinez (Tue Jun 19 2012 - 12:33:13 CDT)
- Problem of 'missing stage' in colvars.state file Shaon Chakrabarti (Tue Jun 19 2012 - 12:15:51 CDT)
- mdff error Hamze Rahimi (Mon Jun 18 2012 - 09:41:08 CDT)
- Problem running NAMD mpahleva_at_abo.fi (Mon Jun 18 2012 - 01:56:37 CDT)
- Erratic pressure values during equilibration of water box Ashwin C.V. (Sun Jun 17 2012 - 08:49:27 CDT)
- [Fwd: Re: FATAL ERROR : Line too long in pdb file] amin_at_imtech.res.in (Fri Jun 15 2012 - 20:25:57 CDT)
- FATAL ERROR : Line too long in pdb file amin_at_imtech.res.in (Fri Jun 15 2012 - 19:43:31 CDT)
- memory-optimized version binary coordinates? Carlos Sosa (Fri Jun 15 2012 - 15:43:58 CDT)
- Re: memory-optimized version binary coordinates? Aron Broom (Fri Jun 15 2012 - 16:18:22 CDT)
- Re: memory-optimized version binary coordinates? Carlos Sosa (Sat Jun 16 2012 - 19:33:36 CDT)
- Re: memory-optimized version binary coordinates? Aron Broom (Sat Jun 16 2012 - 21:22:29 CDT)
- Re: memory-optimized version binary coordinates? Carlos Sosa (Sun Jun 17 2012 - 10:20:38 CDT)
- Re: memory-optimized version binary coordinates? Aron Broom (Sun Jun 17 2012 - 11:10:31 CDT)
- Re: memory-optimized version binary coordinates? Carlos Sosa (Sun Jun 17 2012 - 11:24:50 CDT)
- Re: memory-optimized version binary coordinates? Aron Broom (Sun Jun 17 2012 - 11:34:48 CDT)
- AW: memory-optimized version binary coordinates? Norman Geist (Thu Jun 21 2012 - 00:39:57 CDT)
- Re: memory-optimized version binary coordinates? Carlos Sosa (Mon Jun 25 2012 - 15:06:19 CDT)
- Re: memory-optimized version binary coordinates? Carlos Sosa (Sat Jun 16 2012 - 19:33:36 CDT)
- Re: memory-optimized version binary coordinates? Aron Broom (Fri Jun 15 2012 - 16:18:22 CDT)
- Negative surface area? David Minh (Fri Jun 15 2012 - 09:08:12 CDT)
- running simulations on different machines with different versions of NAMD Puspita Halder (Fri Jun 15 2012 - 01:29:59 CDT)
- AW: namd simulation:protein,ligand,lipid,water and ions Norman Geist (Fri Jun 15 2012 - 01:20:45 CDT)
- minimization and water bubbles Dr. Eddie (Thu Jun 14 2012 - 21:33:27 CDT)
- Multiple copy ligand simulations Vijay Vammi (Thu Jun 14 2012 - 13:32:43 CDT)
- could acpype output file be used for NAMD CHARMM FF? Albert (Thu Jun 14 2012 - 13:29:06 CDT)
- Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 13:26:03 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jun 14 2012 - 13:48:07 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 14:56:30 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jun 14 2012 - 15:20:04 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 15:47:10 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jun 14 2012 - 15:54:17 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 17:12:45 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jun 14 2012 - 17:25:26 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Tue Jul 03 2012 - 20:04:09 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jul 05 2012 - 17:25:02 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jul 05 2012 - 18:01:04 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jul 05 2012 - 18:07:46 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Aron Broom (Thu Jun 14 2012 - 14:56:30 CDT)
- Re: Buffer Underflow in Multiple Walker MetaDynamics Giacomo Fiorin (Thu Jun 14 2012 - 13:48:07 CDT)
- Re: namd simulation:protein,ligand,lipid,water and ions Marlet Martinez (Thu Jun 14 2012 - 12:29:15 CDT)
- Question about optmem input files Carlos Sosa (Thu Jun 14 2012 - 10:33:50 CDT)
- Advice on how to perform multiple copy ligand simulation Vijay Vammi (Thu Jun 14 2012 - 08:09:19 CDT)
- flipdcd corrupting dcd files peter.schmidtke_at_fr.netgrs.com (Thu Jun 14 2012 - 06:30:48 CDT)
- namd simulation:protein,ligand,lipid,water and ions Marlet Martinez (Wed Jun 13 2012 - 18:44:40 CDT)
- making force grids Thomas Brian (Wed Jun 13 2012 - 18:36:00 CDT)
- Only one process running on cluster amin_at_imtech.res.in (Wed Jun 13 2012 - 02:25:14 CDT)
- CUDA error on Pe 4: device cannot map host memory Vignesh (Tue Jun 12 2012 - 18:57:14 CDT)
- keeping a protein in a solvation box Dr. Eddie (Tue Jun 12 2012 - 17:44:26 CDT)
- Re: keeping a protein in a solvation box Aaron Oakley (Tue Jun 12 2012 - 18:45:19 CDT)
- Re: keeping a protein in a solvation box Eduard Schreiner (Tue Jun 12 2012 - 18:19:11 CDT)
- NAMD-INCONSISTENCY IN SCOR jose correa (Tue Jun 12 2012 - 17:23:00 CDT)
- Trying to run a setup with amber force field in NAMD scott davis (Tue Jun 12 2012 - 16:49:55 CDT)
- Re: Trying to run a setup with amber force field in NAMD Aron Broom (Tue Jun 12 2012 - 21:34:09 CDT)
- AW: Trying to run a setup with amber force field in NAMD Norman Geist (Wed Jun 13 2012 - 00:50:10 CDT)
- Re: Trying to run a setup with amber force field in NAMD johan strumpfer (Tue Jun 12 2012 - 17:49:46 CDT)
- Re: Trying to run a setup with amber force field in NAMD Eduard Schreiner (Tue Jun 12 2012 - 18:32:08 CDT)
- how to solve such kind of crossterm parameter problem? Liqun Zhang (Tue Jun 12 2012 - 10:28:09 CDT)
- Targeted Molecular Dynamics Miguel Ángel Mompeán García (Tue Jun 12 2012 - 06:02:17 CDT)
- Force field parameter and topology for zinc finger protein sudipta (Mon Jun 11 2012 - 20:09:56 CDT)
- Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions MARK PLUMMER (Mon Jun 11 2012 - 17:14:51 CDT)
- (no subject) Francesco Pietra (Sun Jun 10 2012 - 12:45:22 CDT)
- membrane GPCR-ligands simulations jose correa (Fri Jun 08 2012 - 20:23:46 CDT)
- Query about compressing PSF files Seetha Pothapragada (Fri Jun 08 2012 - 15:44:22 CDT)
- please help Adeleke Adebayo Abayomi (Fri Jun 08 2012 - 14:38:18 CDT)
- using CHARMM22STAR forcefield in NAMD Aaron Oakley (Fri Jun 08 2012 - 03:23:07 CDT)
- help on building PATCH Matteo Pappalardo (Fri Jun 08 2012 - 03:15:53 CDT)
- AW: compress PSF into INTER Norman Geist (Thu Jun 07 2012 - 05:15:09 CDT)
- cell shape after increasing margin (parm7 ff) Francesco Pietra (Thu Jun 07 2012 - 01:26:35 CDT)
- compress PSF into INTER Cruz-Chu Eduardo Roberto (Wed Jun 06 2012 - 13:37:34 CDT)
- pulling force doesn't drop to zero in SMD Luthur Cheung (Tue Jun 05 2012 - 19:06:17 CDT)
- pulling force didn't drop to zero in SMD Luthur Cheung (Wed Jun 06 2012 - 08:31:43 CDT)
- namd/vmd support to GTX-6## series Francesco Pietra (Wed Jun 06 2012 - 03:43:38 CDT)
- Psfgen CTER issues Evgeny Bulat (Tue Jun 05 2012 - 13:00:52 CDT)
- FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Francesco Pietra (Tue Jun 05 2012 - 02:16:40 CDT)
- NAMD 2.9 Replica Exchange (+replicas error) Cade Markegard (Mon Jun 04 2012 - 16:57:06 CDT)
- RE: charmm to namd conversion Felipe Merino (Mon Jun 04 2012 - 16:39:55 CDT)
- Workshop In Aspen Colorado - Molecular Physics of Non-Bonded Biomolecular Interactions MARK PLUMMER (Mon Jun 04 2012 - 15:06:18 CDT)
- charmm to namd conversion Matthew B. Roark (Mon Jun 04 2012 - 12:29:55 CDT)
- NOTICE: mail delivery status Jim Phillips (Sun Jun 03 2012 - 23:52:37 CDT)
- cuda_check_local_progress polled 1000000 times Francesco Pietra (Sat Jun 02 2012 - 14:06:49 CDT)
- Re: cuda_check_local_progress polled 1000000 times Francesco Pietra (Mon Jun 04 2012 - 12:20:56 CDT)
- AW: cuda_check_local_progress polled 1000000 times Norman Geist (Tue Jun 05 2012 - 00:29:17 CDT)
- Re: cuda_check_local_progress polled 1000000 times Francesco Pietra (Tue Jun 05 2012 - 02:28:30 CDT)
- Re: cuda_check_local_progress polled 1000000 times Francesco Pietra (Tue Jun 05 2012 - 08:34:47 CDT)
- Re: cuda_check_local_progress polled 1000000 times Francesco Pietra (Wed Jun 06 2012 - 02:29:18 CDT)
- Re: cuda_check_local_progress polled 1000000 times Francesco Pietra (Mon Jun 04 2012 - 12:20:56 CDT)
- issue with solute that splits Massimiliano Porrini (Fri Jun 01 2012 - 13:52:45 CDT)
- Benefits of SandyBridge EP in NAMD2.9 Florian Mrugalla (Fri Jun 01 2012 - 06:52:19 CDT)
- NAMD fixes for dummy atoms & parameters for divalent metal ions Francesco Pietra (Fri Jun 01 2012 - 03:15:21 CDT)
- charmm toppar in namd Matthew B. Roark (Thu May 31 2012 - 14:04:18 CDT)
- Writing an output file into pdb format in a simulation. Ajith Rathnaweera Rajapaksha Mudalige (Thu May 31 2012 - 15:20:58 CDT)
- Re: Writing an output file into pdb format in a simulation. Axel Kohlmeyer (Thu May 31 2012 - 15:57:33 CDT)
- Re: Writing an output file into pdb format in a simulation. JC Gumbart (Thu May 31 2012 - 16:10:38 CDT)
- Re: Writing an output file into pdb format in a simulation. Nicholas M Glykos (Fri Jun 01 2012 - 02:18:01 CDT)
- Writing an output file into pdb format in a simulation. Ajith Rathnaweera Rajapaksha Mudalige (Thu May 31 2012 - 15:20:58 CDT)
- (no subject) Marc Charendoff (Thu May 31 2012 - 12:09:43 CDT)
- AW: NAMD feature request Hydrogenscale Norman Geist (Thu May 31 2012 - 01:09:59 CDT)
- Breaking of Disulfide Bonds Kapil jain (Wed May 30 2012 - 23:09:25 CDT)
- How to restraint pairinteractions sanxing.xu_at_gmail.com (Wed May 30 2012 - 17:01:20 CDT)
- Fwd: Three GPU cards on shared-mem motherboard Francesco Pietra (Wed May 30 2012 - 12:33:47 CDT)
- question about dcd file Hasan haska (Wed May 30 2012 - 07:22:11 CDT)
- Re: NAMD feature request Hydrogenscale Axel Kohlmeyer (Wed May 30 2012 - 04:20:03 CDT)
- Re: NAMD feature request Hydrogenscale Ajasja LjubetiÄ (Wed May 30 2012 - 06:16:46 CDT)
- Re: NAMD feature request Hydrogenscale Jérôme Hénin (Wed May 30 2012 - 06:51:47 CDT)
- Re: NAMD feature request Hydrogenscale Axel Kohlmeyer (Wed May 30 2012 - 07:14:40 CDT)
- Re: NAMD feature request Hydrogenscale Vincent Leroux (Wed May 30 2012 - 08:04:01 CDT)
- AW: NAMD feature request Hydrogenscale Norman Geist (Wed May 30 2012 - 09:17:48 CDT)
- Re: AW: NAMD feature request Hydrogenscale Vincent Leroux (Wed May 30 2012 - 10:27:47 CDT)
- AW: AW: NAMD feature request Hydrogenscale Norman Geist (Thu May 31 2012 - 01:06:29 CDT)
- Re: AW: AW: NAMD feature request Hydrogenscale Vincent Leroux (Thu May 31 2012 - 10:40:32 CDT)
- AW: AW: AW: NAMD feature request Hydrogenscale Norman Geist (Fri Jun 01 2012 - 01:33:48 CDT)
- Re: NAMD feature request Hydrogenscale Ajasja LjubetiÄ (Wed May 30 2012 - 06:16:46 CDT)
- NAMD feature request Hydrogenscale Norman Geist (Wed May 30 2012 - 02:36:16 CDT)
- about trajectory analysis oguz gurbulak (Wed May 30 2012 - 01:43:42 CDT)
- About the correction of charging two ion water box by using FEP Win Liu (Mon May 28 2012 - 11:59:33 CDT)
- Three GPU cards on shared-mem motherboard Francesco Pietra (Mon May 28 2012 - 03:53:02 CDT)
- Re: Three GPU cards on shared-mem motherboard Axel Kohlmeyer (Mon May 28 2012 - 05:35:51 CDT)
- Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Mon May 28 2012 - 11:03:43 CDT)
- Re: Three GPU cards on shared-mem motherboard Axel Kohlmeyer (Mon May 28 2012 - 11:20:13 CDT)
- Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Mon May 28 2012 - 14:46:54 CDT)
- Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Tue May 29 2012 - 16:59:32 CDT)
- AW: Three GPU cards on shared-mem motherboard Norman Geist (Wed May 30 2012 - 01:55:50 CDT)
- Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Wed May 30 2012 - 02:45:24 CDT)
- Re: Three GPU cards on shared-mem motherboard Francesco Pietra (Mon May 28 2012 - 11:03:43 CDT)
- AW: Three GPU cards on shared-mem motherboard Norman Geist (Tue May 29 2012 - 01:24:34 CDT)
- Re: Three GPU cards on shared-mem motherboard Axel Kohlmeyer (Mon May 28 2012 - 05:35:51 CDT)
- About the correction of charging two ion water box by using FEP Win Liu (Mon May 28 2012 - 02:06:09 CDT)
- protein folding by simulated anneling Puspita Halder (Mon May 28 2012 - 01:11:53 CDT)
- AW: AW: Generating force field for novel molecules Norman Geist (Fri May 25 2012 - 00:56:07 CDT)
- Re: AW: AW: Generating force field for novel molecules Sajad Falsafi-Zadeh (Fri May 25 2012 - 01:50:35 CDT)
- Re: AW: AW: Generating force field for novel molecules Jeffrey Potoff (Fri May 25 2012 - 09:34:11 CDT)
- Re: AW: AW: Generating force field for novel molecules Mayne, Christopher G (Fri May 25 2012 - 12:07:43 CDT)
- queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 00:06:28 CDT)
- AW: queries about "Tclforces" utility in NAMD Norman Geist (Fri May 25 2012 - 01:11:47 CDT)
- Re: queries about "Tclforces" utility in NAMD Jérôme Hénin (Fri May 25 2012 - 02:48:01 CDT)
- Re: queries about "Tclforces" utility in NAMD Axel Kohlmeyer (Fri May 25 2012 - 05:54:27 CDT)
- Re: queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 10:06:39 CDT)
- Re: queries about "Tclforces" utility in NAMD Jérôme Hénin (Fri May 25 2012 - 11:11:23 CDT)
- Re: queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 11:25:10 CDT)
- Re: queries about "Tclforces" utility in NAMD Jérôme Hénin (Fri May 25 2012 - 12:17:14 CDT)
- Re: queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 12:43:50 CDT)
- Re: queries about "Tclforces" utility in NAMD harish vashisth (Sun May 27 2012 - 17:39:01 CDT)
- Advertisement Workshop Aspen Center for Physics MARK PLUMMER (Thu May 24 2012 - 16:04:35 CDT)
- Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Thu May 24 2012 - 04:51:06 CDT)
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Norman Geist (Fri May 25 2012 - 01:10:17 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Axel Kohlmeyer (Fri May 25 2012 - 05:39:37 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Sun May 27 2012 - 09:10:59 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Axel Kohlmeyer (Mon May 28 2012 - 14:58:53 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Francesco Pietra (Mon May 28 2012 - 17:11:54 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Axel Kohlmeyer (Mon May 28 2012 - 17:19:42 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Francesco Pietra (Tue May 29 2012 - 00:10:08 CDT)
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Norman Geist (Tue May 29 2012 - 01:05:16 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Sun May 27 2012 - 09:10:59 CDT)
- hbonds colvar component Vlad Cojocaru (Thu May 24 2012 - 02:13:29 CDT)
- protein folding by simulated annealing method Puspita Halder (Thu May 24 2012 - 00:01:25 CDT)
- Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Wed May 23 2012 - 14:48:35 CDT)
- Re: Issues with 'Gyration' in Colvars module Aron Broom (Wed May 23 2012 - 14:56:49 CDT)
- Re: Issues with 'Gyration' in Colvars module Giacomo Fiorin (Wed May 23 2012 - 15:27:51 CDT)
- Re: Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Wed May 23 2012 - 17:11:13 CDT)
- Re: Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Wed May 23 2012 - 17:25:09 CDT)
- Re: Issues with 'Gyration' in Colvars module Aron Broom (Wed May 23 2012 - 18:09:29 CDT)
- Re: Issues with 'Gyration' in Colvars module Giacomo Fiorin (Thu May 24 2012 - 09:01:09 CDT)
- Re: Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Thu May 24 2012 - 20:53:25 CDT)
- Re: Issues with 'Gyration' in Colvars module Aron Broom (Thu May 24 2012 - 21:37:42 CDT)
- Re: Issues with 'Gyration' in Colvars module Jérôme Hénin (Fri May 25 2012 - 11:08:58 CDT)
- Issues with 'Gyration' in Colvars module Jérôme Hénin (Fri May 25 2012 - 13:20:49 CDT)
- Re: Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Sat Jun 02 2012 - 14:29:52 CDT)
- Re: Issues with 'Gyration' in Colvars module Giacomo Fiorin (Wed May 23 2012 - 15:27:51 CDT)
- Re: Issues with 'Gyration' in Colvars module Aron Broom (Wed May 23 2012 - 14:56:49 CDT)
- (no subject) Puspita Halder (Wed May 23 2012 - 07:45:48 CDT)
- Generating force field for novel molecules MOHAMMAD JAVAD AGHAEI (Wed May 23 2012 - 03:16:36 CDT)
- TMD output format Payne, Christy (Mon May 21 2012 - 10:00:24 CDT)
- Parameters for Cesium Burgess, Don E (Thu May 17 2012 - 11:43:44 CDT)
- FEP - Dynamic charges John Baker (Tue May 15 2012 - 12:38:59 CDT)
- MDFF for protein complex Hamze Rahimi (Mon May 14 2012 - 09:22:42 CDT)
- five 'ERROR' in the log file of NAMD2.9 ypg (Sun May 13 2012 - 02:15:27 CDT)
- Problem with Methane-Methane PMF Shaon Chakrabarti (Fri May 11 2012 - 16:08:23 CDT)
- Atomic Radii for GB Implicit Solvent Aron Broom (Fri May 11 2012 - 14:40:12 CDT)
- fixed bond length Mortaza Aghtar (Fri May 11 2012 - 10:51:01 CDT)
- Multicore executable error Caitlin Scott (Wed May 09 2012 - 13:05:20 CDT)
- Fwd: AW: stereo-chemical inversion during MD Gordon Wells (Wed May 09 2012 - 10:04:04 CDT)
- Fwd: Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 03:26:25 CDT)
- Fwd: stereo-chemical inversion during MD Francesco Pietra (Tue May 08 2012 - 01:59:49 CDT)
- stereo-chemical inversion during MD Gordon Wells (Mon May 07 2012 - 12:01:24 CDT)
- Specific colvar component needed. Germán Andrés Miño (Mon May 07 2012 - 10:55:14 CDT)
- Hole Buddhadev Maiti (Fri May 04 2012 - 22:47:27 CDT)
- Fwd: Re: charmrun setup Branko (Sat May 05 2012 - 13:37:05 CDT)
- charmrun setup Pedro Armando Ojeda May (Sat May 05 2012 - 13:14:12 CDT)
- Applying TclBC script every x steps Error Maria Pikoula (Fri May 04 2012 - 16:46:03 CDT)
- Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 15:52:41 CDT)
- A question about the CHARMM force field Hall McDull (Fri May 04 2012 - 03:32:30 CDT)
- Umbrella sampling-reliability of results Parisa Akhski (Fri May 04 2012 - 09:20:17 CDT)
- Periodic cell has become too small lecan (Fri May 04 2012 - 00:19:38 CDT)
- forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 15:43:50 CDT)
- Re: forces saved in forcedcd Chris Harrison (Thu May 03 2012 - 18:42:19 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 19:51:36 CDT)
- Re: forces saved in forcedcd JC Gumbart (Thu May 03 2012 - 20:11:32 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 21:57:20 CDT)
- Re: forces saved in forcedcd JC Gumbart (Thu May 03 2012 - 22:05:40 CDT)
- Re: forces saved in forcedcd Chris Harrison (Thu May 03 2012 - 22:22:58 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 22:45:37 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 22:40:34 CDT)
- Re: forces saved in forcedcd JC Gumbart (Fri May 04 2012 - 00:58:54 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Fri May 04 2012 - 08:49:14 CDT)
- RE: forces saved in forcedcd JC Gumbart (Fri May 04 2012 - 08:51:43 CDT)
- Re: forces saved in forcedcd Jérôme Hénin (Fri May 04 2012 - 09:32:29 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Fri May 04 2012 - 10:31:41 CDT)
- Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 19:51:36 CDT)
- Re: forces saved in forcedcd Chris Harrison (Thu May 03 2012 - 18:42:19 CDT)
- NAMD 2.9 released Jim Phillips (Thu May 03 2012 - 10:27:09 CDT)
- Need help preventing hydration of the lipid-protein interface in my system Syed Kashif Zafar (Thu May 03 2012 - 05:48:48 CDT)
- a question about ensemble Albert (Thu May 03 2012 - 01:04:58 CDT)
- tclBC incorrect output P.-L. Chau (Wed May 02 2012 - 22:18:21 CDT)
- AW: tclBC incorrect output Norman Geist (Thu May 03 2012 - 00:55:58 CDT)
- Re: AW: tclBC incorrect output P.-L. Chau (Thu May 03 2012 - 01:44:17 CDT)
- AW: AW: tclBC incorrect output Norman Geist (Fri May 04 2012 - 01:10:57 CDT)
- Re: AW: AW: tclBC incorrect output P.-L. Chau (Fri May 04 2012 - 01:26:49 CDT)
- AW: AW: AW: tclBC incorrect output Norman Geist (Fri May 04 2012 - 02:03:02 CDT)
- Re: AW: AW: AW: tclBC incorrect output P.-L. Chau (Fri May 04 2012 - 02:19:02 CDT)
- Re: AW: AW: AW: tclBC incorrect output Cruz-Chu Eduardo Roberto (Fri May 04 2012 - 02:43:20 CDT)
- Re: AW: AW: AW: tclBC incorrect output P.-L. Chau (Fri May 04 2012 - 03:33:57 CDT)
- AW: AW: AW: AW: tclBC incorrect output Norman Geist (Mon May 07 2012 - 00:26:11 CDT)
- Re: AW: AW: AW: AW: tclBC incorrect output P.-L. Chau (Mon May 07 2012 - 20:59:14 CDT)
- Re: AW: tclBC incorrect output P.-L. Chau (Thu May 03 2012 - 01:44:17 CDT)
- AW: tclBC incorrect output Norman Geist (Thu May 03 2012 - 00:55:58 CDT)
- Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 08:52:26 CDT)
- ion placement method vs total energy of the system raghav singh (Mon Apr 30 2012 - 10:25:42 CDT)
- non integral charges raghav singh (Mon Apr 30 2012 - 08:06:15 CDT)
- nucleic acids - total charge raghav singh (Mon Apr 30 2012 - 04:55:38 CDT)
- AW: AW: Set up NPT simulation in cubic PBC-box Norman Geist (Mon Apr 30 2012 - 00:29:21 CDT)
- AW: AW: Set up NPT simulation in cubic PBC-box Norman Geist (Mon Apr 30 2012 - 00:21:02 CDT)
- non integer total charge raghav singh (Sat Apr 28 2012 - 21:16:02 CDT)
- fwd: sara (Fri Apr 27 2012 - 21:51:50 CDT)
- fwd: sara (Fri Apr 27 2012 - 21:51:49 CDT)
- Go model in NAMD? Bin Zhang (Thu Apr 26 2012 - 16:52:26 CDT)
- Set up NPT simulation in cubic PBC-box Xi Cheng (Thu Apr 26 2012 - 16:22:33 CDT)
- GPCR MD Tutorial Anirban Ghosh (Thu Apr 26 2012 - 04:18:08 CDT)
- constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Wed Apr 25 2012 - 14:41:06 CDT)
- Re: constant pulling velocity in SMD Axel Kohlmeyer (Wed Apr 25 2012 - 17:16:15 CDT)
- constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Thu Apr 26 2012 - 11:33:07 CDT)
- Re: constant pulling velocity in SMD JC Gumbart (Thu Apr 26 2012 - 18:15:42 CDT)
- RE: [EXTERNAL] Re: constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Thu Apr 26 2012 - 23:10:55 CDT)
- Re: [EXTERNAL] Re: constant pulling velocity in SMD JC Gumbart (Thu Apr 26 2012 - 23:21:25 CDT)
- Re: [EXTERNAL] Re: constant pulling velocity in SMD JC Gumbart (Fri Apr 27 2012 - 12:30:53 CDT)
- Re: [EXTERNAL] Re: constant pulling velocity in SMD tillmann.utesch_at_mail.tu-berlin.de (Mon Apr 30 2012 - 03:12:07 CDT)
- Re: constant pulling velocity in SMD JC Gumbart (Thu Apr 26 2012 - 18:15:42 CDT)
- About error in .pgn error in vmd cmd prompt Vidhya Sankar (Wed Apr 25 2012 - 03:00:33 CDT)
- In-Residence Training at the Theoretical & Computational Biophysics Group, July 16-27, 2012 TCBG Workshop (Tue Apr 24 2012 - 14:06:22 CDT)
- FEP using amber topologies felmerino_at_uchile.cl (Mon Apr 23 2012 - 17:46:17 CDT)
- Question about GPUs hardware. Cesar Millan (Mon Apr 23 2012 - 17:32:01 CDT)
- FEP difficulties between two ion species Jeremy Parlin (Mon Apr 23 2012 - 16:38:31 CDT)
- AW: vmd-l: segmentation fault with NAMDenergy Norman Geist (Mon Apr 23 2012 - 00:52:17 CDT)
- AW: problem with gpu namd 2.9b3 Norman Geist (Mon Apr 23 2012 - 00:45:58 CDT)
- (no subject) Taruna Gupta (Sun Apr 22 2012 - 12:37:42 CDT)
- Simulation Using Both NAMD and VMD Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 17:05:28 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 17:10:30 CDT)
- Re: Simulation Using Both NAMD and VMD Aron Broom (Fri Apr 20 2012 - 17:30:14 CDT)
- Re: Simulation Using Both NAMD and VMD Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 18:14:17 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 19:04:54 CDT)
- Re: Simulation Using Both NAMD and VMD Chris Harrison (Fri Apr 20 2012 - 19:34:48 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 19:37:12 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 19:42:49 CDT)
- Re: Simulation Using Both NAMD and VMD Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 20:19:17 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 20:28:15 CDT)
- Re: Simulation Using Both NAMD and VMD Aron Broom (Fri Apr 20 2012 - 23:46:53 CDT)
- Re: Simulation Using Both NAMD and VMD Ajith Rathnaweera Rajapaksha Mudalige (Sat Apr 21 2012 - 00:22:33 CDT)
- Re: Simulation Using Both NAMD and VMD Aron Broom (Fri Apr 20 2012 - 17:30:14 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 17:10:30 CDT)
- Bug with BOUNDARY energy in postprocessing? David Minh (Fri Apr 20 2012 - 13:03:31 CDT)
- Re: problem with gpu namd 2.9b3 Aron Broom (Fri Apr 20 2012 - 09:25:40 CDT)
- What is the means of system-min.conf in the Residue-Based Coarse tutorial? javacfish (Fri Apr 20 2012 - 01:17:57 CDT)
- segmentation fault with NAMDenergy amin_at_imtech.res.in (Thu Apr 19 2012 - 10:19:55 CDT)
- problem with gpu namd 2.9b3 Peter Jones (Thu Apr 19 2012 - 04:30:42 CDT)
- Using Measure SASA in NAMD Simulations Ajith Rathnaweera Rajapaksha Mudalige (Mon Apr 16 2012 - 20:22:28 CDT)
- Amber topology felmerino_at_uchile.cl (Mon Apr 16 2012 - 16:13:54 CDT)
- creating a protonated cytidine entry raghav singh (Mon Apr 16 2012 - 06:35:15 CDT)
- psfgen warnings Vidhya Sankar (Sun Apr 15 2012 - 01:27:14 CDT)
- Abouf Psfgen error Syed Kashif Zafar (Sat Apr 14 2012 - 14:50:37 CDT)
- About psfgen error Vidhya Sankar (Sat Apr 14 2012 - 11:15:01 CDT)
- namd and x-plor Hasan haska (Sat Apr 14 2012 - 06:19:57 CDT)
- About error during creation of psf file Vidhya Sankar (Sat Apr 14 2012 - 01:28:27 CDT)
- (no subject) Vidhya Sankar (Sat Apr 14 2012 - 01:26:21 CDT)
- about molecular axis Namd Namd (Wed Apr 11 2012 - 05:40:30 CDT)
- fatal error running namd on Mac Jiao, Dian NMN (-EXP) (Tue Apr 10 2012 - 17:53:54 CDT)
- Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 14:58:30 CDT)
- Re: Importing a DCD into Mathematica Branko (Tue Apr 10 2012 - 15:09:51 CDT)
- Re: Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 16:38:24 CDT)
- Re: Importing a DCD into Mathematica Axel Kohlmeyer (Tue Apr 10 2012 - 16:53:26 CDT)
- Re: Importing a DCD into Mathematica Ajasja LjubetiÄ (Wed Apr 11 2012 - 07:20:59 CDT)
- Re: Importing a DCD into Mathematica Joshua Adelman (Wed Apr 11 2012 - 07:36:07 CDT)
- Re: Importing a DCD into Mathematica Ajasja LjubetiÄ (Wed Apr 11 2012 - 11:37:56 CDT)
- Re: Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 16:38:24 CDT)
- Re: Importing a DCD into Mathematica Branko (Tue Apr 10 2012 - 15:09:51 CDT)
- User-defined forces in NAMD Ali Ghaffaari (Tue Apr 10 2012 - 06:38:13 CDT)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE AUC Kiarash Hosseini (Tue Apr 10 2012 - 04:24:10 CDT)
- NAMD 2.9b3 colvars oddity Aron Broom (Mon Apr 09 2012 - 20:48:32 CDT)
- how to generate psf for membrane+protein Jiao, Dian NMN (-EXP) (Mon Apr 09 2012 - 18:16:59 CDT)
- Nonzero BOUNDARY ENERGY without periodic boundary conditions David Minh (Mon Apr 09 2012 - 12:36:25 CDT)
- Galilean Invariant Thermostat Ismail, Mohd F. (Sun Apr 08 2012 - 18:26:38 CDT)
- Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Nikolaos Glykos (Sun Apr 08 2012 - 12:25:15 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Thomas Albers (Sat Apr 07 2012 - 16:44:35 CDT)
- NAMD 2.9b3 released Jim Phillips (Fri Apr 06 2012 - 08:38:23 CDT)
- multicore versus net-linux Gianluca Interlandi (Thu Apr 05 2012 - 20:04:57 CDT)
- DCD Buddhadev Maiti (Thu Apr 05 2012 - 15:44:43 CDT)
- changing harmonic restraints (colvars) Jon Phillips (Thu Apr 05 2012 - 06:52:46 CDT)
- Re: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:57:03 CDT)
- AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 03:24:12 CDT)
- Fwd: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:02:14 CDT)
- how to edit restart.coor Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:29:26 CDT)
- MetaDynamics in 2.9b2 Question Aron Broom (Wed Apr 04 2012 - 14:54:39 CDT)
- CUDA problem? Albert (Wed Apr 04 2012 - 14:02:49 CDT)
- CUDA problem with 2.9b2 Albert (Thu Apr 05 2012 - 00:51:05 CDT)
- AW: CUDA problem? Norman Geist (Thu Apr 05 2012 - 01:12:24 CDT)
- Re: AW: CUDA problem? Albert (Thu Apr 05 2012 - 01:15:52 CDT)
- AW: AW: CUDA problem? Norman Geist (Thu Apr 05 2012 - 01:22:38 CDT)
- Re: AW: AW: CUDA problem? Jim Phillips (Thu Apr 05 2012 - 22:37:53 CDT)
- Re: AW: AW: CUDA problem? Albert (Fri Apr 06 2012 - 00:07:53 CDT)
- Re: AW: AW: CUDA problem? Jim Phillips (Fri Apr 06 2012 - 08:26:18 CDT)
- Re: AW: AW: CUDA problem? Francesco Pietra (Fri Apr 06 2012 - 02:59:59 CDT)
- Re: AW: AW: CUDA problem? Albert (Fri Apr 06 2012 - 07:39:09 CDT)
- AW: AW: AW: CUDA problem? Norman Geist (Wed Apr 11 2012 - 01:07:16 CDT)
- Re: AW: AW: CUDA problem? Jim Phillips (Fri Apr 06 2012 - 08:10:47 CDT)
- Re: AW: AW: CUDA problem? Francesco Pietra (Sat Apr 07 2012 - 00:40:04 CDT)
- AW: AW: AW: CUDA problem? Norman Geist (Wed Apr 11 2012 - 01:04:08 CDT)
- Re: AW: CUDA problem? Albert (Thu Apr 05 2012 - 01:15:52 CDT)
- Line minimizerfailure because of IMPR? Francesco Pietra (Wed Apr 04 2012 - 10:01:45 CDT)
- mdff energy calculation snoze pa (Mon Apr 02 2012 - 10:56:28 CDT)
- Protonated nucleotides Zack Scholl (Mon Apr 02 2012 - 07:49:53 CDT)
- psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 09:53:13 CDT)
- NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Thomas Albers (Sat Mar 31 2012 - 18:00:06 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Nicholas M Glykos (Sun Apr 01 2012 - 03:41:08 CDT)
- AW: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Norman Geist (Mon Apr 02 2012 - 01:43:07 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Thomas Albers (Mon Apr 02 2012 - 14:17:13 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Thomas Albers (Tue Apr 03 2012 - 07:37:54 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Nicholas M Glykos (Sun Apr 01 2012 - 03:41:08 CDT)
- Bug in SASA for alanin example John Jumper (Fri Mar 30 2012 - 15:10:44 CDT)
- Dielectric constant for MDFF of a membrane protein. Raul Araya (Fri Mar 30 2012 - 09:18:22 CDT)
- Compiling NAMD_2.9b2_Source with GCC 4.7.0 Fabien Archambault (Fri Mar 30 2012 - 08:25:18 CDT)
- CHARMM-GUI running error for ligand Hannes Loeffler (Fri Mar 30 2012 - 05:39:17 CDT)
- CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 02:37:10 CDT)
- The simplest pair list generation scheme anaome_at_fundp.ac.be (Thu Mar 29 2012 - 14:01:45 CDT)
- PDB sugar unit residue name Massimiliano Porrini (Thu Mar 29 2012 - 06:03:40 CDT)
- Re: PDB sugar unit residue name Aron Broom (Thu Mar 29 2012 - 07:52:20 CDT)
- Re: PDB sugar unit residue name Michelle Kuttel (Thu Mar 29 2012 - 09:30:25 CDT)
- GBIS and thermostats Gianluca Interlandi (Wed Mar 28 2012 - 21:48:40 CDT)
- output nonbonded and bonded terms separately chris liopiri (Wed Mar 28 2012 - 04:59:36 CDT)
- collective variable component -- eigenvector usage chang (Tue Mar 27 2012 - 19:46:04 CDT)
- NAMD 2.9b2 released Jim Phillips (Tue Mar 27 2012 - 15:17:30 CDT)
- 2.9b1 crashes Francesco Pietra (Tue Mar 27 2012 - 09:56:15 CDT)
- Re: How to Get Bonded Pair Force Calculation with NAMD Ehsan Ban (Tue Mar 27 2012 - 09:01:04 CDT)
- AW: AW: conf file question Norman Geist (Mon Mar 26 2012 - 00:39:38 CDT)
- How to Get Bonded Pair Force Calculation with NAMD Ehsan Ban (Mon Mar 26 2012 - 07:41:01 CDT)
- accelMD parameter choice Grant Schauer (Sat Mar 24 2012 - 17:08:55 CDT)
- AW: conf file question Norman Geist (Fri Mar 23 2012 - 06:09:41 CDT)
- Nonbonded 3-body potential Xavier Bidault (Fri Mar 23 2012 - 05:44:59 CDT)
- Umbrella sampling with hbond Payne, Christy (Thu Mar 22 2012 - 19:05:24 CDT)
- NAMD 2.9b1 crashes during minimization Francesco Pietra (Thu Mar 22 2012 - 10:28:04 CDT)
- Glycosaminoglycan sulfate group with CHARMM Massimiliano Porrini (Thu Mar 22 2012 - 10:09:03 CDT)
- problem with paramters? Albert (Thu Mar 22 2012 - 00:25:27 CDT)
- conf file question Molecular Dynamics (Wed Mar 21 2012 - 04:19:57 CDT)
- 2.9b1 and GPU accelerated GB implicit solvent Aron Broom (Tue Mar 20 2012 - 23:16:57 CDT)
- NAMD 2.9b1 released Jim Phillips (Tue Mar 20 2012 - 20:35:59 CDT)
- will Jaguar enough for NAMD partial charge? Albert (Tue Mar 20 2012 - 02:18:54 CDT)
- Collective variable on COM instead of COG poker_at_physics.usyd.edu.au (Mon Mar 19 2012 - 20:47:53 CDT)
- Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Mon Mar 19 2012 - 18:31:40 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Tue Mar 20 2012 - 01:36:34 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Tue Mar 20 2012 - 08:32:49 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Wed Mar 21 2012 - 02:02:41 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Thu Mar 22 2012 - 14:28:54 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Fri Mar 23 2012 - 02:09:28 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Sat Mar 24 2012 - 18:03:28 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Mon Mar 26 2012 - 00:43:17 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Wed Mar 28 2012 - 09:10:26 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Wed Mar 28 2012 - 09:48:15 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Tue Mar 20 2012 - 08:32:49 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Tue Mar 20 2012 - 01:36:34 CDT)
- DNA system and PH control raghav singh (Mon Mar 19 2012 - 12:42:31 CDT)
- SMD under NPT ensemble raghav singh (Mon Mar 19 2012 - 10:12:17 CDT)
- is it possible to strip the restrain linearly? Albert (Mon Mar 19 2012 - 08:29:00 CDT)
- FEP tutorial-my molecule doesn't show up in VMD Alisha \ (Mon Mar 19 2012 - 01:20:44 CDT)
- Tyrosine ligand at Fe(II) Francesco Pietra (Sun Mar 18 2012 - 11:34:57 CDT)
- what does .inp do from CHARMM GUI? Albert (Sun Mar 18 2012 - 07:19:22 CDT)
- jobs failed Albert (Sat Mar 17 2012 - 14:33:19 CDT)
- Simulations with alpha methylated amino acids amin_at_imtech.res.in (Fri Mar 16 2012 - 20:23:33 CDT)
- NAMD on Bluegene Thomas Lemmin (Fri Mar 16 2012 - 12:39:16 CDT)
- ABF - coordNum collective variable Adam Skelton (Thu Mar 15 2012 - 15:27:07 CDT)
- External electric field using Grid Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 14:47:12 CDT)
- selecting multiple fixed atom in SMD raghav singh (Thu Mar 15 2012 - 11:47:30 CDT)
- Announcement: Large biomolecule benchmark report Hannes Loeffler (Thu Mar 15 2012 - 07:51:36 CDT)
- restart a simulation upayan baul (Thu Mar 15 2012 - 07:20:42 CDT)
- Apply two Different eFeild on the same Direction Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 02:34:46 CDT)
- center of mass movement removal throughout simulation? Markus K. Dahlgren (Mon Mar 12 2012 - 18:53:53 CDT)
- AW: center of mass movement removal throughout simulation? Norman Geist (Tue Mar 13 2012 - 01:32:45 CDT)
- AW: center of mass movement removal throughout simulation? Norman Geist (Tue Mar 13 2012 - 01:36:16 CDT)
- Regarding Installing NAMD in Ubuntu amit majhi (Mon Mar 12 2012 - 11:44:48 CDT)
- Fw: forough askari (Sun Mar 11 2012 - 11:54:25 CDT)
- Fwd: SOLVED, however multiple CUDA efficiency? Francesco Pietra (Sun Mar 11 2012 - 11:36:55 CDT)
- CUDA error 0 attaching to node Francesco Pietra (Fri Mar 09 2012 - 09:12:19 CST)
- is zeroMomentum safe in a steered MD simulation? Jose Borreguero (Fri Mar 09 2012 - 09:08:41 CST)
- Compiling NAMD Marcel UJI (IMAP) (Fri Mar 09 2012 - 06:49:34 CST)
- Missing angle parameters in the ffTK ¼¿ëÀÏ (Fri Mar 09 2012 - 01:38:08 CST)
- Compiling NAMD on NICS Kraken Alexander Predeus (Thu Mar 08 2012 - 22:39:05 CST)
- TclForces clearconfig cancels addforce calls? Niklaus Johner (Thu Mar 08 2012 - 15:32:39 CST)
- Metadynamics Problems Aron Broom (Wed Mar 07 2012 - 17:13:23 CST)
- geometry deformation lecan (Wed Mar 07 2012 - 15:10:27 CST)
- charmm param ... wrong charges raghav singh (Wed Mar 07 2012 - 08:44:50 CST)
- How to set protonation states of certain atom in DNA with namd/vmd raghav singh (Wed Mar 07 2012 - 07:15:55 CST)
- how to calculate the box size mjyang (Tue Mar 06 2012 - 01:48:45 CST)
- Re: how to calculate the box size Aron Broom (Tue Mar 06 2012 - 08:44:57 CST)
- Re: how to calculate the box size Axel Kohlmeyer (Tue Mar 06 2012 - 08:52:59 CST)
- RE: how to calculate the box size JC Gumbart (Tue Mar 06 2012 - 09:00:14 CST)
- Re: how to calculate the box size Chris Harrison (Tue Mar 06 2012 - 09:23:01 CST)
- Re: how to calculate the box size Ajasja LjubetiÄ (Tue Mar 06 2012 - 09:32:43 CST)
- Re: how to calculate the box size Chris Harrison (Tue Mar 06 2012 - 09:44:47 CST)
- Re: how to calculate the box size Axel Kohlmeyer (Tue Mar 06 2012 - 09:55:42 CST)
- Re: how to calculate the box size Chris Harrison (Tue Mar 06 2012 - 10:11:24 CST)
- Re: how to calculate the box size Axel Kohlmeyer (Tue Mar 06 2012 - 08:52:59 CST)
- Re: how to calculate the box size Cristhian Boetsch (Tue Mar 06 2012 - 10:48:30 CST)
- Re: how to calculate the box size Aron Broom (Tue Mar 06 2012 - 08:44:57 CST)
- Replica exchange and multiple time-stepping Niklaus Johner (Mon Mar 05 2012 - 10:19:10 CST)
- Constant Pull Velocity ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 09:11:28 CST)
- SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* raghav singh (Mon Mar 05 2012 - 08:12:33 CST)
- system splitted lecan (Fri Mar 02 2012 - 06:54:50 CST)
- Internal Unit system Niklaus Johner (Thu Mar 01 2012 - 11:21:53 CST)
- SHAKE Tolerance and Performance Aron Broom (Thu Mar 01 2012 - 01:04:28 CST)
- Re: SHAKE Tolerance and Performance Nicholas M Glykos (Thu Mar 01 2012 - 03:16:05 CST)
- Protein ligand simulation Tutorial sai nitin (Wed Feb 29 2012 - 06:47:38 CST)
- drude water simulation bug ? radial distrubuion function Sergey (Wed Feb 29 2012 - 01:22:30 CST)
- problem with installing NAMD in Linux Red Hat rukman kesh (Wed Feb 29 2012 - 00:40:12 CST)
- Re: problem with installing NAMD in Linux Red Hat Chris Harrison (Thu Mar 01 2012 - 00:17:28 CST)
- Re: problem with installing NAMD in Linux Red Hat rukman kesh (Mon Mar 05 2012 - 01:39:38 CST)
- Re: problem with installing NAMD in Linux Red Hat Aron Broom (Mon Mar 05 2012 - 01:50:12 CST)
- Re: problem with installing NAMD in Linux Red Hat Andreas Förster (Mon Mar 05 2012 - 03:20:03 CST)
- Re: problem with installing NAMD in Linux Red Hat rukman kesh (Mon Mar 05 2012 - 08:24:16 CST)
- Re: problem with installing NAMD in Linux Red Hat Aron Broom (Mon Mar 05 2012 - 08:33:01 CST)
- Re: problem with installing NAMD in Linux Red Hat Axel Kohlmeyer (Mon Mar 05 2012 - 08:57:35 CST)
- Re: problem with installing NAMD in Linux Red Hat rukman kesh (Mon Mar 05 2012 - 01:39:38 CST)
- Re: problem with installing NAMD in Linux Red Hat Chris Harrison (Thu Mar 01 2012 - 00:17:28 CST)
- rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Tue Feb 28 2012 - 21:58:25 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) JC Gumbart (Thu Mar 01 2012 - 12:49:09 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) Aron Broom (Thu Mar 01 2012 - 13:27:59 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) Victor Ovchinnikov (Thu Mar 01 2012 - 13:56:41 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) Aron Broom (Thu Mar 01 2012 - 14:32:20 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) Aron Broom (Fri Mar 02 2012 - 10:49:34 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) Aron Broom (Thu Mar 01 2012 - 13:27:59 CST)
- Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Jim Phillips (Thu Mar 01 2012 - 14:47:48 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) JC Gumbart (Thu Mar 01 2012 - 12:49:09 CST)
- drude water simulation bug ? Sergey (Tue Feb 28 2012 - 14:35:26 CST)
- Drug design issue. Boyang Wang (Tue Feb 28 2012 - 02:08:07 CST)
- R: restart file Chiara.cosenza (Sat Feb 25 2012 - 09:16:29 CST)
- Re: R: restart file Nicholas M Glykos (Sat Feb 25 2012 - 09:38:27 CST)
- Re: R: restart file Aron Broom (Sat Feb 25 2012 - 11:00:24 CST)
- Re: R: restart file Chris Harrison (Sat Feb 25 2012 - 11:50:08 CST)
- R: restart file Namd Namd (Mon Feb 27 2012 - 01:57:04 CST)
- Re: R: restart file Namd Namd (Mon Feb 27 2012 - 02:42:32 CST)
- "Warning" meaning Cosseddu, Salvatore (Mon Feb 27 2012 - 13:55:50 CST)
- Re: "Warning" meaning Chris Harrison (Thu Mar 01 2012 - 00:23:26 CST)
- Re: "Warning" meaning Salvatore Mario Cosseddu (Thu Mar 01 2012 - 04:27:12 CST)
- AW: "Warning" meaning Norman Geist (Fri Mar 02 2012 - 01:03:10 CST)
- Re: AW: "Warning" meaning Salvatore Mario Cosseddu (Fri Mar 02 2012 - 04:53:19 CST)
- Re: R: restart file Aron Broom (Sat Feb 25 2012 - 11:00:24 CST)
- Re: R: restart file Nicholas M Glykos (Sat Feb 25 2012 - 09:38:27 CST)
- restart file Namd Namd (Sat Feb 25 2012 - 07:31:18 CST)
- Re: Consistent temperature increase in CUDA runs Aron Broom (Fri Feb 24 2012 - 14:49:28 CST)
- regarding ion concentration in implicit solvent Prathit Chatterjee (Fri Feb 24 2012 - 05:19:51 CST)
- Consistent temperature increase in CUDA runs Norman Geist (Fri Feb 24 2012 - 00:51:38 CST)
- what restraint can I use to prevent membrane diffusion on the Z-axis? Jose Borreguero (Wed Feb 22 2012 - 14:07:30 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Chris Harrison (Sat Feb 25 2012 - 11:59:43 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Sun Feb 26 2012 - 10:39:42 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Mon Feb 27 2012 - 22:49:02 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Aron Broom (Mon Feb 27 2012 - 23:15:41 CST)
- AW: what restraint can I use to prevent membrane diffusion on the Z-axis? Norman Geist (Tue Feb 28 2012 - 00:42:24 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Tue Feb 28 2012 - 11:58:49 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Jose Borreguero (Tue Feb 28 2012 - 13:30:16 CST)
- Fwd: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Tue Feb 28 2012 - 13:50:50 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Aron Broom (Tue Feb 28 2012 - 16:46:23 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Jose Borreguero (Wed Feb 29 2012 - 16:38:44 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Aron Broom (Wed Feb 29 2012 - 16:46:05 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Axel Kohlmeyer (Wed Feb 29 2012 - 16:53:59 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Sun Feb 26 2012 - 10:39:42 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Chris Harrison (Sat Feb 25 2012 - 11:59:43 CST)
- Error in NAMD 2.8 function Sereda, Yuriy Vladimirovich (Wed Feb 22 2012 - 11:02:09 CST)
- Re: Keep PBC box size in Z-direction constant? Bjoern Olausson (Wed Feb 22 2012 - 03:36:42 CST)
- AW: Keep PBC box size in Z-direction constant? Norman Geist (Wed Feb 22 2012 - 00:24:02 CST)
- Keep PBC box size in Z-direction constant? Bjoern Olausson (Mon Feb 20 2012 - 06:37:05 CST)
- FW: vmd-l: Stand-alone VMD ? Mark Cunningham (Thu Feb 16 2012 - 15:45:55 CST)
- Re: Possible bug or inconvenience Chris Harrison (Wed Feb 15 2012 - 15:12:03 CST)
- RMSD metadynamics simone bardwell (Wed Feb 15 2012 - 13:25:16 CST)
- how can i demonstrate that a chain-like molecule within a membrane. superdirac (Wed Feb 15 2012 - 07:19:36 CST)
- Possible bug or inconvenience Norman Geist (Wed Feb 15 2012 - 04:06:34 CST)
- Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 01:14:04 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Cruz-Chu Eduardo Roberto (Wed Feb 15 2012 - 05:06:31 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen kanchi subbarao rao (Wed Feb 15 2012 - 08:11:10 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 20:06:01 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Axel Kohlmeyer (Wed Feb 15 2012 - 20:13:44 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 20:50:30 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Axel Kohlmeyer (Wed Feb 15 2012 - 20:57:14 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 23:04:53 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Axel Kohlmeyer (Wed Feb 15 2012 - 23:13:47 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 23:58:52 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Axel Kohlmeyer (Thu Feb 16 2012 - 00:09:13 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Thu Feb 16 2012 - 00:36:20 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Axel Kohlmeyer (Thu Feb 16 2012 - 07:39:36 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Cruz-Chu Eduardo Roberto (Wed Feb 15 2012 - 05:06:31 CST)
- martini force field Swarna M Patra (Tue Feb 14 2012 - 21:41:19 CST)
- Regarding thermostats felmerino_at_uchile.cl (Mon Feb 13 2012 - 09:21:33 CST)
- where is psf develop in ffTK ¼¿ëÀÏ (Mon Feb 13 2012 - 06:55:37 CST)
- 2CPU+1GPU vs 1CPU+2GPU Marcel UJI (IMAP) (Mon Feb 13 2012 - 05:21:18 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Mon Feb 13 2012 - 05:44:59 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Aron Broom (Mon Feb 13 2012 - 08:26:30 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Ajasja LjubetiÄ (Mon Feb 13 2012 - 09:08:30 CST)
- AW: 2CPU+1GPU vs 1CPU+2GPU Norman Geist (Tue Feb 14 2012 - 01:18:44 CST)
- Re: AW: 2CPU+1GPU vs 1CPU+2GPU Marcel UJI (IMAP) (Tue Feb 14 2012 - 03:26:50 CST)
- Re: AW: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Tue Feb 14 2012 - 04:04:20 CST)
- AW: AW: 2CPU+1GPU vs 1CPU+2GPU Norman Geist (Tue Feb 14 2012 - 06:14:22 CST)
- Re: AW: 2CPU+1GPU vs 1CPU+2GPU Marcel UJI (IMAP) (Tue Feb 14 2012 - 05:07:26 CST)
- Re: AW: 2CPU+1GPU vs 1CPU+2GPU Axel Kohlmeyer (Tue Feb 14 2012 - 08:24:53 CST)
- Re: AW: 2CPU+1GPU vs 1CPU+2GPU Axel Kohlmeyer (Tue Feb 14 2012 - 08:19:59 CST)
- AW: AW: 2CPU+1GPU vs 1CPU+2GPU Norman Geist (Wed Feb 15 2012 - 01:45:32 CST)
- Re: AW: AW: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Wed Feb 15 2012 - 03:22:43 CST)
- AW: AW: AW: 2CPU+1GPU vs 1CPU+2GPU Norman Geist (Wed Feb 15 2012 - 03:46:09 CST)
- Re: AW: AW: AW: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Wed Feb 15 2012 - 03:55:01 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Aron Broom (Mon Feb 13 2012 - 08:26:30 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Mon Feb 13 2012 - 05:44:59 CST)
- how to understand vdwForceSwitching Liqun Zhang (Sat Feb 11 2012 - 17:09:48 CST)
- parameter file for POPC (RBCG model) Swarna M Patra (Thu Feb 09 2012 - 22:29:21 CST)
- RBCG-configuration file Swarna M Patra (Thu Feb 09 2012 - 05:53:15 CST)
- Re: Copper ion moving out of the protein towards bulk solvent poker_at_physics.usyd.edu.au (Wed Feb 08 2012 - 18:24:50 CST)
- How to calculate surface tension properly Bjoern Olausson (Wed Feb 08 2012 - 07:59:15 CST)
- Copper ion moving out of the protein towards bulk solvent SUBHA KALYAANAMOORTHY (Tue Feb 07 2012 - 19:16:26 CST)
- crossing the border by protein/ion complex Maria Bykhovskaia (Tue Feb 07 2012 - 17:16:30 CST)
- Ewald contribution to pressure profile only working on single core Bjoern Olausson (Tue Feb 07 2012 - 06:59:43 CST)
- Question about "Free Energy of Conformational Change Calculations" Shen, Han (Mon Feb 06 2012 - 11:03:44 CST)
- gurukatagi@gmail.com Gurunath Katagi (Mon Feb 06 2012 - 10:37:49 CST)
- ffTK in the just released VMD 1.9.1 JC Gumbart (Sat Feb 04 2012 - 15:04:05 CST)
- Hard sphere potential M.Raviprasad (Thu Feb 02 2012 - 20:20:14 CST)
- one question about gtp flipping in namd simulation Liqun Zhang (Thu Feb 02 2012 - 13:42:27 CST)
- RMSD collective variable - Different atons to align and to calculate RMSD Paulo Cesar Telles de Souza (Thu Feb 02 2012 - 12:19:10 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Giacomo Fiorin (Thu Feb 02 2012 - 13:52:49 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Chris Harrison (Thu Feb 02 2012 - 13:54:55 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Jérôme Hénin (Thu Feb 02 2012 - 15:40:47 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Paulo Cesar Telles de Souza (Mon Feb 06 2012 - 08:39:02 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Paulo Cesar Telles de Souza (Tue Feb 07 2012 - 11:53:47 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Branko (Tue Feb 07 2012 - 12:49:37 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Jérôme Hénin (Thu Feb 02 2012 - 15:40:47 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Davide Branduardi (Thu Feb 02 2012 - 14:27:18 CST)
- NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Thu Feb 02 2012 - 11:06:20 CST)
- Re: NAMDenergy plugin_van der Waal interactions Chris Harrison (Wed Feb 15 2012 - 15:27:12 CST)
- RE: NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Mon Feb 20 2012 - 07:01:14 CST)
- AW: NAMDenergy plugin_van der Waal interactions Norman Geist (Tue Feb 21 2012 - 00:16:40 CST)
- RE: NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Tue Feb 21 2012 - 18:05:44 CST)
- Re: NAMDenergy plugin_van der Waal interactions Axel Kohlmeyer (Tue Feb 21 2012 - 18:19:26 CST)
- AW: NAMDenergy plugin_van der Waal interactions Norman Geist (Wed Feb 22 2012 - 00:20:15 CST)
- RE: NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Mon Feb 20 2012 - 07:01:14 CST)
- Re: NAMDenergy plugin_van der Waal interactions Chris Harrison (Wed Feb 15 2012 - 15:27:12 CST)
- Energy minimization of membrane R. Charbel Maroun (Thu Feb 02 2012 - 06:37:42 CST)
- Re: Energy minimization of membrane Boyang Wang (Thu Feb 02 2012 - 23:31:28 CST)
- AW: Energy minimization of membrane Norman Geist (Fri Feb 03 2012 - 01:14:50 CST)
- Re: AW: Energy minimization of membrane R. Charbel Maroun (Fri Feb 03 2012 - 04:58:17 CST)
- Re: AW: Energy minimization of membrane Ajasja LjubetiÄ (Fri Feb 03 2012 - 05:25:01 CST)
- Re: AW: Energy minimization of membrane R. Charbel Maroun (Fri Feb 03 2012 - 08:53:37 CST)
- AW: AW: Energy minimization of membrane Norman Geist (Mon Feb 06 2012 - 01:01:41 CST)
- Re: AW: Energy minimization of membrane Chris Harrison (Thu Feb 09 2012 - 01:25:56 CST)
- Re: AW: Energy minimization of membrane Chris Harrison (Thu Feb 09 2012 - 01:28:36 CST)
- AW: AW: Energy minimization of membrane Norman Geist (Fri Feb 03 2012 - 06:02:39 CST)
- Re: AW: Energy minimization of membrane kanchi subbarao rao (Fri Feb 03 2012 - 05:20:29 CST)
- AW: AW: Energy minimization of membrane Norman Geist (Fri Feb 03 2012 - 05:54:19 CST)
- AW: Energy minimization of membrane Norman Geist (Fri Feb 03 2012 - 01:14:50 CST)
- Re: Energy minimization of membrane Boyang Wang (Thu Feb 02 2012 - 23:31:28 CST)
- rigidBonds water option Hasan haska (Thu Feb 02 2012 - 01:48:22 CST)
- Gromacs analysis tools for Namd output PAUL NEWMAN (Wed Feb 01 2012 - 11:41:40 CST)
- Analysis of FEP output file sudipta (Tue Jan 31 2012 - 11:41:33 CST)
- Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Tue Jan 31 2012 - 08:30:05 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Tue Jan 31 2012 - 12:28:24 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Wed Feb 01 2012 - 03:44:26 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Wed Feb 01 2012 - 19:31:53 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Thu Feb 02 2012 - 09:06:37 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Thu Feb 02 2012 - 17:02:08 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Jérôme Hénin (Fri Feb 03 2012 - 05:20:31 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Mon Feb 06 2012 - 15:04:56 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Mon Feb 06 2012 - 16:55:26 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Tue Feb 07 2012 - 16:57:33 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Thu Feb 09 2012 - 12:05:19 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Wed Feb 01 2012 - 03:44:26 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Tue Jan 31 2012 - 12:28:24 CST)
- Fwd: Madhulika Gupta (Mon Jan 30 2012 - 22:10:37 CST)
- problem to analyze the output of FEP file using vmd plugin sudipta (Mon Jan 30 2012 - 15:58:41 CST)
- Installing NAMD on a 64-bit linux (NVIDIA CUDA) Shyno Mathew (Mon Jan 30 2012 - 12:15:15 CST)
- Alchemical free-energy methods and electroneutrality Thomas Albers (Sat Jan 28 2012 - 13:35:27 CST)
- Output of thermodynamic integration Kei-ichi Okazaki (Fri Jan 27 2012 - 18:16:47 CST)
- (no subject) Madhulika Gupta (Tue Jan 24 2012 - 23:08:52 CST)
- NAMD on ranger.tacc Jesper Sørensen (Mon Jan 23 2012 - 10:28:33 CST)
- Umbrella sampling using dihedral angle Buddhadev Maiti (Sun Jan 22 2012 - 22:17:25 CST)
- (no subject) Basak Isin (Mon Jan 23 2012 - 01:16:45 CST)
- Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Fri Jan 20 2012 - 17:52:14 CST)
- Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Gungor Ozer (Thu Jan 19 2012 - 11:44:29 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Giacomo Fiorin (Thu Jan 19 2012 - 11:56:00 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Boyang Wang (Thu Jan 19 2012 - 17:45:41 CST)
- RE: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 13:06:47 CST)
- Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 12:32:32 CST)
- namd question in parameter conversion Liqun Zhang (Wed Jan 18 2012 - 10:27:12 CST)
- questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Wed Jan 18 2012 - 08:12:20 CST)
- Re: questions regarding ABF sampling in a DMPC bilayer Jérôme Hénin (Wed Jan 18 2012 - 12:00:28 CST)
- Re: questions regarding ABF sampling in a DMPC bilayer Giacomo Fiorin (Wed Jan 18 2012 - 12:05:02 CST)
- question about NPT oguz gurbulak (Wed Jan 18 2012 - 02:06:19 CST)
- target pressure value Namd Namd (Tue Jan 17 2012 - 06:30:20 CST)
- Problems in setting up low pH systems Sheng, Zi-Zhang (Wed Jan 11 2012 - 09:43:31 CST)
- surfaceTensionTarget - Surface Tension per interface or per bilayer Jon Fuller (Wed Jan 11 2012 - 04:25:24 CST)
- how does namd handle violations of the minimum image convention? Ana Celia Vila Verde (Mon Jan 09 2012 - 05:32:32 CST)
- Re: incompatibility between NAMD and amber topology files Osman, Roman (Tue Jan 10 2012 - 15:33:43 CST)
- ERROR: 0031-250 task 0: Terminated Gurunath Katagi (Mon Jan 09 2012 - 23:42:53 CST)
- incompatibility between NAMD and amber topology files Osman, Roman (Mon Jan 09 2012 - 16:13:24 CST)
- ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Gurunath Katagi (Tue Jan 10 2012 - 14:03:03 CST)
- Problem with parameter file in Pair Interaction Calculation M Mahjour (Mon Jan 09 2012 - 05:47:20 CST)
- can TMD alignment prior to force calculation be turned off? Michael Zimmermann (Sun Jan 08 2012 - 15:04:15 CST)
- Problem with parameter file in Pair Interaction Calculation M Mahjour (Sun Jan 08 2012 - 00:14:50 CST)
- IB fabrics Thomas Bishop (Fri Jan 06 2012 - 11:42:53 CST)
- ABF simulation Tugba Nogay (Fri Jan 06 2012 - 10:53:36 CST)
- Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Fri Jan 06 2012 - 09:29:18 CST)
- TIP5P simulation Mallajosyula, Sairam (Thu Jan 05 2012 - 21:41:05 CST)
- Problem with NVE simulation gaborekt_at_duq.edu (Thu Jan 05 2012 - 15:42:10 CST)
- TIP4P force field Udaysankar Midya (Tue Jan 03 2012 - 21:46:52 CST)
- Re: Replica Exchange Discrete Molecular Dynamics for structure based models bharat gupta (Tue Jan 03 2012 - 00:48:16 CST)
- water molecules oguz gurbulak (Mon Jan 02 2012 - 06:04:08 CST)
- (no subject) ÐìÖÓºÓ (Mon Jan 02 2012 - 03:03:31 CST)
- GPRESSURE becomes nan in TIP4P simulation Udaysankar Midya (Sat Dec 31 2011 - 05:23:35 CST)
- tabulatd potentials Arturas (Thu Dec 29 2011 - 13:09:17 CST)
- Coarse-Graining MD don't work perfect as expected ÐìÖÓºÓ (Thu Dec 29 2011 - 00:50:31 CST)
- scaling Neelanjana Sengupta (Wed Dec 28 2011 - 22:56:45 CST)
- Fwd: about md in npt Boyang Wang (Wed Dec 28 2011 - 02:54:01 CST)
- about md in npt Hasan haska (Wed Dec 28 2011 - 02:18:30 CST)
- equilibrate the system in NPT Hasan haska (Mon Dec 26 2011 - 13:57:37 CST)
- Parse Fep plugin error Joseph Antoine Garate (Fri Dec 23 2011 - 08:27:39 CST)
- collective variable calculation from dcd file Giovanni Bellesia (Wed Dec 21 2011 - 14:44:47 CST)
- AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Wed Dec 21 2011 - 00:54:50 CST)
- AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Tue Dec 20 2011 - 06:45:32 CST)
- coordNum colvar with dummyAtom Ernesto Vargas (Mon Dec 19 2011 - 18:56:40 CST)
- Re: Generating .tpr file using NAMD files rajitha tatikonda (Mon Dec 19 2011 - 00:32:56 CST)
- Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Mon Dec 19 2011 - 05:04:40 CST)
- AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Mon Dec 19 2011 - 07:35:58 CST)
- Re: glycosaminoglycan with GLYCAM06 in amber format Lachele Foley (Lists) (Tue Dec 20 2011 - 08:53:59 CST)
- Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Tue Dec 20 2011 - 08:55:58 CST)
- Sticking TIP4P water molecules AMBER Norman Geist (Mon Dec 19 2011 - 04:33:25 CST)
- Fwd: Generating .tpr file using NAMD files rajitha rajeshwar (Mon Dec 19 2011 - 03:05:34 CST)
- glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Sun Dec 18 2011 - 10:44:48 CST)
- Interfaces in NAMD Hasan haska (Sat Dec 17 2011 - 14:20:25 CST)
- New physical understanding. Boyang Wang (Fri Dec 16 2011 - 00:39:27 CST)
- Re: New physical understanding. Axel Kohlmeyer (Fri Dec 16 2011 - 05:47:48 CST)
- Re: New physical understanding. Boyang Wang (Fri Dec 16 2011 - 06:56:42 CST)
- Re: New physical understanding. Chris Harrison (Fri Dec 16 2011 - 09:20:53 CST)
- Re: New physical understanding. Boyang Wang (Sat Dec 17 2011 - 08:52:28 CST)
- Re: New physical understanding. Axel Kohlmeyer (Sat Dec 17 2011 - 13:42:31 CST)
- Re: New physical understanding. Boyang Wang (Sat Dec 17 2011 - 21:24:21 CST)
- Re: New physical understanding. Boyang Wang (Fri Dec 16 2011 - 06:56:42 CST)
- Re: New physical understanding. Axel Kohlmeyer (Fri Dec 16 2011 - 05:47:48 CST)
- Umbrella sampling-NAMD Parisa Akhski (Thu Dec 15 2011 - 09:24:36 CST)
- cell size Hasan haska (Tue Dec 13 2011 - 08:10:49 CST)
- tclforces and extrabonds Jian Dai (Mon Dec 12 2011 - 10:13:16 CST)
- correlation functions Molecular Dynamics (Sat Dec 10 2011 - 05:18:50 CST)
- MMTools for analysis Namd Namd (Sat Dec 10 2011 - 05:07:19 CST)
- Peptide planarity Dihedral angle restraints Vijay Vammi (Thu Dec 08 2011 - 20:07:12 CST)
- NAMD FEP - Bad Hydrogen group size John Baker (Wed Dec 07 2011 - 05:38:11 CST)
- stochastical boundary conditions in NAMD mjyang (Tue Dec 06 2011 - 19:24:17 CST)
- Re: xplor-formated parameters Chris Harrison (Tue Dec 06 2011 - 12:41:05 CST)
- Thermodynamic integration questions pepe barrientos (Tue Dec 06 2011 - 10:39:38 CST)
- mmView - a tool for mmCIF exploration Daniel Svozil (Tue Dec 06 2011 - 05:38:35 CST)
- Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 14:54:27 CST)
- AW: installing namd on ibm cluster (powerpc) Norman Geist (Mon Dec 05 2011 - 03:30:48 CST)
- AW: installing namd on ibm cluster (powerpc) Norman Geist (Mon Dec 05 2011 - 00:29:43 CST)
- Coulomb 1-4 interactions oguz gurbulak (Fri Dec 02 2011 - 10:11:24 CST)
- cpu-gpu vs cpu Francesco Pietra (Tue Nov 29 2011 - 00:44:10 CST)
- paper/articule on colvars module Leonardo Herrera (Mon Nov 28 2011 - 19:35:37 CST)
- help in a FEP restart? Bruno Luís Pinto de Oliveira (Sat Nov 26 2011 - 10:15:13 CST)
- charmrun constantly hanging jani vinod (Fri Nov 25 2011 - 00:59:35 CST)
- equilibrate water molecules Hasan haska (Thu Nov 24 2011 - 01:43:38 CST)
- AW: AW: AW: AW: namd-ibverbs fails to start Norman Geist (Thu Nov 24 2011 - 00:15:52 CST)
- HEME and Cystein instead of His Raul Araya (Wed Nov 23 2011 - 13:10:36 CST)
- Is it possible to print out the force of one specific atom? Wenhao Liu (Wed Nov 23 2011 - 08:29:23 CST)
- Re: Predicting the binding affinity and anion bharat gupta (Wed Nov 23 2011 - 07:23:29 CST)
- AW: AW: Norman Geist (Wed Nov 23 2011 - 01:00:42 CST)
- AW: AW: Norman Geist (Wed Nov 23 2011 - 00:59:15 CST)
- AW: AW: AW: namd-ibverbs fails to start Norman Geist (Wed Nov 23 2011 - 00:09:41 CST)
- OpenCL and AMD GPUs Aron Broom (Tue Nov 22 2011 - 22:04:13 CST)
- (no subject) Chandra Ramananjara (Tue Nov 22 2011 - 12:31:08 CST)
- Re: AW: namd-ibverbs fails to start Axel Kohlmeyer (Tue Nov 22 2011 - 08:02:12 CST)
- (no subject) Chandra Ramananjara (Tue Nov 22 2011 - 06:53:15 CST)
- namd force field Molecular Dynamics (Tue Nov 22 2011 - 06:21:16 CST)
- AW: AW: namd-ibverbs fails to start Norman Geist (Tue Nov 22 2011 - 00:49:46 CST)
- AW: AW: namd-ibverbs fails to start Norman Geist (Tue Nov 22 2011 - 00:47:00 CST)
- Segmentation violation with adaptive tempering. Nicholas M Glykos (Sun Nov 20 2011 - 05:13:02 CST)
- Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Mon Nov 21 2011 - 04:45:39 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 08:16:58 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Giacomo Fiorin (Wed Nov 23 2011 - 09:28:50 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Wed Nov 23 2011 - 10:41:58 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 14:03:22 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Aron Broom (Wed Nov 23 2011 - 14:36:42 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 23:33:26 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Thu Nov 24 2011 - 03:51:51 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Thu Nov 24 2011 - 06:33:58 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Thu Nov 24 2011 - 07:24:58 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Thu Nov 24 2011 - 08:18:07 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Thu Nov 24 2011 - 09:39:56 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Giacomo Fiorin (Wed Nov 23 2011 - 14:40:34 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 23:31:14 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Giacomo Fiorin (Wed Nov 23 2011 - 09:28:50 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 08:16:58 CST)
- intermittent non-execution of NAMD on tesla P.-L. Chau (Mon Nov 21 2011 - 04:09:04 CST)
- fullSamples in ABF: applied at restart? Neelanjana Sengupta (Sun Nov 20 2011 - 22:14:15 CST)
- problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Sun Nov 20 2011 - 16:43:01 CST)
- Fwd: restrain on COM Swarna M Patra (Fri Nov 18 2011 - 23:33:09 CST)
- namd-ibverbs fails to start David Hemmendinger (Fri Nov 18 2011 - 21:39:20 CST)
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois David Brandon (Thu Nov 17 2011 - 13:46:56 CST)
- Umbrella sampling Parisa Akhski (Wed Nov 16 2011 - 15:12:17 CST)
- Resend - ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 19:56:39 CST)
- ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 12:10:52 CST)
- Steered dynamics Jacopo Sgrignani (Fri Nov 11 2011 - 04:56:32 CST)
- improper angle Marco Sant (Fri Nov 11 2011 - 02:34:42 CST)
- Assertion failed in file @ KRAKEN PAUL NEWMAN (Wed Nov 09 2011 - 10:07:07 CST)
- PLUMED release 1.3 available Massimiliano Bonomi (Wed Nov 09 2011 - 09:05:09 CST)
- Pressure Problems, Excessively High Readings Rajan Vatassery (Tue Nov 08 2011 - 20:43:10 CST)
- Low global exclusion count matziast_at_med.uth.gr (Tue Nov 08 2011 - 04:23:47 CST)
- Extra bonds-ABF Parisa Akhski (Mon Nov 07 2011 - 10:53:18 CST)
- dextran and or poly-D-glucosamine topology Raul Araya (Fri Nov 04 2011 - 16:58:34 CDT)
- membrane simulation at high Temp Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 16:50:20 CDT)
- Running NAMD CUDA Steven Cox (Fri Nov 04 2011 - 15:06:31 CDT)
- AW: Reading files for multiple threaded simulations Norman Geist (Fri Nov 04 2011 - 02:28:50 CDT)
- (no subject) Gurunath Katagi (Thu Nov 03 2011 - 03:01:19 CDT)
- (no subject) Gurunath Katagi (Thu Nov 03 2011 - 03:00:22 CDT)
- Re: Reading files for multiple threaded simulations Chris Harrison (Wed Nov 02 2011 - 01:57:36 CDT)
- selection of cholesterol molecules Swarna M Patra (Tue Nov 01 2011 - 23:54:06 CDT)
- Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained rohan uttarwar (Tue Nov 01 2011 - 13:13:20 CDT)
- Reading files for multiple threaded simulations Yi He (Tue Nov 01 2011 - 12:16:52 CDT)
- Cluster on commodity hardware Thomas Albers (Mon Oct 31 2011 - 12:37:30 CDT)
- (no subject) Buddhadev Maiti (Fri Oct 28 2011 - 22:14:30 CDT)
- minimization and gradient trend Francesco Pietra (Mon Oct 31 2011 - 03:57:10 CDT)
- installing namd on ibm cluster (powerpc) Gurunath Katagi (Fri Oct 28 2011 - 15:14:02 CDT)
- question about namd simulation on protein in tip4p water box Liqun Zhang (Fri Oct 28 2011 - 13:14:36 CDT)
- ForceConstant in Umbrella Sampling Buddhadev Maiti (Fri Oct 28 2011 - 12:38:24 CDT)
- NAMD on KRAKEN PAUL NEWMAN (Fri Oct 28 2011 - 02:04:00 CDT)
- Carma v.1.1 released. Nicholas M Glykos (Thu Oct 27 2011 - 12:54:24 CDT)
- PME and net charge in the system Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:00:12 CDT)
- Evaluated heat capacities via NAMD are larger than experimental values Mert Gür (Wed Oct 26 2011 - 13:44:35 CDT)
- Error with "namd" Bob Masong (Wed Oct 26 2011 - 00:01:21 CDT)
- Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 16:11:54 CDT)
- PMF jafar azamat (Tue Oct 25 2011 - 06:52:28 CDT)
- different velocities problem Hasan haska (Tue Oct 25 2011 - 01:28:22 CDT)
- Error with ubqp.pdb in NAMD tutorial Bob Masong (Mon Oct 24 2011 - 22:43:46 CDT)
- What is the proper value of TMDk in TMD simulations? 常姗燕 (Sun Oct 23 2011 - 23:21:19 CDT)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) Jens K. Munk (Sun Oct 23 2011 - 14:39:24 CDT)
- GBIS and hydrophobic term, in replay to Jerome and David discussion Branko (Sun Oct 23 2011 - 09:36:17 CDT)
- * CGtool force field * HAMID - (Sat Oct 22 2011 - 12:00:19 CDT)
- About "alchDecouple" in FEP wenhao_at_uchicago.edu (Sat Oct 22 2011 - 10:47:14 CDT)
- Problems Bionanotechnology Tutorial Salvador H-V (Fri Oct 21 2011 - 22:19:01 CDT)
- cellBasisvectors/.xsc fixing/colvars while running amber ff Francesco Pietra (Fri Oct 21 2011 - 13:13:57 CDT)
- Error with tclBC to induce shear flow KONG Xian (Thu Oct 20 2011 - 20:59:42 CDT)
- coloring method in VMD lam nguyen (Thu Oct 20 2011 - 18:19:14 CDT)
- RBCG electrostatic term HAMID - (Thu Oct 20 2011 - 12:43:33 CDT)
- rigid body Dimitrios Tragoudaras (Thu Oct 20 2011 - 12:33:45 CDT)
- Sampling schemes with FEP Patargias, George (Thu Oct 20 2011 - 08:13:19 CDT)
- how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 06:27:47 CDT)
- Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 09:02:34 CDT)
- RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 13:28:13 CDT)
- Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 14:02:59 CDT)
- RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 15:10:28 CDT)
- Re: how to visualize an alchemical FEP transformation?? Chris Harrison (Thu Oct 20 2011 - 15:21:59 CDT)
- RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 16:19:38 CDT)
- Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 16:42:02 CDT)
- Re: how to visualize an alchemical FEP transformation?? Chris Harrison (Thu Oct 20 2011 - 18:02:32 CDT)
- RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 09:58:42 CDT)
- Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Sat Oct 22 2011 - 11:33:47 CDT)
- RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 12:31:01 CDT)
- Re: how to visualize an alchemical FEP transformation?? Chris Harrison (Sat Oct 22 2011 - 12:48:16 CDT)
- RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 13:28:13 CDT)
- Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 09:02:34 CDT)
- TClforce Swarna M Patra (Thu Oct 20 2011 - 03:11:01 CDT)
- fftw libraries for ppc Gurunath Katagi (Wed Oct 19 2011 - 22:04:42 CDT)
- Using CHARMM Compatible Amber Parameters Ehsan Ban (Wed Oct 19 2011 - 20:10:30 CDT)
- Multiple dihedral parameters in X-PLOR format Joe Yelk (Tue Oct 18 2011 - 17:46:57 CDT)
- Question about silver nanoparticle simulation Yao Xiao (Wed Oct 19 2011 - 08:37:23 CDT)
- Running AMBER FF with NAMD 2.8-CUDA Francesco Pietra (Wed Oct 19 2011 - 08:14:59 CDT)
- Area per lipid error Andres Morales N (Mon Oct 17 2011 - 21:12:33 CDT)
- tclforces- tcl extension written in c and built with swig Eva Gonzalez Noya (Mon Oct 17 2011 - 18:30:33 CDT)
- membrane moving up in simulation box kanchi subbarao rao (Mon Oct 17 2011 - 01:09:17 CDT)
- RE: Hello imran.1.618_at_gmail.com (Sat Oct 15 2011 - 00:32:59 CDT)
- Re: what is wrong with this pdb to simulate with NAMD raghav singh (Fri Oct 14 2011 - 12:04:20 CDT)
- rigid bonds Francesco Pietra (Fri Oct 14 2011 - 09:24:41 CDT)
- RBCG water HAMID - (Thu Oct 13 2011 - 17:45:14 CDT)
- unit of force constant for dihedral angle restrain with extrabonds command Ling Wu (Thu Oct 13 2011 - 15:43:13 CDT)
- Restarting protein system simulation using different ligand Kevin Kastner (Thu Oct 13 2011 - 12:22:41 CDT)
- Re: iron sulphur cluster parametrization francesco oteri (Thu Oct 13 2011 - 09:03:43 CDT)
- membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 01:54:32 CDT)
- Boundary potential of colvar alpha not working? Yun Luo (Wed Oct 12 2011 - 09:34:27 CDT)
- rsh not working Neelanjana Sengupta (Tue Oct 11 2011 - 00:58:27 CDT)
- Questions Kevin Littrell (Mon Oct 10 2011 - 21:20:37 CDT)
- PBC Wrap + TMD Gianluca Interlandi (Mon Oct 10 2011 - 14:02:58 CDT)
- GBIS and hydrophobic solvation Jérôme Hénin (Mon Oct 10 2011 - 07:24:50 CDT)
- install NAMD 2.8 v Namd Namd (Mon Oct 10 2011 - 05:50:53 CDT)
- Force Vector Between Two Atoms Ehsan Ban (Fri Oct 07 2011 - 17:14:02 CDT)
- namd log file Namd Namd (Fri Oct 07 2011 - 07:20:02 CDT)
- Re: Minimization doesn't stop when converged Boyang Wang (Fri Oct 07 2011 - 03:56:01 CDT)
- Minimization doesn't stop when converged Norman Geist (Fri Oct 07 2011 - 03:48:36 CDT)
- iron sulphur cluster parametrization francesco oteri (Thu Oct 06 2011 - 09:24:31 CDT)
- Compiled Windows HPC version. Chewning, Joseph (Tue Oct 04 2011 - 07:04:31 CDT)
- Restart from anywhere in DCD trajectory Zack Scholl (Mon Oct 03 2011 - 13:19:41 CDT)
- How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 13:21:36 CDT)
- Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 13:26:54 CDT)
- Re: How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 14:07:47 CDT)
- Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 14:13:03 CDT)
- Re: How to write a dcd in fortran? Joshua D. Moore (Mon Oct 03 2011 - 15:56:57 CDT)
- Re: How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 18:03:37 CDT)
- Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 18:13:20 CDT)
- Re: How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 14:07:47 CDT)
- Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 13:26:54 CDT)
- Help in reverse Free Energy perturbation - hysteresis Bruno Luís Pinto de Oliveira (Mon Oct 03 2011 - 05:24:58 CDT)
- script for equilibration matziast_at_med.uth.gr (Sun Oct 02 2011 - 04:19:19 CDT)
- refphrasing of the question for equilibration script matziast_at_med.uth.gr (Fri Sep 30 2011 - 04:16:27 CDT)
- refphrasing of the question for equilibration script matziast_at_med.uth.gr (Fri Sep 30 2011 - 03:43:13 CDT)
- Periodic cell has become too small for original patch grid!†Andres Morales N (Thu Sep 29 2011 - 23:52:39 CDT)
- an important question for equilibration script matziast_at_med.uth.gr (Thu Sep 29 2011 - 15:44:58 CDT)
- Dangling Bonds? atsuiai_at_aim.com (Wed Sep 28 2011 - 17:35:12 CDT)
- TMD and binary coordinate files Bryan Roessler (Wed Sep 28 2011 - 16:40:49 CDT)
- ABF with Alpha colvar can't be used on supercomputer? Yun Luo (Wed Sep 28 2011 - 15:38:02 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? JC Gumbart (Thu Sep 29 2011 - 01:05:53 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 05:04:42 CDT)
- RE: ABF with Alpha colvar can't be used on supercomputer? JC Gumbart (Thu Sep 29 2011 - 08:05:19 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 09:56:46 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? Chris Harrison (Thu Sep 29 2011 - 10:11:32 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? Yun Luo (Thu Sep 29 2011 - 14:25:57 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 05:04:42 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? JC Gumbart (Thu Sep 29 2011 - 01:05:53 CDT)
- Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 Irene Newhouse (Wed Sep 28 2011 - 15:40:24 CDT)
- CUDA compiled code for Windows HPC Chewning, Joseph (Wed Sep 28 2011 - 14:52:29 CDT)
- restraining residues in NAMD Haydee Valdes (Wed Sep 28 2011 - 10:59:20 CDT)
- membrane simulation and mobility of lipids - blocking ion channel Jorgen Simonsen (Wed Sep 28 2011 - 09:07:50 CDT)
- Trouble running NAMD on win7 Haque-Student,STW, Farhadul (Sun Sep 25 2011 - 23:44:14 CDT)
- colvar and tclForces with CUDA Jiyong Park (Sun Sep 25 2011 - 02:02:29 CDT)
- Epsilon, Rmin for copper ions Francesco Pietra (Sat Sep 24 2011 - 03:55:34 CDT)
- how to use variables in colvar configuration file Ling Wu (Fri Sep 23 2011 - 12:26:08 CDT)
- Fwd: Solved stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 10:13:06 CDT)
- velocity information Molecular Dynamics (Fri Sep 23 2011 - 08:20:29 CDT)
- stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 03:10:52 CDT)
- Help in FEP backward/reverse calculation Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 14:36:38 CDT)
- namd 2.8 new feature Hasan haska (Thu Sep 22 2011 - 08:37:27 CDT)
- ABF & distanceZ projection axis more HAMID - (Thu Sep 22 2011 - 03:05:07 CDT)
- force question Hasan haska (Thu Sep 22 2011 - 02:50:18 CDT)
- save the last frame as a pdb file using dcd file Namd Namd (Thu Sep 22 2011 - 02:02:53 CDT)
- Quick TCl scripting question Anthony Rey (Wed Sep 21 2011 - 20:57:07 CDT)
- ABF & distanceZ projection axis HAMID - (Wed Sep 21 2011 - 16:15:45 CDT)
- ABF results interpretation HAMID - (Wed Sep 21 2011 - 10:22:38 CDT)
- Re: ABF question Jérôme Hénin (Wed Sep 21 2011 - 07:01:50 CDT)
- membrane system ipsita basu (Wed Sep 21 2011 - 01:30:00 CDT)
- NAMD running on windows HPC question Chewning, Joseph (Tue Sep 20 2011 - 07:58:43 CDT)
- NOE Jacopo Sgrignani (Tue Sep 20 2011 - 07:27:09 CDT)
- Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 04:27:23 CDT)
- Heating in NPT Pellegrini Eric (Mon Sep 19 2011 - 07:44:04 CDT)
- Infiniband and commodity hardware Thomas Albers (Sat Sep 17 2011 - 14:59:20 CDT)
- phosphorilated serine Branko (Sat Sep 17 2011 - 11:01:42 CDT)
- Setting up a membrane simulation Pellegrini Eric (Fri Sep 16 2011 - 02:52:05 CDT)
- Invitation to connect on LinkedIn Ahlam Al-Rawi (Thu Sep 15 2011 - 16:11:12 CDT)
- SMD Jacopo Sgrignani (Thu Sep 15 2011 - 07:12:26 CDT)
- Na ion, Cl ion in TIP4P divya nayar (Thu Sep 15 2011 - 02:42:54 CDT)
- time step and total simulation time in conf file Namd Namd (Wed Sep 14 2011 - 09:41:00 CDT)
- Constraint failure during equalibration Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:45:50 CDT)
- Differences between ABF and metadynamics Alex (Tue Sep 13 2011 - 05:13:34 CDT)
- question about Distance XY Song, Hyundeok (songhk) (Mon Sep 12 2011 - 23:27:05 CDT)
- Unsubscribe Gmail (Mon Sep 12 2011 - 14:33:58 CDT)
- SMD Jacopo Sgrignani (Mon Sep 12 2011 - 02:53:30 CDT)
- restraint with colvars mocule Ling Wu (Sun Sep 11 2011 - 16:25:39 CDT)
- Nice paper on MD Simulations pawan raghav (Sat Sep 10 2011 - 13:37:00 CDT)
- difference between run and minimize snoze pa (Fri Sep 09 2011 - 16:01:55 CDT)
- TopoTools for tpr file Hasan haska (Fri Sep 09 2011 - 09:01:44 CDT)
- can we run FEP calculation in water sphere? wenhao_at_uchicago.edu (Fri Sep 09 2011 - 03:21:01 CDT)
- RE: Temperature during membrane equilibration Andres Morales N (Thu Sep 08 2011 - 18:33:47 CDT)
- help in FEP calculations : analysis/confirmation of results Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 13:59:23 CDT)
- Temperature during membrane equilibration Andres Morales N (Wed Sep 07 2011 - 23:57:10 CDT)
- Bonds are too long after simulation Anthony Rey (Wed Sep 07 2011 - 10:32:11 CDT)
- Re: Bonds are too long after simulation Markus K. Dahlgren (Wed Sep 07 2011 - 12:54:16 CDT)
- Re: Bonds are too long after simulation flavio seixas (Wed Sep 07 2011 - 13:10:13 CDT)
- Re: Bonds are too long after simulation Axel Kohlmeyer (Wed Sep 07 2011 - 13:18:26 CDT)
- namd2_ti.pl Modification of non-creatable array value attempted, subscript -49999 Pete Kekenes-Huskey (Tue Sep 06 2011 - 17:22:26 CDT)
- mean square displacement Molecular Dynamics (Mon Sep 05 2011 - 08:15:28 CDT)
- Density Profile in VMD oguz gurbulak (Mon Sep 05 2011 - 02:30:50 CDT)
- Patch at AutoPsfBuilder flavio seixas (Sun Sep 04 2011 - 14:17:38 CDT)
- POPC membrane model in pH 4 zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 09:36:58 CDT)
- Hints for building namd2.8 on charm++ ibverbs layer? Bennion, Brian (Fri Sep 02 2011 - 18:06:15 CDT)
- (solved) charmrun: ssh_exchange_identification: Connection closed by remote host Leandro Martínez (Fri Sep 02 2011 - 14:44:24 CDT)
- Pressure Calculation Priyan Amaras (Fri Sep 02 2011 - 12:43:25 CDT)
- Component distanceZ-ABF Parisa Akhski (Fri Sep 02 2011 - 11:21:56 CDT)
- Namd-I: A question about constant force pulling of a group of atoms Ye Yang (Thu Sep 01 2011 - 10:16:18 CDT)
- help in FEP calculations_binding free energy difference between 2 inhibitors Bruno Luís Pinto de Oliveira (Thu Sep 01 2011 - 10:04:41 CDT)
- Margin Value in NAMD Andrea Holfelder (Wed Aug 31 2011 - 21:42:05 CDT)
- Keeping rigidBonds during Minimization David Huggins (Wed Aug 31 2011 - 19:05:05 CDT)
- Dock a metal ion into a peptide/protein Andrea Holfelder (Wed Aug 31 2011 - 14:29:39 CDT)
- HETATM vs ATOM in .pdb file Andrea Holfelder (Wed Aug 31 2011 - 04:56:35 CDT)
- about extrabonds restrain Ling Wu (Mon Aug 29 2011 - 16:22:53 CDT)
- FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Massimiliano Porrini (Mon Aug 29 2011 - 09:36:55 CDT)
- colvar restrain of water in lipid system Ling Wu (Mon Aug 29 2011 - 09:13:58 CDT)
- Using 'Alignment to principal axes ' Andres Morales N (Mon Aug 29 2011 - 00:38:44 CDT)
- RNA simulation Juan Antonio Raygoza Garay (Fri Aug 26 2011 - 15:38:38 CDT)
- colvar restrain of water in lipid system Ling Wu (Fri Aug 26 2011 - 14:44:21 CDT)
- dummyAtom-ABF Parisa Akhski (Fri Aug 26 2011 - 09:57:13 CDT)
- combining metadynamics simulations Giovanni Bellesia (Fri Aug 26 2011 - 08:40:29 CDT)
- Heating /Equilibration Babban Mia (Fri Aug 26 2011 - 05:20:23 CDT)
- SMD-extension MOhan maruthi sena (Fri Aug 26 2011 - 05:18:25 CDT)
- About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Thu Aug 25 2011 - 18:02:04 CDT)
- How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? ÕÅÓÂ (Thu Aug 25 2011 - 01:32:33 CDT)
- Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Boyang Wang (Thu Aug 25 2011 - 01:41:51 CDT)
- Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Salvador H-V (Thu Aug 25 2011 - 11:12:49 CDT)
- SWM4-NDP Simulation David Huggins (Wed Aug 24 2011 - 14:49:33 CDT)
- convert pdb format to normal pdb format hamze rahimi (Wed Aug 24 2011 - 04:48:09 CDT)
- Heating /Equilibration Babban Mia (Wed Aug 24 2011 - 02:56:37 CDT)
- About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 17:28:04 CDT)
- Memory leak patch Andy Somogyi (Tue Aug 23 2011 - 09:20:09 CDT)
- Logfile flooded with "The last position output [...]" when IMDon is used. Bjoern Olausson (Tue Aug 23 2011 - 04:32:47 CDT)
- 'firsttimestep' treated as signed integer ? Nicholas M Glykos (Mon Aug 22 2011 - 12:01:26 CDT)
- Ib version and nodelist Neelanjana Sengupta (Mon Aug 22 2011 - 00:36:09 CDT)
- distanceXY colvar-ABF Parisa Akhski (Sun Aug 21 2011 - 09:05:16 CDT)
- SASA of PBD files Andrea Holfelder (Sat Aug 20 2011 - 04:11:25 CDT)
- CUDA on GPU Cluster Arvind Kannan (Fri Aug 19 2011 - 17:31:06 CDT)
- PBB File Format/Setup for PBC Anna James (Fri Aug 19 2011 - 07:24:11 CDT)
- remove translation of protein under spherical boundary conditions kakali sen (Fri Aug 19 2011 - 04:39:24 CDT)
- Restarting MD (Disabling Checklist) Babban Mia (Thu Aug 18 2011 - 10:58:55 CDT)
- Re: Multinode NAMD CUDA GPU Selection Axel Kohlmeyer (Thu Aug 18 2011 - 10:39:18 CDT)
- Heating in NAMD Babban Mia (Thu Aug 18 2011 - 10:13:08 CDT)
- Relationship between High temperature and the boiling point of water albus hawking (Wed Aug 17 2011 - 13:29:56 CDT)
- (no subject) Andrea Holfelder (Thu Aug 18 2011 - 04:59:05 CDT)
- RHDO lattice as a PBC unit Cell in NAMD Andrea Holfelder (Thu Aug 18 2011 - 04:59:59 CDT)
- Multinode NAMD CUDA GPU Selection Norman Geist (Thu Aug 18 2011 - 01:25:00 CDT)
- differences in multiprocessor energy minimization results Markus Metz (Wed Aug 17 2011 - 11:44:19 CDT)
- Relative RMSD constraint jiyong (Wed Aug 17 2011 - 02:00:57 CDT)
- Truncated octahedron - unwrapping the trajectory etc Alexander Predeus (Tue Aug 16 2011 - 21:46:22 CDT)
- MMTools Chathurika Abeyrathne (Tue Aug 16 2011 - 20:03:45 CDT)
- low dielectric constants in GBIS Branko (Tue Aug 16 2011 - 15:41:04 CDT)
- Generalized Born calcs Thomas Bishop (Tue Aug 16 2011 - 14:53:17 CDT)
- PME Grid Settings and its significance relative to a cutoff value Andrea Holfelder (Tue Aug 16 2011 - 15:07:14 CDT)
- Namd / gromacs Sara baretller (Tue Aug 16 2011 - 09:17:41 CDT)
- (no subject) Anna James (Tue Aug 16 2011 - 08:38:14 CDT)
- Re: AW: Letzte Hilfe Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
- convergence and stability of simulation Jorgen Simonsen (Mon Aug 15 2011 - 14:08:29 CDT)
- AW: Letzte Hilfe Norman Geist (Mon Aug 15 2011 - 07:16:39 CDT)
- AW: Batch Mode MD simulation Script for NAMD Norman Geist (Mon Aug 15 2011 - 00:29:43 CDT)
- Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:11:06 CDT)
- Lingand Unbinding using SMD Jacopo Sgrignani (Mon Aug 15 2011 - 02:19:17 CDT)
- Re: Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed Ehsan Ban (Mon Aug 15 2011 - 00:01:22 CDT)
- Periodic Boundary Condition for a 630 Amino Acid Protein Babban Mia (Sun Aug 14 2011 - 08:15:28 CDT)
- MD condition hamze rahimi (Sun Aug 14 2011 - 05:02:36 CDT)
- .COOR TO PDB FILE Babban Mia (Sat Aug 13 2011 - 01:11:48 CDT)
- Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 05:46:32 CDT)
- Re: Batch Mode MD simulation Script for NAMD Jeffrey Potoff (Fri Aug 12 2011 - 06:45:12 CDT)
- AW: Batch Mode MD simulation Script for NAMD Norman Geist (Fri Aug 12 2011 - 07:02:29 CDT)
- Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 12:06:28 CDT)
- Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 12:59:45 CDT)
- RE: Batch Mode MD simulation Script for NAMD Ismail, Mohd F. (Fri Aug 12 2011 - 13:07:59 CDT)
- Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 13:55:03 CDT)
- RE: Batch Mode MD simulation Script for NAMD Ismail, Mohd F. (Fri Aug 12 2011 - 14:40:31 CDT)
- Re: Batch Mode MD simulation Script for NAMD Babban Mia (Sat Aug 13 2011 - 07:36:56 CDT)
- Re: Batch Mode MD simulation Script for NAMD JC Gumbart (Sat Aug 13 2011 - 08:45:56 CDT)
- AW: Batch Mode MD simulation Script for NAMD Norman Geist (Mon Aug 15 2011 - 00:34:15 CDT)
- Batch Mode MD simulation Script for NAMD Babban Mia (Thu Aug 11 2011 - 18:56:19 CDT)
- Mixed TIP3/TIP4 Waters Keith Battle (Thu Aug 11 2011 - 06:29:18 CDT)
- image centering problem ipsita basu (Thu Aug 11 2011 - 00:41:20 CDT)
- sodium ion in water divya nayar (Thu Aug 11 2011 - 00:17:27 CDT)
- Re: Topology file for ethanol Babban Mia (Wed Aug 10 2011 - 23:35:37 CDT)
- Topology file for ethanol Babban Mia (Wed Aug 10 2011 - 22:58:19 CDT)
- Solvation in VMD using Non Standard Solvent System Babban Mia (Wed Aug 10 2011 - 07:35:32 CDT)
- Compiling Namd on MAC with Cuda Stan Skafidas (Wed Aug 10 2011 - 07:16:49 CDT)
- Custom CHARMM forcefield usage problem Jernej Zidar (Tue Aug 09 2011 - 23:12:04 CDT)
- Fwd: Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Branko (Tue Aug 09 2011 - 13:29:52 CDT)
- Blue Waters Andy Somogyi (Tue Aug 09 2011 - 10:18:49 CDT)
- Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Tue Aug 09 2011 - 09:42:26 CDT)
- minimization problem Narasimhan LOGANATHAN (Tue Aug 09 2011 - 07:00:28 CDT)
- Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Tue Aug 09 2011 - 01:20:20 CDT)
- patch becoming too small Jorgen Simonsen (Tue Aug 09 2011 - 01:14:33 CDT)
- Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Andres Morales N (Sun Aug 07 2011 - 21:00:38 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Mon Aug 08 2011 - 02:57:08 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! flavio seixas (Mon Aug 08 2011 - 21:12:24 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Jeffrey Potoff (Mon Aug 08 2011 - 21:12:39 CDT)
- NAMD on PS3 Ali Khanlarkhani (Sat Aug 06 2011 - 11:02:22 CDT)
- nvidia cuda driver version Francesco Pietra (Fri Aug 05 2011 - 08:44:44 CDT)
- Minimization is taking a lot of computing time. Kartheek (Fri Aug 05 2011 - 04:53:42 CDT)
- AW: Minimization is taking a lot of computing time. Norman Geist (Fri Aug 05 2011 - 05:54:49 CDT)
- Minimization is taking a lot of computing time. Kartheek (Tue Aug 09 2011 - 06:06:57 CDT)
- GBIS on GPU? Danny Xu (Thu Aug 04 2011 - 11:51:57 CDT)
- error: expected floating-point number but got Shen, Han (Thu Aug 04 2011 - 10:21:32 CDT)
- online guide for using amber ff in NAMD George Madalin Giambasu (Wed Aug 03 2011 - 11:18:10 CDT)
- Re: [ppl] Regarding Compiling in Redhat linux. Phil Miller (Wed Aug 03 2011 - 09:30:01 CDT)
- Re: Namd-I: namd compiling problem Ye Yang (Wed Aug 03 2011 - 10:46:13 CDT)
- Namd-I: namd compiling problem Ye Yang (Tue Aug 02 2011 - 22:28:05 CDT)
- RE: System net charge Andres Morales N (Tue Aug 02 2011 - 19:20:38 CDT)
- Re: [ppl] Compliling NAMD in RedHat Phil Miller (Tue Aug 02 2011 - 10:10:18 CDT)
- Pair interaction and thermo integration Courtney Taylor (Mon Aug 01 2011 - 09:32:38 CDT)
- Temperature bath Chathurika Abeyrathne (Mon Aug 01 2011 - 02:20:15 CDT)
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany David Brandon (Fri Jul 29 2011 - 14:13:05 CDT)
- Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed Ehsan Ban (Fri Jul 29 2011 - 12:40:27 CDT)
- namd-I: cionize problem in vmd Ye Yang (Fri Jul 29 2011 - 11:17:10 CDT)
- Dividing a 2D ABF simulations into regions (on nodes with different speeds) Ajasja LjubetiÄ (Fri Jul 29 2011 - 04:44:38 CDT)
- About fastest CUDA cards Francesco Pietra (Fri Jul 29 2011 - 04:09:37 CDT)
- about D amino acid AB (Fri Jul 29 2011 - 03:50:16 CDT)
- System net charge Andres Morales N (Fri Jul 29 2011 - 03:25:11 CDT)
- RE: DPPC membrane Andres Morales N (Fri Jul 29 2011 - 03:16:50 CDT)
- "Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Thu Jul 28 2011 - 12:21:28 CDT)
- NAMD energy plugin politr_at_fh.huji.ac.il (Thu Jul 28 2011 - 04:22:42 CDT)
- DPPC membrane Andres Morales N (Thu Jul 28 2011 - 01:29:36 CDT)
- Quartz modelling Nikita Vakula (Thu Jul 28 2011 - 00:46:05 CDT)
- Trp-cage folding simulation divya nayar (Thu Jul 28 2011 - 00:09:07 CDT)
- colvars, discontinuous rotation JC Gumbart (Wed Jul 27 2011 - 20:41:30 CDT)
- Setting integrator parameters for ABF Ajasja LjubetiÄ (Wed Jul 27 2011 - 12:49:24 CDT)
- nitrogen in namd Marco Sant (Wed Jul 27 2011 - 04:47:15 CDT)
- using colvars for bending modulus? JC Gumbart (Tue Jul 26 2011 - 15:43:50 CDT)
- NAMD 2.8 on Cray XE6 segfaulting Tim Robinson (Tue Jul 26 2011 - 05:46:01 CDT)
- NAMD 2.8 job submission script for queenbee cnu gromacs (Mon Jul 25 2011 - 18:29:51 CDT)
- Segmentation Faults on Mac OS X Lion Arvind Kannan (Mon Jul 25 2011 - 16:48:21 CDT)
- Segmentation Faults on Mac OS X Lion Arvind Kannan (Mon Jul 25 2011 - 16:39:31 CDT)
- is there any difference between non-constrained equilibrium and normal MD production? AB (Mon Jul 25 2011 - 13:04:35 CDT)
- combining thermodynamic integration with replica exchange in NAMD Hugh Heldenbrand (Mon Jul 25 2011 - 10:05:50 CDT)
- how to generate transparent figures? AB (Sat Jul 23 2011 - 09:59:07 CDT)
- SOLVED: Failure to run namd-cuda with gtx-470 Francesco Pietra (Fri Jul 22 2011 - 09:56:34 CDT)
- Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Fri Jul 22 2011 - 05:24:26 CDT)
- Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Fri Jul 22 2011 - 08:56:17 CDT)
- Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Fri Jul 22 2011 - 09:12:29 CDT)
- Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Fri Jul 22 2011 - 09:19:59 CDT)
- Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Mon Jan 16 2012 - 19:29:26 CST)
- Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Tue Jan 17 2012 - 08:25:29 CST)
- Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Tue Jan 17 2012 - 08:35:42 CST)
- Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Tue Jan 17 2012 - 09:10:51 CST)
- Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Fri Jul 22 2011 - 09:12:29 CDT)
- Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Fri Jul 22 2011 - 08:56:17 CDT)
- Re: Yan: analysis question Bjoern Olausson (Fri Jul 22 2011 - 03:01:05 CDT)
- how to calculate partial charge for ligand based on CHARMM principle? AB (Thu Jul 21 2011 - 11:49:39 CDT)
- Molecule2.C Andy Somogyi (Thu Jul 21 2011 - 11:45:11 CDT)
- Suspend NAMD (to RAM) Ajasja LjubetiÄ (Wed Jul 20 2011 - 17:10:06 CDT)
- namd files Hasan haska (Wed Jul 20 2011 - 08:17:34 CDT)
- TIP4P water model Molecular Dynamics (Wed Jul 20 2011 - 07:34:47 CDT)
- Equilibration Andres Morales N (Tue Jul 19 2011 - 13:39:37 CDT)
- Re: Equilibration bharat gupta (Wed Jun 29 2011 - 01:06:10 CDT)
- Re: Equilibration Chris Harrison (Tue Jul 19 2011 - 14:42:06 CDT)
- Membranes Andres Morales N (Tue Jul 19 2011 - 15:46:54 CDT)
- expect NAMD survey emails this week Jim Phillips (Tue Jul 19 2011 - 11:51:22 CDT)
- Query about switch function using AMBER ff99SB forcefield and NAMD simulation code Madhurima Jana (Tue Jul 19 2011 - 06:41:25 CDT)
- analysis question Namd Namd (Tue Jul 19 2011 - 04:32:06 CDT)
- vmd-l: No APBS output: 'cannot access output file' error Christian Jorgensen (Mon Jul 18 2011 - 18:44:07 CDT)
- zinc-finger protein simulation hamze rahimi (Mon Jul 18 2011 - 06:55:08 CDT)
- PME or not PME? What happens if PME is turned off? Bjoern Olausson (Mon Jul 18 2011 - 04:10:08 CDT)
- Re: PME or not PME? What happens if PME is turned off? Jérôme Hénin (Mon Jul 18 2011 - 15:27:09 CDT)
- Re: PME or not PME? What happens if PME is turned off? Bjoern Olausson (Tue Jul 19 2011 - 01:48:50 CDT)
- Re: PME or not PME? What happens if PME is turned off? Chris Harrison (Tue Jul 19 2011 - 14:45:48 CDT)
- Re: PME or not PME? What happens if PME is turned off? Bjoern Olausson (Wed Jul 20 2011 - 03:03:10 CDT)
- alchDecouple esmael (Fri Jul 22 2011 - 19:10:59 CDT)
- Re: alchDecouple Jérôme Hénin (Sat Jul 23 2011 - 02:44:36 CDT)
- Re: alchDecouple Jérôme Hénin (Mon Jul 25 2011 - 15:19:14 CDT)
- Re: PME or not PME? What happens if PME is turned off? esmael (Tue Aug 02 2011 - 18:54:03 CDT)
- Re: PME or not PME? What happens if PME is turned off? Chris Harrison (Wed Aug 03 2011 - 14:48:12 CDT)
- Re: PME or not PME? What happens if PME is turned off? Jérôme Hénin (Mon Jul 18 2011 - 15:27:09 CDT)
- Pico scale to nanoscale simulation....alteration if .conf files required amit banerjee (Sun Jul 17 2011 - 21:28:43 CDT)
- control distance between solvent and solute Kang Hee Cho (Fri Jul 15 2011 - 20:07:56 CDT)
- FATAL ERROR: Setting parameter fixedAtomsFile from script failed! Jorgen Simonsen (Fri Jul 15 2011 - 15:55:26 CDT)
- how to define the numsteps in ABF or metadynamics simulation? ÕÅÓÂ (Thu Jul 14 2011 - 19:48:32 CDT)
- TIP5P-model Maria Kamm (Thu Jul 14 2011 - 19:07:48 CDT)
- hi kanchi subbarao rao (Thu Jul 14 2011 - 12:31:06 CDT)
- FATAL ERROR: Unable to open binary file sibel.cakan (Thu Jul 14 2011 - 05:34:57 CDT)
- Colvars "tilt" component force constant units for WHAM Robert Elder (Tue Jul 12 2011 - 16:36:55 CDT)
- hi kanchi subbarao rao (Wed Jul 13 2011 - 13:47:30 CDT)
- Low global exclusion count errors Austin B. Yongye (Wed Jul 13 2011 - 13:10:10 CDT)
- protein moving out during npt equilibration bharat gupta (Wed Jul 13 2011 - 10:48:48 CDT)
- Help required for nanoscale simulation amit banerjee (Wed Jul 13 2011 - 03:03:45 CDT)
- unsubscribe Tibbitt, Jeffrey A. (Tue Jul 12 2011 - 19:32:21 CDT)
- Low global exclusion count Austin B. Yongye (Tue Jul 12 2011 - 15:08:51 CDT)
- Problem while using MARTINI force field with NAMD 2.8 rohan uttarwar (Tue Jul 12 2011 - 11:42:14 CDT)
- how to define the numsteps in ABF or metadynamics simulation? Clark Zhang (Wed Jul 06 2011 - 23:08:50 CDT)
- tesla 2050 benchmark Burgess, Don E (Tue Jul 12 2011 - 13:56:45 CDT)
- where can I find parameters for t-BuO(C=O)NH-? AlbertAlbert (Tue Jul 12 2011 - 12:33:39 CDT)
- Filtered mail? Austin B. Yongye (Tue Jul 12 2011 - 09:04:32 CDT)
- Using VMD paratool æŽä½³é”® (Mon Jul 11 2011 - 16:24:12 CDT)
- Fixed COM Ali Khanlarkhani (Mon Jul 11 2011 - 13:30:32 CDT)
- NAMD chares Andy Somogyi (Mon Jul 11 2011 - 10:35:17 CDT)
- Possibility of modifying the non-bonded terms of the potential Ali Emileh (Fri Jul 08 2011 - 16:58:44 CDT)
- Patch link flavio seixas (Fri Jul 08 2011 - 14:11:38 CDT)
- temperature-TS with NAMDplot Molecular Dynamics (Fri Jul 08 2011 - 05:44:50 CDT)
- Implicit solvent simulation jaya c.jose (Fri Jul 08 2011 - 05:35:40 CDT)
- does any body have the parameter file for aldehyde group? AlbertAlbert (Fri Jul 08 2011 - 01:34:22 CDT)
- free energy of binding Francesco Pietra (Thu Jul 07 2011 - 04:52:38 CDT)
- AW: free energy of binding Norman Geist (Thu Jul 07 2011 - 05:35:07 CDT)
- Re: free energy of binding Dong Luo (Thu Jul 07 2011 - 10:50:07 CDT)
- Re: free energy of binding Francesco Pietra (Thu Jul 07 2011 - 16:50:12 CDT)
- Re: free energy of binding Gianluca Interlandi (Thu Jul 07 2011 - 17:08:55 CDT)
- Re: free energy of binding Jeffrey Potoff (Thu Jul 07 2011 - 17:16:02 CDT)
- Re: free energy of binding Gianluca Interlandi (Thu Jul 07 2011 - 17:29:18 CDT)
- Re: free energy of binding Jeff Wereszczynski (Thu Jul 07 2011 - 18:27:55 CDT)
- Re: free energy of binding Richard Wood (Thu Jul 07 2011 - 18:56:48 CDT)
- Re: free energy of binding Chris Harrison (Thu Jul 07 2011 - 17:12:34 CDT)
- Re: free energy of binding Francesco Pietra (Thu Jul 07 2011 - 16:50:12 CDT)
- Failure to run namd-cuda with gtx-470 Francesco Pietra (Wed Jul 06 2011 - 10:44:38 CDT)
- Transferring environment variables when using charmrun Ajasja LjubetiÄ (Wed Jul 06 2011 - 05:08:54 CDT)
- Difference between cwd and cd Ajasja LjubetiÄ (Wed Jul 06 2011 - 04:43:43 CDT)
- membrane simulation ERROR rattle algorithm Jorgen Simonsen (Tue Jul 05 2011 - 10:13:57 CDT)
- Re: membrane simulation ERROR rattle algorithm sajad falsafi (Tue Jul 05 2011 - 11:44:10 CDT)
- Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ (Tue Jul 05 2011 - 12:01:53 CDT)
- Re: membrane simulation ERROR rattle algorithm Jorgen Simonsen (Tue Jul 05 2011 - 12:41:49 CDT)
- Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ (Tue Jul 05 2011 - 12:54:40 CDT)
- Re: membrane simulation ERROR rattle algorithm Axel Kohlmeyer (Tue Jul 05 2011 - 13:05:18 CDT)
- Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ (Tue Jul 05 2011 - 13:40:44 CDT)
- Re: membrane simulation ERROR rattle algorithm Jorgen Simonsen (Wed Jul 06 2011 - 03:36:22 CDT)
- Re: membrane simulation ERROR rattle algorithm Salvatore Mario Cosseddu (Wed Jul 06 2011 - 06:15:46 CDT)
- Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ (Wed Jul 06 2011 - 06:37:10 CDT)
- Re: membrane simulation ERROR rattle algorithm snoze pa (Wed Jul 06 2011 - 10:06:03 CDT)
- Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ (Tue Jul 05 2011 - 12:01:53 CDT)
- Re: membrane simulation ERROR rattle algorithm sajad falsafi (Tue Jul 05 2011 - 11:44:10 CDT)
- clustering of trajectory Bala subramanian (Tue Jul 05 2011 - 09:46:24 CDT)
- Re: Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 03:40:59 CDT)
- Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Tue Jul 05 2011 - 04:22:50 CDT)
- Re: Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 21:25:04 CDT)
- Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Fri Jul 08 2011 - 02:50:29 CDT)
- DNA terminal Patch / How could I retain the primes in DNA raghav singh (Tue Jul 05 2011 - 03:23:21 CDT)
- Win64-MPI Patriche Simona (Tue Jul 05 2011 - 02:04:17 CDT)
- Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 00:33:30 CDT)
- Re: distortion of some bonds during structure preparation bharat gupta (Mon Jul 04 2011 - 03:36:39 CDT)
- bigdcd file help snoze pa (Mon Jul 04 2011 - 01:29:23 CDT)
- Hi: some doubt about nvt and npt equilibration bharat gupta (Sun Jul 03 2011 - 20:36:19 CDT)
- a bundle of coor files Massimiliano Porrini (Sat Jul 02 2011 - 13:21:56 CDT)
- restart simulation writing in the same .dcd file. Ranyere Deyler (Sat Jul 02 2011 - 02:25:51 CDT)
- Re: NPT equilibration bharat gupta (Fri Jul 01 2011 - 04:04:56 CDT)
- Re: Fatal Error Periodic cell has become too small for original patch grid bharat gupta (Fri Jul 01 2011 - 00:59:56 CDT)
- Re: Final production run in MD bharat gupta (Thu Jun 30 2011 - 18:42:23 CDT)
- Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM Francesco Pietra (Thu Jun 30 2011 - 14:49:56 CDT)
- can RHDO crystal shape works in NAMD pxq_at_dicp.ac.cn (Fri Jul 01 2011 - 01:33:14 CDT)
- Accessing Colvars Within NAMD TCL David Rogers (Thu Jun 30 2011 - 10:28:33 CDT)
- nvidia 275.09.07 driver Francesco Pietra (Thu Jun 30 2011 - 03:24:48 CDT)
- Re: Equilibration - NVT & NPT bharat gupta (Thu Jun 30 2011 - 01:36:56 CDT)
- Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 16:07:55 CDT)
- Re: Namd-I: Implicit solvent problem Francesco Oteri (Wed Jun 29 2011 - 16:17:21 CDT)
- Re: Namd-I: Implicit solvent problem Gianluca Interlandi (Wed Jun 29 2011 - 16:31:49 CDT)
- Re: Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 17:38:54 CDT)
- Re: Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 17:44:55 CDT)
- Re: Namd-I: Implicit solvent problem Giovanni Settanni (Thu Jun 30 2011 - 01:56:13 CDT)
- Re: Namd-I: Implicit solvent problem Matteo Rotter (Wed Jul 20 2011 - 11:04:03 CDT)
- Re: Re: Namd-I: Implicit solvent problem Enrico Guarnera (Wed Jul 20 2011 - 11:22:46 CDT)
- Re: Re: Namd-I: Implicit solvent problem Matteo Rotter (Wed Jul 20 2011 - 16:06:29 CDT)
- Re: Namd-I: Implicit solvent problem Gianluca Interlandi (Wed Jun 29 2011 - 17:49:51 CDT)
- Re: Namd-I: Implicit solvent problem Gianluca Interlandi (Wed Jun 29 2011 - 16:31:49 CDT)
- Re: Namd-I: Implicit solvent problem Francesco Oteri (Wed Jun 29 2011 - 16:17:21 CDT)
- How to simulate a charged surface Yingzhe Liu (Wed Jun 22 2011 - 02:53:56 CDT)
- Charmm parameter for H2 gas Zhao Lina (Wed Jun 29 2011 - 04:41:15 CDT)
- AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 04:08:26 CDT)
- AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 04:04:42 CDT)
- Re: Energy minimization bharat gupta (Tue Jun 28 2011 - 18:49:01 CDT)
- Cannot find bond parameters Gayatri Rathod (Tue Jun 28 2011 - 11:03:45 CDT)
- SWM4 water model simulation saman amiri (Mon Jun 27 2011 - 12:27:34 CDT)
- Restarting an alchemic FEP calculation Giovanni Bellesia (Mon Jun 27 2011 - 09:32:25 CDT)
- Implicit solvent Massimiliano Porrini (Mon Jun 27 2011 - 06:35:00 CDT)
- Re: vmd-l: protein-water RDF Ajasja LjubetiÄ (Mon Jun 27 2011 - 03:29:44 CDT)
- Methanol - Autocorrelation of total dipole moment Chathurika Abeyrathne (Sat Jun 25 2011 - 03:36:06 CDT)
- Memory leak and crash before first step Pedro Gonnet (Fri Jun 24 2011 - 14:28:08 CDT)
- interpretation of timing data in output Hannes Loeffler (Fri Jun 24 2011 - 04:29:42 CDT)
- CG-MD high electrostatic energy values sibel.cakan (Fri Jun 24 2011 - 03:40:32 CDT)
- Re: formyl and ethanolamide parameters and topology flavio seixas (Thu Jun 23 2011 - 12:08:58 CDT)
- formyl and ethanolamide parameters and topology Jorgen Simonsen (Thu Jun 23 2011 - 09:52:18 CDT)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) Jorgen Simonsen (Thu Jun 23 2011 - 08:51:52 CDT)
- slow heating md Hasan haska (Thu Jun 23 2011 - 06:11:51 CDT)
- How to simulate a charged surface Yingzhe Liu (Thu Jun 23 2011 - 05:43:49 CDT)
- finding water around protein divya nayar (Thu Jun 23 2011 - 00:59:56 CDT)
- how to get the energy in vacuum of a molecule in NAMD jnsong (Wed Jun 22 2011 - 08:36:40 CDT)
- Re: patch for phosphotyrosine residue bharat gupta (Tue Jun 21 2011 - 20:53:38 CDT)
- NAMD with TIP5P water David Huggins (Tue Jun 21 2011 - 13:24:49 CDT)
- hello murffyp_at_gmail.com (Tue Jun 21 2011 - 07:54:59 CDT)
- simulated annealing protocol Massimiliano Porrini (Tue Jun 21 2011 - 07:41:00 CDT)
- Re: aligning two molecules by principal axes of inertia using measure.c Ajasja LjubetiÄ (Mon Jun 20 2011 - 09:40:20 CDT)
- aligning two molecules by principal axes of inertia using measure.c Ada Sedova (Mon Jun 20 2011 - 08:18:41 CDT)
- restraining groups of atoms Massimiliano Porrini (Mon Jun 20 2011 - 07:03:09 CDT)
- Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Mon Jun 20 2011 - 06:11:49 CDT)
- vdw value in parameter file ÅÓ´ºÀö (Mon Jun 20 2011 - 02:26:06 CDT)
- Re: phosphotyrosine bharat gupta (Sun Jun 19 2011 - 19:26:37 CDT)
- patch needed for tuple is missing JC Gumbart (Sat Jun 18 2011 - 23:49:47 CDT)
- How to calculate Binding Free energy in NAMD jnsong (Sat Jun 18 2011 - 01:00:49 CDT)
- SWM4 water model simulation saman amiri (Fri Jun 17 2011 - 16:07:14 CDT)
- REMD exchange ratios Massimiliano Porrini (Fri Jun 17 2011 - 08:47:48 CDT)
- Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 00:50:05 CDT)
- Tcl issue with config script opronkri_at_msu.edu (Fri Jun 17 2011 - 00:06:53 CDT)
- rescaling velocity esmael (Wed Jun 15 2011 - 18:17:58 CDT)
- namd-I: Problems with Namd coarsegrain and Gromacs top file Ye Yang (Wed Jun 15 2011 - 14:50:23 CDT)
- Channel flow equilibration Mao Mao (Wed Jun 15 2011 - 11:46:26 CDT)
- NAMD-l: Get the PDB file from Steered Molecular Dynamics output files albus hawking (Tue Jun 14 2011 - 22:56:55 CDT)
- Question about equilibration snoze pa (Wed Jun 15 2011 - 11:02:53 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:07:51 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:20:04 CDT)
- Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 11:27:45 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:38:17 CDT)
- Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 11:48:06 CDT)
- Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 12:35:44 CDT)
- Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 13:10:10 CDT)
- Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 13:16:00 CDT)
- Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 13:22:56 CDT)
- Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 13:47:59 CDT)
- Re: Question about equilibration Gianluca Interlandi (Wed Jun 15 2011 - 14:03:57 CDT)
- Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 14:12:14 CDT)
- Re: Question about equilibration Gianluca Interlandi (Wed Jun 15 2011 - 14:18:43 CDT)
- RE: Question about equilibration Reichert, David (Wed Jun 15 2011 - 14:21:33 CDT)
- Re: Question about equilibration snoze pa (Thu Jun 16 2011 - 17:33:37 CDT)
- Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 11:19:17 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 12:06:57 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:20:04 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:07:51 CDT)
- Re: AW: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Wed Jun 15 2011 - 09:10:28 CDT)
- hi all kanchi subbarao rao (Wed Jun 15 2011 - 04:14:04 CDT)
- Fwd: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Wed Jun 15 2011 - 02:45:26 CDT)
- AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 01:01:25 CDT)
- water is forming bonds between oxigens PAUL NEWMAN (Tue Jun 14 2011 - 16:36:33 CDT)
- Impropers in Charmm and OPLS Henriette Elisabeth Autzen (Tue Jun 14 2011 - 08:33:58 CDT)
- umbrella sampling by NAMD jafar azamat (Tue Jun 14 2011 - 06:27:45 CDT)
- cuda error cudastreamcreate Francesco Pietra (Tue Jun 14 2011 - 00:45:37 CDT)
- A question on Jarkynski equation Jun Zhang (Mon Jun 13 2011 - 22:01:59 CDT)
- namd ( please help me!!! ) Namd Namd (Mon Jun 13 2011 - 14:29:40 CDT)
- NAMD crashes with OpenMPI/OpenMX Thomas Albers (Mon Jun 13 2011 - 11:50:35 CDT)
- Re: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Tue Jun 14 2011 - 11:33:35 CDT)
- Protein distort during equilibration snoze pa (Mon Jun 13 2011 - 10:22:10 CDT)
- changing solventDielectric in GBIS Andres Colubri (Mon Jun 13 2011 - 07:36:41 CDT)
- force field Namd Namd (Mon Jun 13 2011 - 03:36:04 CDT)
- Iron Oxide and Arsenic Salvador H-V (Sat Jun 11 2011 - 17:09:20 CDT)
- Compiling NAMD for CUDA Thomas Albers (Sat Jun 11 2011 - 16:23:01 CDT)
- about charmm force field oguz gurbulak (Fri Jun 10 2011 - 09:55:26 CDT)
- Re: max number of CPU PEs per GPU? Ajasja LjubetiÄ (Fri Jun 10 2011 - 06:50:44 CDT)
- AW: max number of CPU PEs per GPU? Norman Geist (Fri Jun 10 2011 - 06:25:45 CDT)
- max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 01:17:53 CDT)
- Re: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Jim Phillips (Thu Jun 09 2011 - 10:53:46 CDT)
- about log file Molecular Dynamics (Thu Jun 09 2011 - 04:30:30 CDT)
- Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." David McGiven (Wed Jun 08 2011 - 09:00:34 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:26:13 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:36:44 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:44:01 CDT)
- Multiple Runs in a Single Conf File Rajan Vatassery (Wed Jun 08 2011 - 03:00:55 CDT)
- Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink juan du (Tue Jun 07 2011 - 18:27:25 CDT)
- Re: atom select within hbond analysis sajad falsafi (Tue Jun 07 2011 - 09:21:09 CDT)
- question about v2.8 sibel.cakan (Tue Jun 07 2011 - 09:01:58 CDT)
- atom select within hbond analysis Branko (Tue Jun 07 2011 - 07:40:09 CDT)
- Re: Gibbs potential sajad falsafi (Tue Jun 07 2011 - 02:14:40 CDT)
- Gibbs potential Patriche Simona (Mon Jun 06 2011 - 10:10:01 CDT)
- water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:07:38 CDT)
- Re: water equilibration Wang Yi (Mon Jun 06 2011 - 08:42:26 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:55:39 CDT)
- Re: water equilibration Bjoern Olausson (Mon Jun 06 2011 - 09:12:33 CDT)
- Re: water equilibration johan strumpfer (Mon Jun 06 2011 - 08:59:05 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Tue Jun 07 2011 - 09:03:23 CDT)
- Re: water equilibration johan strumpfer (Tue Jun 07 2011 - 09:44:33 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Tue Jun 07 2011 - 11:15:10 CDT)
- Re: water equilibration johan strumpfer (Tue Jun 07 2011 - 11:20:16 CDT)
- Re: water equilibration Gurunath Katagi (Tue Jun 07 2011 - 15:14:51 CDT)
- Re: water equilibration Jim Phillips (Wed Jun 08 2011 - 14:40:03 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Tue Aug 02 2011 - 08:42:11 CDT)
- water equilibration Narasimhan LOGANATHAN (Fri Aug 05 2011 - 05:41:27 CDT)
- AW: water equilibration Norman Geist (Fri Aug 05 2011 - 05:56:04 CDT)
- Re: AW: water equilibration Narasimhan LOGANATHAN (Fri Aug 05 2011 - 07:53:22 CDT)
- Re: water equilibration Jeffrey Potoff (Fri Aug 05 2011 - 09:32:23 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Wed Jun 08 2011 - 05:17:17 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Thu Aug 04 2011 - 03:25:07 CDT)
- Re: water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:55:39 CDT)
- Re: water equilibration Wang Yi (Mon Jun 06 2011 - 08:42:26 CDT)
- Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 05:50:24 CDT)
- AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 02:54:52 CDT)
- MARTINI parameters and Bead definitions Edroaldo Lummertz da Rocha (Fri Jun 03 2011 - 18:56:49 CDT)
- I M wants to share "legis_2011" with you Dropbox (Fri Jun 03 2011 - 15:20:24 CDT)
- metadynamics combined with PCV Anurag Sethi (Fri Jun 03 2011 - 12:14:18 CDT)
- Ä°lt: Re: heat annealing conf file Molecular Dynamics (Fri Jun 03 2011 - 09:57:07 CDT)
- prm and top files for charmm19 force field oguz gurbulak (Fri Jun 03 2011 - 09:22:47 CDT)
- CthCreate failed to create fiber Patriche Simona (Fri Jun 03 2011 - 08:52:28 CDT)
- conf file script ( help needed ) Molecular Dynamics (Fri Jun 03 2011 - 08:37:57 CDT)
- Alpha P.M.F. with NAMD 2.8 Prathit Chatterjee (Fri Jun 03 2011 - 06:21:46 CDT)
- Periodic Boundary Condition in NAMD Van Ngo (Thu Jun 02 2011 - 23:55:08 CDT)
- lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 06:53:05 CDT)
- heat annealing conf file Molecular Dynamics (Thu Jun 02 2011 - 05:26:17 CDT)
- Re: Advice on buying GPUs Ajasja LjubetiÄ (Thu Jun 02 2011 - 03:13:10 CDT)
- regarding vmd kamal Kishor Thakur (Thu Jun 02 2011 - 01:28:36 CDT)
- question on residue rmsd.tcl amit banerjee (Wed Jun 01 2011 - 22:49:17 CDT)
- problem in distance.tcl amit banerjee (Wed Jun 01 2011 - 22:37:42 CDT)
- Fwd: Fwd: hi kanchi subbarao rao (Wed Jun 01 2011 - 13:32:41 CDT)
- Advice on buying GPUs Ajasja LjubetiÄ (Wed Jun 01 2011 - 09:43:24 CDT)
- PBC Werner Crous (Wed Jun 01 2011 - 05:09:27 CDT)
- Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Tue May 31 2011 - 21:57:03 CDT)
- NAMD 2.8 released Jim Phillips (Tue May 31 2011 - 14:55:34 CDT)
- restart a simulation Mao Mao (Tue May 31 2011 - 14:50:22 CDT)
- Fail to Run VMD Àî¼Ñ¼ü (Tue May 31 2011 - 13:53:07 CDT)
- Fwd: hi kanchi subbarao rao (Tue May 31 2011 - 05:10:32 CDT)
- vdw parameter of metal ion ÅÓ´ºÀö (Tue May 31 2011 - 04:49:55 CDT)
- Script Help flavio seixas (Sun May 29 2011 - 18:16:51 CDT)
- Question about end of log file Rajan Vatassery (Sun May 29 2011 - 14:14:34 CDT)
- Re PMF Branko (Sat May 28 2011 - 12:18:22 CDT)
- RBCG water simulation Cristhian Boetsch (Fri May 27 2011 - 12:17:38 CDT)
- NADPH topology flavio seixas (Fri May 27 2011 - 08:58:17 CDT)
- NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE" David McGiven (Fri May 27 2011 - 06:12:42 CDT)
- TIP5P water simulation David Huggins (Thu May 26 2011 - 15:57:25 CDT)
- Re: vmd-l: measure fit - wrong alignment Jérôme Hénin (Thu May 26 2011 - 13:09:29 CDT)
- about conf file oguz gurbulak (Thu May 26 2011 - 09:11:29 CDT)
- PSF and PDB file for SWM4 water models saman amiri (Thu May 26 2011 - 07:37:04 CDT)
- Truncated octahedron box issues (?) Massimiliano Porrini (Wed May 25 2011 - 10:38:03 CDT)
- restart with constraints causes RMSD "jump" P.-L. Chau (Wed May 25 2011 - 07:24:11 CDT)
- The Nudged Elastic Band Approach to Find the Lowest Energy Pathway Between two States Buddhadev Maiti (Tue May 24 2011 - 22:14:14 CDT)
- Joining PSF Files PAUL NEWMAN (Tue May 24 2011 - 08:58:24 CDT)
- the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file jnsong (Tue May 24 2011 - 03:12:57 CDT)
- Coulombic component of configurational energy divya nayar (Tue May 24 2011 - 03:12:24 CDT)
- Development plan of NAMD? Norman Geist (Tue May 24 2011 - 02:03:37 CDT)
- PMF jafar azamat (Tue May 24 2011 - 00:47:30 CDT)
- AW: AW: AW: question about wrap atoms to its original coordinates Norman Geist (Mon May 23 2011 - 01:03:53 CDT)
- PMF calculation jafar azamat (Mon May 23 2011 - 07:31:13 CDT)
- Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 05:47:08 CDT)
- Re: Problem building NAMD (multiple definitions) Jim Phillips (Mon May 23 2011 - 17:08:21 CDT)
- Re: Problem building NAMD (multiple definitions) Axel Kohlmeyer (Mon May 23 2011 - 17:12:21 CDT)
- Re: Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 17:38:47 CDT)
- Re: Problem building NAMD (multiple definitions) Axel Kohlmeyer (Mon May 23 2011 - 17:41:37 CDT)
- Re: Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 17:49:59 CDT)
- Re: Problem building NAMD (multiple definitions) Jim Phillips (Mon May 23 2011 - 17:57:27 CDT)
- Re: Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 18:14:35 CDT)
- Re: Problem building NAMD (multiple definitions) Axel Kohlmeyer (Mon May 23 2011 - 17:12:21 CDT)
- Re: Problem building NAMD (multiple definitions) Jim Phillips (Mon May 23 2011 - 17:08:21 CDT)
- hi murffyp_at_gmail.com (Sun May 22 2011 - 23:14:11 CDT)
- Dear friend Niraj kumar (Sun May 22 2011 - 20:29:53 CDT)
- questions about the heat diffusion calculation in the tutorial charlie (Sun May 22 2011 - 11:57:56 CDT)
- dcd files Molecular Dynamics (Sun May 22 2011 - 08:02:48 CDT)
- error in the orientationAngle Prathit Chatterjee (Sat May 21 2011 - 03:51:10 CDT)
- SMD of three atom at a time snoze pa (Fri May 20 2011 - 11:32:03 CDT)
- Re: simulation box PAUL NEWMAN (Fri May 20 2011 - 11:11:52 CDT)
- simulation box PAUL NEWMAN (Fri May 20 2011 - 10:39:48 CDT)
- NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ (Fri May 20 2011 - 05:16:30 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ (Fri May 20 2011 - 05:25:31 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Fri May 20 2011 - 08:45:46 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ (Tue May 24 2011 - 07:25:25 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Thu May 26 2011 - 09:12:02 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Fri May 20 2011 - 17:06:32 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ (Fri May 20 2011 - 05:25:31 CDT)
- My benchmark results with TeslaC2050 Norman Geist (Fri May 20 2011 - 01:02:36 CDT)
- Minimisation algorithm Christian Jorgensen (Thu May 19 2011 - 18:31:03 CDT)
- NAMD 2.8b3 released Jim Phillips (Thu May 19 2011 - 16:28:04 CDT)
- Build .pdb and .psf after coarse graining results in errors Edroaldo Lummertz da Rocha (Thu May 19 2011 - 13:37:15 CDT)
- last frame and restart are different Francesco Oteri (Thu May 19 2011 - 11:12:22 CDT)
- unsubscribe Cole Gleason (Thu May 19 2011 - 09:37:36 CDT)
- Typo in NAMD 2.8b2 output for Accelerated MD Bjoern Olausson (Thu May 19 2011 - 07:25:51 CDT)
- AW: AW: Automatic GPU selection in NAMD ? Norman Geist (Thu May 19 2011 - 01:41:37 CDT)
- Is there any difference between SMD and tclForces? Jun Zhang (Wed May 18 2011 - 20:29:07 CDT)
- RE: CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 05:55:59 CDT)
- CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 05:03:17 CDT)
- hi kanchi subbarao rao (Wed May 18 2011 - 03:43:25 CDT)
- question about wrap atoms to its original coordinates jnsong (Wed May 18 2011 - 00:06:20 CDT)
- Umbrella Sampling Buddhadev Maiti (Tue May 17 2011 - 21:52:38 CDT)
- trajectory_path.tcl Jacopo Sgrignani (Tue May 17 2011 - 09:16:47 CDT)
- Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 06:17:43 CDT)
- Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 04:58:56 CDT)
- RE: Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 05:05:27 CDT)
- Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 05:34:21 CDT)
- RE: Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 05:41:03 CDT)
- Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 06:02:29 CDT)
- Re: Automatic GPU selection in NAMD ? Axel Kohlmeyer (Tue May 17 2011 - 07:19:44 CDT)
- Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 09:35:57 CDT)
- AW: Automatic GPU selection in NAMD ? Norman Geist (Wed May 18 2011 - 00:24:45 CDT)
- Re: Automatic GPU selection in NAMD ? Jim Phillips (Wed May 18 2011 - 13:22:57 CDT)
- Re: Automatic GPU selection in NAMD ? David McGiven (Thu May 19 2011 - 04:42:39 CDT)
- Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 05:34:21 CDT)
- RE: Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 05:05:27 CDT)
- GPU-CPU small-scale machine for NAMD Francesco Pietra (Mon May 16 2011 - 03:45:37 CDT)
- deca-Ala simulations with different cutoff produce different results Jun Zhang (Mon May 16 2011 - 00:48:36 CDT)
- (no subject) Chandra Ramananjara (Sun May 15 2011 - 12:32:07 CDT)
- NAMD question snoze pa (Fri May 13 2011 - 16:34:16 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Fri May 13 2011 - 13:10:46 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Fri May 13 2011 - 14:52:53 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 04:02:51 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 13:45:14 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Tue May 17 2011 - 13:21:49 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Wed May 18 2011 - 08:44:48 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Wed May 18 2011 - 17:58:16 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Thu May 19 2011 - 04:00:33 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Tue May 17 2011 - 13:21:49 CDT)
- REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 07:58:45 CDT)
- PhD position in Computational Structural Biology at MPI Muenster Vlad Cojocaru (Fri May 13 2011 - 04:47:24 CDT)
- parameter for TFA (trifluoroacetic acid) liupeng012_at_mail.nankai.edu.cn (Fri May 13 2011 - 03:36:55 CDT)
- (no subject) Chandra Ramananjara (Thu May 12 2011 - 19:58:21 CDT)
- NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Thu May 12 2011 - 17:20:09 CDT)
- Error when run Replica Exchange Method on Ranger Guoxiong Su (Thu May 12 2011 - 14:13:59 CDT)
- FATAL error when run Replica Exchange Method on Franklin Guoxiong Su (Thu May 12 2011 - 14:03:58 CDT)
- CUDA limitations Ajasja LjubetiÄ (Thu May 12 2011 - 03:07:02 CDT)
- NAMD 2.8b2 released Jim Phillips (Wed May 11 2011 - 17:15:43 CDT)
- Re: NAMDEnergy Plugin - setting PMEGridSize / mesh density Michael S. Sellers (Cont, ARL/WMRD) (Wed May 11 2011 - 15:29:25 CDT)
- NAMDEnergy Plugin - setting PMEGridSize / mesh density Lela Vukovic (Wed May 11 2011 - 14:48:51 CDT)
- Corrupt dcd files Marc Baaden (Wed May 11 2011 - 11:15:55 CDT)
- what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Arun Kumar Subramanian (Sat May 07 2011 - 21:20:29 CDT)
- Namdstats.tcl flavio seixas (Tue May 10 2011 - 14:51:13 CDT)
- print center of mass Jacopo Sgrignani (Tue May 10 2011 - 10:54:09 CDT)
- force field for 2-methyl-2,4-pentanediol (MPD) Yang Gao (Tue May 10 2011 - 10:40:40 CDT)
- A newer version of win32 libraries Ajasja LjubetiÄ (Mon May 09 2011 - 07:35:47 CDT)
- large load rate using implicit solvent charlie (Sun May 08 2011 - 20:45:10 CDT)
- (no subject) Chandra Ramananjara (Sun May 08 2011 - 09:37:04 CDT)
- ABF atom selection Parisa Akhski (Sat May 07 2011 - 18:14:24 CDT)
- (no subject) Chandra Ramananjara (Sat May 07 2011 - 14:00:37 CDT)
- Re: compilation of namd johan strumpfer (Fri May 06 2011 - 09:09:35 CDT)
- Q=AD=94=E5=A4=8D:__compilation_of_namd?= TAO WANG (Sun May 08 2011 - 19:34:03 CDT)
- Q=AD=94=E5=A4=8D:__compilation_of_namd?= TAO WANG (Mon May 09 2011 - 01:27:12 CDT)
- unsubscribe Gary M. Skinner (Mon May 09 2011 - 03:31:45 CDT)
- Re: Q=AD=94=E5=A4=8D:__compilation_of_namd?= Jim Phillips (Tue May 10 2011 - 20:32:27 CDT)
- Q=AD=94=E5=A4=8D:_=E7=AD=94=E5=A4=8D:__compilation_of_n?= amd TAO WANG (Tue May 10 2011 - 20:42:49 CDT)
- Re: ç”å¤: compilation of namd Axel Kohlmeyer (Tue May 10 2011 - 22:14:26 CDT)
- Re: Re: ç”å¤: compilation of namd Jim Phillips (Wed May 11 2011 - 10:53:59 CDT)
- Re: Re: ç”å¤: compilation of namd Axel Kohlmeyer (Wed May 11 2011 - 11:16:29 CDT)
- Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 02:45:49 CDT)
- Re: Re: ç”å¤: compilation of namd Axel Kohlmeyer (Thu May 12 2011 - 04:53:58 CDT)
- Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 08:11:57 CDT)
- Re: Re: ç”å¤: compilation of namd Axel Kohlmeyer (Thu May 12 2011 - 08:34:14 CDT)
- Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 09:58:47 CDT)
- Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 11:13:21 CDT)
- Re: Re: Re: ç”å¤: compilation of namd Jim Phillips (Thu May 12 2011 - 12:32:28 CDT)
- REMD across gpus Massimiliano Porrini (Fri May 06 2011 - 07:39:56 CDT)
- AW: AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 01:36:20 CDT)
- ABF atom selection question Parisa Akhski (Thu May 05 2011 - 21:50:00 CDT)
- compilation of namd TAO WANG (Thu May 05 2011 - 21:08:37 CDT)
- msd calculation for lipid bilayers cnu gromacs (Thu May 05 2011 - 14:22:24 CDT)
- Running NAMD parallel on two machines with 3 CUDAs Darko Stefanovski (Thu May 05 2011 - 11:53:40 CDT)
- AMD Multicore + CUDA Benchmarks, are them ok ? David McGiven (Thu May 05 2011 - 04:08:30 CDT)
- alpha pmf Prathit Chatterjee (Wed May 04 2011 - 00:55:40 CDT)
- Re: alpha pmf felmerino_at_uchile.cl (Wed May 04 2011 - 02:37:06 CDT)
- Re: alpha pmf Ajasja LjubetiÄ (Wed May 04 2011 - 03:04:14 CDT)
- Re: alpha pmf Jérôme Hénin (Wed May 04 2011 - 04:17:16 CDT)
- Re: alpha pmf Prathit Chatterjee (Thu May 05 2011 - 01:21:02 CDT)
- Re: alpha pmf Giacomo Fiorin (Thu May 05 2011 - 09:31:51 CDT)
- Re: alpha pmf Prathit Chatterjee (Fri May 06 2011 - 05:54:55 CDT)
- Re: alpha pmf Jérôme Hénin (Fri May 06 2011 - 07:58:37 CDT)
- Re: alpha pmf Prathit Chatterjee (Sat May 07 2011 - 00:33:28 CDT)
- Re: alpha pmf Giacomo Fiorin (Mon May 09 2011 - 16:05:19 CDT)
- Re: alpha pmf Jérôme Hénin (Tue May 10 2011 - 03:37:24 CDT)
- Re: alpha pmf Ajasja LjubetiÄ (Wed May 04 2011 - 03:04:14 CDT)
- Re: alpha pmf felmerino_at_uchile.cl (Wed May 04 2011 - 02:37:06 CDT)
- (no subject) Nicolas Sapay (Tue May 03 2011 - 11:51:42 CDT)
- run tests with CUDA Massimiliano Porrini (Mon May 02 2011 - 16:25:17 CDT)
- implicit solvent and cuda Francesco Oteri (Mon May 02 2011 - 16:03:15 CDT)
- Forcefield for simulating peptide with heparin!!!! Aditya Ranganathan (Mon May 02 2011 - 07:24:56 CDT)
- WG: Abnormal EOF Error in Extra Bonds File Norman Geist (Mon May 02 2011 - 06:48:41 CDT)
- NAMD_2.7_AIX-POWER-MPI Buddhadev Maiti (Sun May 01 2011 - 21:28:41 CDT)
- Add bonds and topology file problem Edroaldo Lummertz da Rocha (Sun May 01 2011 - 16:57:16 CDT)
- Add bonds and topology file problem Edroaldo Lummertz da Rocha (Sun May 01 2011 - 15:20:01 CDT)
- non-bonded potential in NAMD Molecular Dynamics (Sat Apr 30 2011 - 15:06:58 CDT)
- colvars orientation problem appears in 2.8 only? JC Gumbart (Thu Apr 28 2011 - 18:41:17 CDT)
- ERROR: CUDA-enabled NAMD requires at least one patch per process Arash Azari (Wed Apr 27 2011 - 23:49:56 CDT)
- question about rotation force in SMD jnsong (Wed Apr 27 2011 - 09:34:09 CDT)
- freeEnergy parsing error Lada Biedermannová (Wed Apr 27 2011 - 09:08:46 CDT)
- how to apply different temperature simultaneously to different atoms in the same system charlie (Wed Apr 27 2011 - 02:41:08 CDT)
- A namd2.8b1 bug ? charlie (Wed Apr 27 2011 - 02:23:56 CDT)
- modify NAMD code for Lee-Edwards boundary conditions and compute stress tensor Van Ngo (Tue Apr 26 2011 - 19:17:47 CDT)
- Abnormal EOF Error in Extra Bonds File Eli Fine (Tue Apr 26 2011 - 14:22:11 CDT)
- Coarse Graining problem resolved Stefan Franzen (Tue Apr 26 2011 - 05:32:21 CDT)
- Coarse Graining setup question Stefan Franzen (Tue Apr 26 2011 - 05:13:23 CDT)
- CG parameterization problem Stefan Franzen (Tue Apr 26 2011 - 05:07:32 CDT)
- velocity error during steered MD Markus K. Dahlgren (Tue Apr 26 2011 - 09:08:32 CDT)
- ABF calculation using RMSD Buddhadev Maiti (Mon Apr 25 2011 - 22:14:39 CDT)
- Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Mon Apr 25 2011 - 13:14:22 CDT)
- 'cutting' colvars.traj file Branko (Sat Apr 23 2011 - 12:28:58 CDT)
- FATAL ERROR: Bad global angle count! PAUL NEWMAN (Fri Apr 22 2011 - 19:42:02 CDT)
- pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 14:03:29 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Fri Apr 22 2011 - 22:21:56 CDT)
- RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 22:52:11 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Sat Apr 23 2011 - 03:37:20 CDT)
- RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Sun Apr 24 2011 - 12:51:16 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Sun Apr 24 2011 - 13:00:10 CDT)
- RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Sun Apr 24 2011 - 14:44:06 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Sun Apr 24 2011 - 14:53:20 CDT)
- RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Sun Apr 24 2011 - 19:38:43 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Mon Apr 25 2011 - 09:22:29 CDT)
- RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 22:52:11 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Fri Apr 22 2011 - 22:21:56 CDT)
- question on modifyAppliedForces() Bennion, Brian (Fri Apr 22 2011 - 12:11:27 CDT)
- Can I set a range to limit the ABF Shen, Han (Wed Apr 20 2011 - 10:24:46 CDT)
- infrequent rattle failure with charmm36 Edward Lyman (Wed Apr 20 2011 - 08:47:59 CDT)
- new error in NAMD2.8b1 with fixedAtoms dklose_at_uni-osnabrueck.de (Tue Apr 19 2011 - 11:45:25 CDT)
- ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue Apr 19 2011 - 10:55:57 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue Apr 19 2011 - 11:05:09 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Tue Apr 19 2011 - 11:41:55 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue Apr 19 2011 - 12:05:23 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja Ljubetiè (Tue Apr 19 2011 - 12:43:12 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja Ljubetiè (Wed Apr 20 2011 - 09:22:21 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Wed Apr 20 2011 - 11:22:37 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Thu Apr 21 2011 - 06:30:47 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu Apr 21 2011 - 09:43:21 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Fri Apr 22 2011 - 03:34:29 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Fri Apr 22 2011 - 09:27:24 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Fri Apr 22 2011 - 15:38:07 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue May 03 2011 - 08:11:26 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Tue May 03 2011 - 10:23:17 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue May 03 2011 - 11:02:12 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Wed May 04 2011 - 06:31:58 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Thu May 05 2011 - 03:38:16 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 05 2011 - 10:23:23 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Thu May 05 2011 - 15:50:34 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Thu May 05 2011 - 16:22:09 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 05 2011 - 17:02:56 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Thu May 12 2011 - 03:55:03 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 12 2011 - 04:36:20 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Tue Apr 19 2011 - 11:41:55 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue Apr 19 2011 - 11:05:09 CDT)
- Reduce the frequency of load balancer output Ajasja LjubetiÄ (Tue Apr 19 2011 - 09:23:04 CDT)
- Does GB Implicit Solvent handle explicit ions? David Tanner (Sun Apr 17 2011 - 06:39:19 CDT)
- SMD for two steered directions 常姗燕 (Sun Apr 17 2011 - 09:51:12 CDT)
- question on the center of mass calculation in colvar Hyonseok Hwang (Sat Apr 16 2011 - 09:57:16 CDT)
- topology and parameter files Molecular Dynamics (Sat Apr 16 2011 - 07:13:28 CDT)
- NAMDenergy calculations for nucleic acid systems mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 03:22:37 CDT)
- NAMD cell dimension increasing in Z direction, problem with periodic cell snoze pa (Fri Apr 15 2011 - 13:23:53 CDT)
- Oh dear, 'namd2 invoked oom-killer' ... Nicholas M Glykos (Fri Apr 15 2011 - 09:55:35 CDT)
- Error: keyword "group1" is not supported, or not recognized in this context. Shen, Han (Fri Apr 15 2011 - 09:14:11 CDT)
- Replica Exchange alamng_at_uci.edu (Fri Apr 15 2011 - 04:35:47 CDT)
- GeForce vs Tesla GPUs for high performance computing Salvador H-V (Thu Apr 14 2011 - 13:58:30 CDT)
- problem in restarting ipsita basu (Thu Apr 14 2011 - 02:11:24 CDT)
- fixing group of atoms, Proper for manipualation M Mahjour (Wed Apr 13 2011 - 17:06:43 CDT)
- NAMD feture request Ajasja LjubetiÄ (Wed Apr 13 2011 - 09:46:07 CDT)
- Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) Burgess, Don E (Wed Apr 13 2011 - 08:21:15 CDT)
- about rigid bonds oguz gurbulak (Wed Apr 13 2011 - 03:39:34 CDT)
- problem for simulation of membrane protein system Buddhadev Maiti (Tue Apr 12 2011 - 11:06:30 CDT)
- Re: Replica Exchange Simulations on Blue Gene/P Dong Luo (Tue Apr 12 2011 - 09:54:31 CDT)
- Replica Exchange Simulations on Blue Gene/P Jan H. Meinke (Tue Apr 12 2011 - 07:09:32 CDT)
- QM/MM QFrank_X=2E_V=E1zquez=22?= (Mon Apr 11 2011 - 18:23:26 CDT)
- (no subject) Buddhadev Maiti (Mon Apr 11 2011 - 14:27:13 CDT)
- vmd-l: ParseFEP output errors Christian Jorgensen (Mon Apr 11 2011 - 11:27:08 CDT)
- dihedral rotation with ABF kakali sen (Sun Apr 10 2011 - 12:48:17 CDT)
- Help building a desktop for namd Salvador H-V (Sun Apr 10 2011 - 12:40:05 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Sun Apr 10 2011 - 12:52:59 CDT)
- Re: Help building a desktop for namd Salvador H-V (Mon Apr 11 2011 - 12:22:01 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 12:55:34 CDT)
- Re: Help building a desktop for namd Gianluca Interlandi (Mon Apr 11 2011 - 14:41:28 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 15:06:33 CDT)
- Re: Help building a desktop for namd Gianluca Interlandi (Mon Apr 11 2011 - 16:21:27 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 16:34:22 CDT)
- Re: Help building a desktop for namd Gianluca Interlandi (Mon Apr 11 2011 - 16:25:26 CDT)
- Re: Help building a desktop for namd Jim Phillips (Wed Apr 13 2011 - 10:17:27 CDT)
- Re: Help building a desktop for namd Salvador H-V (Wed Apr 13 2011 - 11:34:18 CDT)
- Re: Help building a desktop for namd Gianluca Interlandi (Wed Apr 13 2011 - 17:06:53 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Wed Apr 13 2011 - 17:22:03 CDT)
- Re: Help building a desktop for namd Jeffrey Potoff (Thu Apr 14 2011 - 00:07:16 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Thu Apr 14 2011 - 08:37:20 CDT)
- Re: Help building a desktop for namd Salvador H-V (Mon Apr 11 2011 - 12:22:01 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Sun Apr 10 2011 - 12:52:59 CDT)
- (no subject) Buddhadev Maiti (Fri Apr 08 2011 - 10:45:19 CDT)
- protein on solid surface Giovanni Bellesia (Fri Apr 08 2011 - 09:48:50 CDT)
- SMD simulation: stop applying force during simulation? THANH NGUYEN (Thu Apr 07 2011 - 22:05:35 CDT)
- Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:22:37 CDT)
- Re: Abe versus Lincoln johan strumpfer (Thu Apr 07 2011 - 13:40:13 CDT)
- Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 13:46:34 CDT)
- Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:57:41 CDT)
- Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 14:21:33 CDT)
- Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 15:40:11 CDT)
- Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 16:18:09 CDT)
- Re: Abe versus Lincoln johan strumpfer (Thu Apr 07 2011 - 16:23:16 CDT)
- Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 16:55:51 CDT)
- Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:50:45 CDT)
- Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 13:46:34 CDT)
- Re: Abe versus Lincoln johan strumpfer (Thu Apr 07 2011 - 13:40:13 CDT)
- Fwd: ramd seed Francesco Pietra (Thu Apr 07 2011 - 08:41:08 CDT)
- NVT setup for monolayer Bjoern Olausson (Thu Apr 07 2011 - 08:24:32 CDT)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Gary M. Skinner (Thu Apr 07 2011 - 07:17:14 CDT)
- multilevel summation in NAMD Francesco Oteri (Wed Apr 06 2011 - 17:32:49 CDT)
- FEP with flattened free energy surface? Ivan Vyalov (Wed Apr 06 2011 - 04:49:50 CDT)
- topology for monophosphate Irene Newhouse (Tue Apr 05 2011 - 15:25:52 CDT)
- NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Tue Apr 05 2011 - 13:51:55 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Wed Apr 06 2011 - 11:19:16 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Axel Kohlmeyer (Wed Apr 06 2011 - 12:06:41 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Wed Apr 06 2011 - 15:50:11 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Axel Kohlmeyer (Wed Apr 06 2011 - 16:22:48 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Jim Phillips (Wed Apr 06 2011 - 17:01:31 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Thu Apr 07 2011 - 09:06:03 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Axel Kohlmeyer (Wed Apr 06 2011 - 12:06:41 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Norman Geist (Fri Apr 15 2011 - 07:46:00 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Wed Apr 06 2011 - 11:19:16 CDT)
- NPT simulations in NAMD Hasan haska (Tue Apr 05 2011 - 07:31:52 CDT)
- NAMD for windows cannot run correctly according to namd tutorials sciencekey (Tue Apr 05 2011 - 04:00:11 CDT)
- Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 03:11:29 CDT)
- implicit solvent job error in NAMD2.8b1 harish vashisth (Mon Apr 04 2011 - 15:47:33 CDT)
- gromacs analysis tools Molecular Dynamics (Sun Apr 03 2011 - 04:33:14 CDT)
- gromacs analysis tools Molecular Dynamics (Sun Apr 03 2011 - 04:54:35 CDT)
- Why NAMD writes colvars step by step Leonardo Herrera (Fri Apr 01 2011 - 19:04:21 CDT)
- Why NAMD writes colvars step by step Leonardo Herrera (Fri Apr 01 2011 - 17:06:03 CDT)
- Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 12:32:35 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Axel Kohlmeyer (Fri Apr 01 2011 - 15:02:18 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 15:46:21 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Axel Kohlmeyer (Fri Apr 01 2011 - 16:10:00 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 16:27:08 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Jim Phillips (Wed Apr 06 2011 - 16:17:02 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 15:46:21 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Sergei (Tue Jun 19 2012 - 08:32:39 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Axel Kohlmeyer (Fri Apr 01 2011 - 15:02:18 CDT)
- set dummyAtom position changing christos.lamprakis_at_dcb.unibe.ch (Fri Apr 01 2011 - 09:44:39 CDT)
- Setting up aMD simulation of a membrane protein Raul Araya (Fri Apr 01 2011 - 09:05:32 CDT)
- New collective variable: biolRel Jérôme Hénin (Fri Apr 01 2011 - 09:01:53 CDT)
- Re: vmd-l: No probability distribution plot in ParseFEP liupeng012_at_mail.nankai.edu.cn (Thu Mar 31 2011 - 21:08:46 CDT)
- angles flavio seixas (Thu Mar 31 2011 - 15:57:33 CDT)
- Accelerated MD: question about dual boost mode patrick wintrode (Thu Mar 31 2011 - 15:01:49 CDT)
- vmd-l: No probability distribution plot in ParseFEP Christian Jorgensen (Thu Mar 31 2011 - 13:24:27 CDT)
- unsubscribe Chen, Zhihong (chenz2) (Thu Mar 31 2011 - 13:02:05 CDT)
- reassignFreq expression and relation with SMD Kang Hee Cho (Thu Mar 31 2011 - 10:56:47 CDT)
- Reverse Mapping of RBCG Model Sibel Cakan (Thu Mar 31 2011 - 06:20:08 CDT)
- Reverse Mapping of RBCG Model Sibel Cakan (Thu Mar 31 2011 - 03:51:57 CDT)
- NAMD_CVS_Source Leonardo Herrera (Wed Mar 30 2011 - 16:43:52 CDT)
- The biggest system simulated on one TESLA C2050 ? Marek Maly (Wed Mar 30 2011 - 13:30:11 CDT)
- Generalized Born implicit solvent model in 2.8b1 Enrico Guarnera (Wed Mar 30 2011 - 09:40:45 CDT)
- Switching function for cut-off method yandong Huang (Wed Mar 30 2011 - 08:54:09 CDT)
- Network version gives inconsistent wall clock timings yashodhan karandikar (Wed Mar 30 2011 - 08:39:15 CDT)
- Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 05:04:02 CDT)
- Re: Incompatibility between colvars and tclforces? Ajasja LjubetiÄ (Wed Mar 30 2011 - 06:21:23 CDT)
- Re: Incompatibility between colvars and tclforces? Jérôme Hénin (Wed Mar 30 2011 - 06:23:42 CDT)
- Re: Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 09:06:13 CDT)
- Re: Incompatibility between colvars and tclforces? Jérôme Hénin (Wed Mar 30 2011 - 10:23:45 CDT)
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- initial structures for md simulations oguz gurbulak (Wed Feb 16 2011 - 06:22:11 CST)
- Current status of polarizable force fields in NAMD lucie delemotte (Wed Feb 16 2011 - 04:37:03 CST)
- Setting Up A Langevin Buffer Region David Huggins (Wed Feb 16 2011 - 04:30:44 CST)
- Can I do protein-ligand docking using NAMD? Àî¼Ñ¼ü (Tue Feb 15 2011 - 23:32:03 CST)
- Computing several pair interactions Samy Hamdouche (Tue Feb 15 2011 - 18:11:25 CST)
- energy jump between minimization and simulation Eva Gonzalez Noya (Tue Feb 15 2011 - 18:06:25 CST)
- Re: energy jump between minimization and simulation Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:27:53 CST)
- Re: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 10:14:45 CST)
- RE: energy jump between minimization and simulation Bennion, Brian (Wed Feb 16 2011 - 10:58:33 CST)
- Re: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 13:15:01 CST)
- RE: NAMD-l: energy jump between minimization and simulation Bennion, Brian (Wed Feb 16 2011 - 13:48:34 CST)
- Re: RE: NAMD-l: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 16:37:09 CST)
- Re: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 10:14:45 CST)
- Re: energy jump between minimization and simulation Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:27:53 CST)
- energy jump running a simulation after minimization Eva Gonzalez Noya (Tue Feb 15 2011 - 17:23:07 CST)
- energy jump running a simulation after minimization Eva Gonzalez Noya (Tue Feb 15 2011 - 16:37:59 CST)
- Parameter in configuration NVE or NPT snoze pa (Tue Feb 15 2011 - 11:17:03 CST)
- problem with MD hamze rahimi (Tue Feb 15 2011 - 00:25:25 CST)
- Force constant for Umbrella Sampling Buddhadev Maiti (Mon Feb 14 2011 - 19:19:02 CST)
- ABF calculation using RMSD Buddhadev Maiti (Mon Feb 14 2011 - 19:08:32 CST)
- How to write gradual heating config files Cristina Rodríguez (Mon Feb 14 2011 - 19:08:07 CST)
- Re: Tetramer protein complex snoze pa (Mon Feb 14 2011 - 15:01:31 CST)
- NCS flavio seixas (Mon Feb 14 2011 - 14:09:35 CST)
- New colvar feature request -- angleXY Ajasja LjubetiÄ (Mon Feb 14 2011 - 07:19:46 CST)
- ABF reproducibility Parisa Akhski (Sun Feb 13 2011 - 15:08:26 CST)
- Tetramer protein complex snoze pa (Sun Feb 13 2011 - 00:54:34 CST)
- psfgen - any version capable of reading extended PSF files? Bjoern Olausson (Fri Feb 11 2011 - 05:47:05 CST)
- coarse-grained MD Demet Akten (Fri Feb 11 2011 - 03:34:56 CST)
- job termination ipsita basu (Fri Feb 11 2011 - 00:46:17 CST)
- PME for electrostatics and cutoff for vdW? Christian Jorgensen (Thu Feb 10 2011 - 11:07:53 CST)
- FEP - Protein binding to Membrane surface Bjoern Olausson (Thu Feb 10 2011 - 03:50:37 CST)
- Mirror Image Energy Discrepency Keith Battle (Wed Feb 09 2011 - 13:23:28 CST)
- I need help with this Richard Wood (Wed Feb 09 2011 - 13:01:25 CST)
- water box deformation ais_at_fh.huji.ac.il (Wed Feb 09 2011 - 09:47:27 CST)
- Abf force output stefhoor (Tue Feb 08 2011 - 20:58:39 CST)
- calculating energy term from extrabonds Segun Jung (Mon Feb 07 2011 - 23:50:43 CST)
- rescaling and reassignment parameter Kang Hee Cho (Mon Feb 07 2011 - 22:35:44 CST)
- calculating energy term from extrabonds Segun Jung (Mon Feb 07 2011 - 20:08:33 CST)
- Get number of timesteps from DCD via script Bjoern Olausson (Mon Feb 07 2011 - 06:52:39 CST)
- Re: Get number of timesteps from DCD via script Chris Harrison (Mon Feb 07 2011 - 12:34:25 CST)
- Re: Get number of timesteps from DCD via script Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
- Re: Get number of timesteps from DCD via script Andrew Emerson (Tue Feb 08 2011 - 08:00:07 CST)
- Re: Get number of timesteps from DCD via script Joshua D. Moore (Tue Feb 08 2011 - 17:01:32 CST)
- Re: Get number of timesteps from DCD via script Joshua D. Moore (Tue Feb 08 2011 - 16:56:02 CST)
- Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 06:37:20 CST)
- Re: Get number of timesteps from DCD via script Axel Kohlmeyer (Wed Feb 09 2011 - 07:43:17 CST)
- Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 08:32:13 CST)
- Re: Get number of timesteps from DCD via script Axel Kohlmeyer (Wed Feb 09 2011 - 08:43:21 CST)
- Re: Get number of timesteps from DCD via script Bjoern Olausson (Thu Feb 10 2011 - 03:52:44 CST)
- Re: Get number of timesteps from DCD via script Joshua D. Moore (Wed Feb 09 2011 - 06:41:06 CST)
- Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 08:05:42 CST)
- Re: Get number of timesteps from DCD via script Joshua D. Moore (Wed Feb 09 2011 - 08:40:27 CST)
- Re: Get number of timesteps from DCD via script Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
- Re: Get number of timesteps from DCD via script Chris Harrison (Mon Feb 07 2011 - 12:34:25 CST)
- Re: [ppl] NAMD at linux on sparc Phil Miller (Sun Feb 06 2011 - 21:18:32 CST)
- determining force constant in exterbonds (harmonic potential) Segun Jung (Sat Feb 05 2011 - 10:09:50 CST)
- SMD negative forces S Richmond (Fri Feb 04 2011 - 10:39:44 CST)
- charmm force field Swarna M Patra (Thu Feb 03 2011 - 21:55:22 CST)
- Strange (very large) atom motions Craig Jolley (Thu Feb 03 2011 - 17:14:42 CST)
- (no subject) Alexandra Nemkevich (Thu Feb 03 2011 - 04:30:50 CST)
- Proposed Feature in Targeted MD Ryan McGreevy (Wed Feb 02 2011 - 12:48:58 CST)
- ABF question (sampling and colvars output file) Parisa Akhski (Tue Feb 01 2011 - 10:27:43 CST)
- volume calculation Swarna M Patra (Tue Feb 01 2011 - 04:02:48 CST)
- unsubscribe Purushottam Dixit (Mon Jan 31 2011 - 20:59:01 CST)
- Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 13:12:38 CST)
- Problems compiling NAMD on 8-core Mac Minh, David D. (Mon Jan 31 2011 - 12:25:40 CST)
- Question regarding NAMD membrane tutorial snoze pa (Mon Jan 31 2011 - 10:49:07 CST)
- Help With colvars/abf Please Angelo Rossi (Sun Jan 30 2011 - 07:09:41 CST)
- Coarse_Graining tempetrature Sibel Cakan (Fri Jan 28 2011 - 09:12:43 CST)
- Coarse_Graining tempetrature Sibel Cakan (Fri Jan 28 2011 - 08:31:02 CST)
- CG_MD temperature Sibel Cakan (Fri Jan 28 2011 - 07:52:15 CST)
- topology for DNA Neelanjana Sengupta (Fri Jan 28 2011 - 06:28:03 CST)
- water content Kang Hee Cho (Thu Jan 27 2011 - 23:18:24 CST)
- bond lengths angles in namd oguz gurbulak (Thu Jan 27 2011 - 06:35:34 CST)
- Equilibration when splitting an ABF calculation Ajasja LjubetiÄ (Thu Jan 27 2011 - 06:25:04 CST)
- bond lengths angles in namd oguz gurbulak (Thu Jan 27 2011 - 05:43:09 CST)
- Cu+2 parameters jose correa (Wed Jan 26 2011 - 07:36:59 CST)
- the meaning and effect of reassignFreq and reassignTemp Kang Hee Cho (Tue Jan 25 2011 - 08:46:39 CST)
- mainboard-power source for GPU Francesco Pietra (Tue Jan 25 2011 - 01:47:42 CST)
- NBFIX support in CUDA NAMD Burgess, Don E (Mon Jan 24 2011 - 20:41:26 CST)
- REMD with IBM SP6 LoadLeveler Luca Bellucci (Sat Jan 22 2011 - 11:45:31 CST)
- distance calculation between atoms of two segments mjyang (Sat Jan 22 2011 - 10:51:00 CST)
- the meaning of reassignFreq and reassignTemp Kang Hee Cho (Sat Jan 22 2011 - 04:28:22 CST)
- Missing angle parameters NH1 CT1 NH1 Christian Jorgensen (Fri Jan 21 2011 - 04:39:07 CST)
- discrete energy value after restart Kang Hee Cho (Thu Jan 20 2011 - 21:25:46 CST)
- question from a tutorial Lisa Brown (Thu Jan 20 2011 - 14:17:29 CST)
- 4 x Opteron 12-core or 4 x Xeon 8-core ? David McGiven (Thu Jan 20 2011 - 05:59:13 CST)
- increasing MAX_EXCLUSIONS Francesco Oteri (Wed Jan 19 2011 - 16:07:05 CST)
- non-zero charge Kwee Hong (Wed Jan 19 2011 - 10:17:45 CST)
- peptide structure ipsita basu (Tue Jan 18 2011 - 23:05:34 CST)
- Various practical colvar module related questions Ajasja LjubetiÄ (Tue Jan 18 2011 - 11:31:46 CST)
- Protein-DNA simulations S.Archana (Mon Jan 17 2011 - 04:41:27 CST)
- NBFIX for carbonyl atoms and potassium ions -- User Defined Force -- CUDA Burgess, Don E (Mon Jan 17 2011 - 15:35:28 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:56:28 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Mon Jan 17 2011 - 11:44:24 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Tue Jan 18 2011 - 08:40:56 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Wed Jan 19 2011 - 06:53:41 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Wed Jan 19 2011 - 09:23:03 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Wed Jan 19 2011 - 10:01:42 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Thu Jan 20 2011 - 08:07:36 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Tue Jan 18 2011 - 08:40:56 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Mon Jan 17 2011 - 11:44:24 CST)
- Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:26:47 CST)
- Re: Feature request for the colvars module -- TCL syntax Jérôme Hénin (Mon Jan 17 2011 - 11:52:23 CST)
- Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Tue Jan 18 2011 - 07:17:54 CST)
- Re: Feature request for the colvars module -- TCL syntax Axel Kohlmeyer (Tue Jan 18 2011 - 09:09:54 CST)
- Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Tue Jan 18 2011 - 11:44:54 CST)
- Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Mon Jan 24 2011 - 08:16:01 CST)
- Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Tue Jan 18 2011 - 07:17:54 CST)
- Re: Feature request for the colvars module -- TCL syntax Chris Harrison (Mon Jan 17 2011 - 11:00:22 CST)
- Re: Feature request for the colvars module -- TCL syntax Jérôme Hénin (Mon Jan 17 2011 - 11:52:23 CST)
- temperature range for residue-based CG Demet Akten (Mon Jan 17 2011 - 08:02:59 CST)
- Membrane protein simulaton snoze pa (Fri Jan 14 2011 - 18:19:24 CST)
- NAMD CUDA error message snoze pa (Fri Jan 14 2011 - 11:37:54 CST)
- Can DCD trajectory files contain only protein but water surround yandong Huang (Thu Jan 13 2011 - 08:44:10 CST)
- Error on closing binary file Seren Soner (Thu Jan 13 2011 - 06:42:50 CST)
- Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 14:42:46 CST)
- Re: Constraint failure; simulation has become unstable Athanassios Stavrakoudis (Fri Jan 07 2011 - 15:04:08 CST)
- Re: Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 15:18:20 CST)
- Re: Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 15:25:23 CST)
- Re: Constraint failure; simulation has become unstable Joshua Adelman (Fri Jan 07 2011 - 18:18:05 CST)
- Re: Constraint failure; simulation has become unstable Wendy González (Sat Jan 08 2011 - 07:53:11 CST)
- Re: Constraint failure; simulation has become unstable Athanassios Stavrakoudis (Sat Jan 08 2011 - 08:05:15 CST)
- Re: Constraint failure; simulation has become unstable Wendy González (Sat Jan 08 2011 - 08:29:37 CST)
- Re: Constraint failure; simulation has become unstable Axel Kohlmeyer (Mon Jan 10 2011 - 08:49:07 CST)
- Re: Constraint failure; simulation has become unstable Joshua Adelman (Sat Jan 08 2011 - 09:49:18 CST)
- Re: Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 15:18:20 CST)
- Re: Constraint failure; simulation has become unstable Athanassios Stavrakoudis (Fri Jan 07 2011 - 15:04:08 CST)
- NAMD initial coordinate file Ismail, Mohd F. (Fri Jan 07 2011 - 00:10:47 CST)
- Compiling NAMD 2.7 with the PLUMED patch Gianluca Interlandi (Thu Jan 06 2011 - 16:55:03 CST)
- Fix atoms-Colvars Alex Liu (Thu Jan 06 2011 - 15:46:14 CST)
- NAMD Tutorial Problem Jane Ren (Thu Jan 06 2011 - 13:19:50 CST)
- water sphere sara (Thu Jan 06 2011 - 03:14:01 CST)
- (no subject) Chen, Zhihong (chenz2) (Wed Jan 05 2011 - 18:43:15 CST)
- Benchmark for NAMD2.7 (curent version) Branko (Wed Jan 05 2011 - 14:19:19 CST)
- unsubcribe Charlie Forde (Wed Jan 05 2011 - 10:49:54 CST)
- Distance XY-colvars Alex Liu (Tue Jan 04 2011 - 15:56:56 CST)
- NAG simulation problem with CPS Adrian Jasiñski (Wed Jan 05 2011 - 05:36:00 CST)
- free energy perturbation BIN ZHANG (Wed Jan 05 2011 - 02:07:57 CST)
- restart problem charlie (Wed Jan 05 2011 - 02:07:48 CST)
- parameter file for DMPC lipid and protein system but with CHARMM36 lipids Erica Smith (Mon Jan 03 2011 - 21:53:59 CST)
- .colvars.state file in ABF Alex Liu (Mon Jan 03 2011 - 15:53:45 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Sat Jan 01 2011 - 15:48:06 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ (Sun Jan 02 2011 - 15:03:48 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Giacomo Fiorin (Mon Jan 03 2011 - 18:13:21 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ (Fri Jan 14 2011 - 09:31:49 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Fri Jan 14 2011 - 10:37:17 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ (Mon Jan 17 2011 - 08:40:11 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Mon Jan 17 2011 - 10:35:20 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Giacomo Fiorin (Mon Jan 03 2011 - 18:13:21 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ (Sun Jan 02 2011 - 15:03:48 CST)
- concatenate pmf files in colvars Parisa Akhski (Sat Jan 01 2011 - 12:23:06 CST)
Last message date: Mon Dec 31 2012 - 14:36:03 CST
Archived on: Mon Dec 31 2012 - 23:22:24 CST
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