NAMD-L: By Thread
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About this archive
Starting: Fri Jan 03 2020 - 07:25:25 CST
Ending: Thu Dec 30 2021 - 09:20:14 CST
- Angle parameter errors Pradeepti Kampani (Thu Dec 30 2021 - 03:26:26 CST)
- membrane system displacing in z during ABF or metadynamics Yogesh Sharma (Tue Dec 28 2021 - 04:58:26 CST)
- simulation of protein DNA complex Dhiraj Srivastava (Mon Dec 27 2021 - 19:33:47 CST)
- Re: namd-l digest V1 #3189 Raman Preet Singh (Mon Dec 27 2021 - 07:08:59 CST)
- SMD at constant velocity Almeida-Hernández, Yasser, Dr. (Mon Dec 27 2021 - 04:45:32 CST)
- Question about CHARMM-GUI NAMD Inputs Ahmad Alqaisi (Sun Dec 26 2021 - 18:41:30 CST)
- Position restrain in ABF Yogesh Sharma (Thu Dec 23 2021 - 07:36:28 CST)
- Best performance multi node GPU Luis Cebamanos (Thu Dec 16 2021 - 09:05:56 CST)
- How to run on multi-node environment Luis Cebamanos (Wed Dec 22 2021 - 08:39:58 CST)
- Re: How to run on multi-node environment Vermaas, Josh (Wed Dec 22 2021 - 08:56:03 CST)
- Re: How to run on multi-node environment Luis Cebamanos (Wed Dec 22 2021 - 09:33:16 CST)
- Re: How to run on multi-node environment Axel Kohlmeyer (Wed Dec 22 2021 - 10:37:52 CST)
- Re: How to run on multi-node environment Giacomo Fiorin (Wed Dec 22 2021 - 11:03:32 CST)
- Re: How to run on multi-node environment Axel Kohlmeyer (Wed Dec 22 2021 - 11:28:05 CST)
- Re: How to run on multi-node environment Vermaas, Josh (Wed Dec 22 2021 - 08:56:03 CST)
- How to run on multi-node environment Luis Cebamanos (Wed Dec 22 2021 - 08:39:58 CST)
- tclForce not recognizing group option during cphmd job Diship Srivastava (Wed Dec 15 2021 - 23:42:58 CST)
- Lone pair forces Hsubo Luo (Wed Dec 15 2021 - 11:15:40 CST)
- SMD: Fixing centroid Moumita Saharay (Tue Dec 14 2021 - 04:18:10 CST)
- (no subject) Rakesh Roy (Mon Dec 13 2021 - 07:19:12 CST)
- Initial force for steered MD simulations Hannah Scott (Thu Dec 09 2021 - 14:42:28 CST)
- Problem with titration curve with cphanalyze script CYS and LYS (Constant pH Molecular Dynamics ) Ingrid Bernardes Santana Martins (Thu Dec 09 2021 - 07:00:17 CST)
- Error in running multiple-walkers metadynamics at Bluewaters Chen, Charles (Wed Dec 08 2021 - 18:29:27 CST)
- restarting eABF jobs Ashutosh Shandilya (Wed Dec 08 2021 - 16:50:03 CST)
- Namd can not find parameters for chlorine lonepairs DENILSON FERREIRA DE OLIVEIRA (Wed Dec 08 2021 - 07:38:24 CST)
- Extracting force on subset of atoms from tclForces Nate Walkins (Tue Dec 07 2021 - 04:07:11 CST)
- Dihedral parameters for terminal alkyne DENILSON FERREIRA DE OLIVEIRA (Sun Dec 05 2021 - 12:53:41 CST)
- eFieldNormalized Fateme Ghadirian (Sat Dec 04 2021 - 07:56:47 CST)
- setting the value of qmLinkElement in NAMD/QMMM script jing liang (Thu Dec 02 2021 - 03:23:24 CST)
- NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Vlad Cojocaru (Tue Nov 30 2021 - 04:30:35 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Axel Kohlmeyer (Tue Nov 30 2021 - 05:14:31 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Giacomo Fiorin (Tue Nov 30 2021 - 08:33:18 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Vlad Cojocaru (Tue Nov 30 2021 - 09:14:04 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Giacomo Fiorin (Tue Nov 30 2021 - 09:29:40 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Axel Kohlmeyer (Tue Nov 30 2021 - 09:50:28 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Vermaas, Josh (Tue Nov 30 2021 - 11:10:03 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree James M Davis (Tue Nov 30 2021 - 12:07:32 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree James M Davis (Tue Nov 30 2021 - 12:25:46 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree David Hardy (Mon Dec 06 2021 - 16:51:36 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Giacomo Fiorin (Tue Nov 30 2021 - 08:33:18 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Axel Kohlmeyer (Tue Nov 30 2021 - 05:14:31 CST)
- Re: vmd-l: basic procedure for ABF-PMF calculation JĂ©rĂ´me HĂ©nin (Mon Nov 29 2021 - 06:30:58 CST)
- FEP calculation for Binding of a potassium ion to 18Q=80=93crown=E2=80=936?= SYEDA SABIHA SULTANA LUBNA . (Thu Nov 25 2021 - 04:14:03 CST)
- residue_rmsd.tcl script Alexei Rossokhin (Thu Nov 25 2021 - 02:15:39 CST)
- QMMM convergence/optimization issues in CHCL3 solvent Francesco Pietra (Tue Nov 23 2021 - 10:26:50 CST)
- HarmonicWall colvar ROPĂ“N-PALACIOS G. (Mon Nov 22 2021 - 12:25:57 CST)
- eFieldNormalized Fateme Ghadirian (Sat Nov 20 2021 - 10:26:31 CST)
- applying harmonic constraints in cphmd Diship Srivastava (Fri Nov 19 2021 - 23:29:34 CST)
- colvars.traj file empty Ashutosh Shandilya (Thu Nov 18 2021 - 19:40:50 CST)
- namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 02:27:31 CST)
- Re: namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 04:02:10 CST)
- Re: namd minimization looking for wrong angle Peter Freddolino (Thu Nov 18 2021 - 08:03:40 CST)
- Re: vmd-l: Re: namd minimization looking for wrong angle Francesco Pietra (Fri Nov 19 2021 - 03:32:39 CST)
- Re: vmd-l: Re: namd minimization looking for wrong angle Peter Freddolino (Fri Nov 19 2021 - 07:56:58 CST)
- Re: vmd-l: Re: namd minimization looking for wrong angle Francesco Pietra (Fri Nov 19 2021 - 10:55:59 CST)
- Re: vmd-l: Re: namd minimization looking for wrong angle Peter Freddolino (Fri Nov 19 2021 - 11:02:59 CST)
- Re: vmd-l: Re: namd minimization looking for wrong angle Francesco Pietra (Fri Nov 19 2021 - 15:15:00 CST)
- Re: namd minimization looking for wrong angle Peter Freddolino (Thu Nov 18 2021 - 08:03:40 CST)
- Re: namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 04:02:10 CST)
- colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 09:58:33 CST)
- Re: colvars: Too many iterations in routine jacobi. Giacomo Fiorin (Wed Nov 17 2021 - 10:27:39 CST)
- Re: colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 11:51:32 CST)
- Re: colvars: Too many iterations in routine jacobi. Giacomo Fiorin (Wed Nov 17 2021 - 12:31:47 CST)
- Re: colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 13:08:38 CST)
- Re: colvars: Too many iterations in routine jacobi. Giacomo Fiorin (Wed Nov 17 2021 - 13:42:14 CST)
- Re: colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 11:51:32 CST)
- Re: colvars: Too many iterations in routine jacobi. Giacomo Fiorin (Wed Nov 17 2021 - 10:27:39 CST)
- User defined signal 2 ERROR: One or more process (first noticed rank 7) terminated with signal 12 Ashutosh Shandilya (Wed Nov 17 2021 - 09:09:07 CST)
- QMMM latency in PME correction Wall, Michael E (Tue Nov 16 2021 - 15:39:25 CST)
- Gallium parameters ROPĂ“N-PALACIOS G. (Tue Nov 16 2021 - 11:25:32 CST)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 辛志宏 (Fri Nov 12 2021 - 08:35:40 CST)
- Water molecules "flying away" in Gaussian calculation of "water int" step in FFTK Alexandre Suman de AraĂşjo (Wed Nov 10 2021 - 15:02:08 CST)
- Fujitsu A64FX CPU processor-suitable NAMD Nikhil Maroli (Wed Nov 10 2021 - 13:27:32 CST)
- Colvar Flat-bottom potential "distanceXY" ROPĂ“N-PALACIOS G. (Wed Nov 10 2021 - 12:59:45 CST)
- Protein simulations: why does the structure change so much? Francesco Coppola (Wed Nov 10 2021 - 10:25:47 CST)
- SMD for predetermined Umbrella sampling Windows HANNAH MARIE BURTON (Mon Nov 08 2021 - 22:17:55 CST)
- Why simulation running on linux is damn slow?? Amir Zeb (Mon Nov 08 2021 - 19:31:12 CST)
- Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies JĂ©rĂ´me HĂ©nin (Fri Nov 05 2021 - 11:12:18 CDT)
- REST2 soluteScalingFactor fluctuating between runs Ethan Croitoru (Tue Nov 02 2021 - 17:21:17 CDT)
- Error Tolerance David Tang (Mon Nov 01 2021 - 16:33:01 CDT)
- CONVERT PSF to TOP grimaces ROPĂ“N-PALACIOS G. (Sun Oct 31 2021 - 14:10:14 CDT)
- unable to run NAMD+ORCA on more than 1 cpu jing liang (Sat Oct 30 2021 - 13:09:24 CDT)
- Trouble in fep.tcl file for FEP run in NAMD SYEDA SABIHA SULTANA LUBNA . (Sat Oct 30 2021 - 02:02:39 CDT)
- Rattle algorithm failure while restarting metadynamics simulation Monika Kumari (Fri Oct 29 2021 - 09:40:13 CDT)
- RMSD and RMSF of ligand Only Mi Yang (Thu Oct 28 2021 - 04:48:37 CDT)
- Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Oct 27 2021 - 14:43:12 CDT)
- Re: Error: keyword "abf" found without configuration Michael Robinson (Wed Oct 27 2021 - 19:27:57 CDT)
- Re: Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Nov 10 2021 - 10:39:56 CST)
- Re: Error: keyword "abf" found without configuration Giacomo Fiorin (Wed Nov 10 2021 - 11:10:42 CST)
- Re: Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Nov 10 2021 - 13:23:58 CST)
- Re: Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Nov 10 2021 - 13:26:59 CST)
- Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame Ashutosh Shandilya (Thu Nov 11 2021 - 10:15:37 CST)
- Re: Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Nov 10 2021 - 10:39:56 CST)
- Re: Error: keyword "abf" found without configuration Michael Robinson (Wed Oct 27 2021 - 19:27:57 CDT)
- Script for contact Vs Freq Mi Yang (Thu Oct 21 2021 - 12:41:06 CDT)
- Re: vmd-l: Fwd: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Thu Oct 21 2021 - 04:15:56 CDT)
- NAMD3 information ROPĂ“N-PALACIOS G. (Mon Oct 18 2021 - 17:14:47 CDT)
- Addendum Francesco Pietra (Mon Oct 18 2021 - 15:03:31 CDT)
- Ewald for charged systems Dongyue Liang (Mon Oct 18 2021 - 12:55:27 CDT)
- impropers for protonated 1-methyladenosine Francesco Pietra (Mon Oct 18 2021 - 02:38:14 CDT)
- Re: impropers for protonated 1-methyladenosine Josh Vermaas (Mon Oct 18 2021 - 15:23:30 CDT)
- Re: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 02:32:21 CDT)
- Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 12:29:18 CDT)
- Re: Fwd: impropers for protonated 1-methyladenosine Josh Vermaas (Tue Oct 19 2021 - 13:03:04 CDT)
- Re: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 13:28:23 CDT)
- Fwd: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 13:34:23 CDT)
- Fwd: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 14:04:10 CDT)
- Re: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Wed Oct 20 2021 - 05:41:20 CDT)
- Re: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 02:32:21 CDT)
- Re: impropers for protonated 1-methyladenosine Josh Vermaas (Mon Oct 18 2021 - 15:23:30 CDT)
- Namd3 error message Maria Kontoyianni (Fri Oct 15 2021 - 12:12:36 CDT)
- Re: MD run terminated with singnal 11 Alessandro Ruda (Fri Oct 15 2021 - 07:04:30 CDT)
- Job stopped without any error message (probably a load balancing issue?) Haohao Fu (Fri Oct 15 2021 - 00:14:33 CDT)
- [containerising NAMD with Singularity] Maxim Abalenkov (Wed Oct 13 2021 - 04:28:36 CDT)
- MMPBSA standard deviation Nancy Singh (Mon Oct 11 2021 - 06:53:26 CDT)
- Query about post-process of DCD PREMANANDA BASAK (Thu Oct 07 2021 - 07:10:34 CDT)
- NAMD Cuda on more than one node Alexei Rossokhin (Wed Oct 06 2021 - 02:24:16 CDT)
- QM/MM biding free energy Mi Yang (Sun Oct 03 2021 - 09:58:44 CDT)
- how can email dcd files Asmi Mahmood (Sat Oct 02 2021 - 06:02:11 CDT)
- Salt bridge selection Vidhya Sankar (Fri Oct 01 2021 - 21:25:01 CDT)
- Re: Simulation Box Size & Simulation speed Fateme Ghadirian (Thu Sep 30 2021 - 16:40:12 CDT)
- Simulation Box Size & Simulation speed Fateme Ghadirian (Thu Sep 30 2021 - 11:15:00 CDT)
- ERROR: Atoms moving too fast; simulation has become unstable. Hasith Sathsindu (Wed Sep 29 2021 - 13:23:57 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:36:27 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:40:38 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:50:34 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:53:15 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:54:14 CDT)
- QM/MM live solvent selection - segmentation fault (with ORCA) Oleksii Zdorevskyi (Tue Sep 28 2021 - 10:39:18 CDT)
- Replica run of Constant pH MD Diship Srivastava (Tue Sep 28 2021 - 09:58:32 CDT)
- about compilation Vidhya Sankar (Tue Sep 28 2021 - 02:16:04 CDT)
- SMD in lipid Ishaan Roy (Fri Sep 24 2021 - 12:01:20 CDT)
- Metadynamics Farag Mosa (Thu Sep 23 2021 - 14:21:37 CDT)
- Switching from GPU to CPU: failing with too many CPUs? Smith, Harper E. (Thu Sep 23 2021 - 10:41:47 CDT)
- performance scaling of CUDA accelerated NAMD over multiple nodes Vlad Cojocaru (Fri Sep 17 2021 - 05:11:56 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vermaas, Josh (Fri Sep 17 2021 - 07:31:45 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vlad Cojocaru (Fri Sep 17 2021 - 08:05:40 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Giacomo Fiorin (Fri Sep 17 2021 - 08:41:15 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vlad Cojocaru (Sat Sep 18 2021 - 07:00:44 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Giacomo Fiorin (Sat Sep 18 2021 - 10:52:51 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vlad Cojocaru (Fri Sep 17 2021 - 08:05:40 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vermaas, Josh (Fri Sep 17 2021 - 07:31:45 CDT)
- vdW for atom NRN1 Francesco Pietra (Tue Sep 14 2021 - 08:28:38 CDT)
- MMPBSA calculation using CAFE plugin vmd Nancy Singh (Tue Sep 14 2021 - 06:27:32 CDT)
- Problem with speed of QMMM (namd2-ORCA) Herald Delis (Thu Sep 09 2021 - 05:51:14 CDT)
- Patch for non protonated lysine Francesco Pietra (Wed Sep 08 2021 - 04:19:49 CDT)
- Re: namd-l digest V1 #3135 Venkatareddy Dadireddy (Wed Sep 08 2021 - 02:48:33 CDT)
- Merge ABF windows SĂ©bastien Hoyas (Wed Sep 08 2021 - 01:53:43 CDT)
- GaMD is slower on GPU compared to cMD Venkatareddy Dadireddy (Mon Sep 06 2021 - 11:15:00 CDT)
- Re: Assunto: Re: Binary coordinates NAMD 2.14 Vermaas, Josh (Fri Sep 03 2021 - 19:05:43 CDT)
- Binary coordinates NAMD 2.14 oivalf_nix_at_yahoo.com (Fri Sep 03 2021 - 14:05:39 CDT)
- (no subject) Krithika Unmesh (Thu Sep 02 2021 - 09:40:41 CDT)
- Re: Problem with running replica-exchange umbrella sampling of polarizable system zeynab hosseini (Thu Sep 02 2021 - 02:12:43 CDT)
- Modifying a DRUDE pdb file and producing a new psf file HANNAH MARIE BURTON (Wed Sep 01 2021 - 11:25:17 CDT)
- Problem with running replica-exchange umbrella sampling of polarizable system zeynab hosseini (Wed Sep 01 2021 - 05:20:30 CDT)
- Free energy calculations Nancy Singh (Mon Aug 30 2021 - 08:59:47 CDT)
- Unrealistically High Keq in eABF Seperation Ishaan Roy (Tue Aug 24 2021 - 17:23:39 CDT)
- Asymmetric concentration gradient Ropon-Palacios G. (Mon Aug 23 2021 - 21:08:16 CDT)
- Re: Asymmetric concentration gradient Gumbart, JC (Mon Aug 23 2021 - 23:05:19 CDT)
- Re: Asymmetric concentration gradient Ropon-Palacios G. (Mon Aug 23 2021 - 23:10:52 CDT)
- Re: Asymmetric concentration gradient Gumbart, JC (Tue Aug 24 2021 - 00:11:42 CDT)
- Re: Asymmetric concentration gradient Ropon-Palacios G. (Tue Aug 24 2021 - 10:59:07 CDT)
- Re: Asymmetric concentration gradient Gumbart, JC (Tue Aug 24 2021 - 17:34:23 CDT)
- Re: Asymmetric concentration gradient Ropon-Palacios G. (Tue Aug 24 2021 - 19:45:27 CDT)
- Re: Asymmetric concentration gradient Mohammad Mehdi Pirnia (Tue Aug 24 2021 - 03:25:50 CDT)
- Re: Asymmetric concentration gradient Ropon-Palacios G. (Mon Aug 23 2021 - 23:10:52 CDT)
- Re: Asymmetric concentration gradient Gumbart, JC (Mon Aug 23 2021 - 23:05:19 CDT)
- sphingosine topology and parameter files Capponi, Sara (Mon Aug 23 2021 - 12:22:20 CDT)
- psfgen problem for membrane, LPSA and bacterial lipids Mohammad Mehdi Pirnia (Sat Aug 21 2021 - 19:43:21 CDT)
- eABF Improper Protein Seperation Ishaan Roy (Tue Aug 17 2021 - 15:40:56 CDT)
- eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling René Hafner TUK (Sat Aug 14 2021 - 10:22:37 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling Giacomo Fiorin (Sat Aug 14 2021 - 12:17:53 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling René Hafner TUK (Sat Aug 14 2021 - 12:28:46 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling JĂ©rĂ´me HĂ©nin (Thu Aug 26 2021 - 07:01:19 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling René Hafner TUK (Thu Aug 26 2021 - 13:52:19 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling JĂ©rĂ´me HĂ©nin (Fri Aug 27 2021 - 07:05:16 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling René Hafner TUK (Fri Aug 27 2021 - 08:47:26 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling René Hafner TUK (Sat Aug 14 2021 - 12:28:46 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling Giacomo Fiorin (Sat Aug 14 2021 - 12:17:53 CDT)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 zeynab hosseini (Fri Aug 13 2021 - 03:26:03 CDT)
- Problem in running constant pH NAMD job Diship Srivastava (Wed Aug 11 2021 - 11:02:32 CDT)
- MD simulation Ruturaj warake (Sun Aug 08 2021 - 02:12:11 CDT)
- Compiling issue: selfcompiled NAMD2.14 multicore version factor ~2x slower René Hafner TUK (Sat Aug 07 2021 - 14:16:44 CDT)
- Lowe-Andersen Thermostat default damping value René Hafner TUK (Wed Aug 04 2021 - 14:27:36 CDT)
- Numsteps or Runs? Ruturaj warake (Wed Aug 04 2021 - 10:51:48 CDT)
- FATAL ERROR: UNABLE TO FIND BOND PARAMETERS samaneh ghanbari (Tue Aug 03 2021 - 09:05:36 CDT)
- Running NAMD 3.0 Ruturaj warake (Tue Aug 03 2021 - 04:46:14 CDT)
- constant pH with NAMD3 Jeff Comer (Mon Aug 02 2021 - 22:36:19 CDT)
- Reducing the system size Ruturaj warake (Mon Aug 02 2021 - 09:59:32 CDT)
- Mail About error in CV Vidhya Sankar (Mon Aug 02 2021 - 03:31:16 CDT)
- Problem with creating Drude-compatible .psf file for amino acid zeynab hosseini (Fri Jul 30 2021 - 07:05:13 CDT)
- Fatal Error: Error in the configuration file Amir Zeb (Fri Jul 30 2021 - 01:06:18 CDT)
- mail about error in namd configuration file Vidhya Sankar (Thu Jul 29 2021 - 07:50:15 CDT)
- about usage of eABF method Vidhya Sankar (Thu Jul 29 2021 - 04:10:52 CDT)
- NUMA Node and CUDA GPU Acceleration Gawtak Kim (Thu Jul 29 2021 - 02:23:09 CDT)
- Mail about path CV Vidhya Sankar (Wed Jul 28 2021 - 05:09:19 CDT)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER samaneh ghanbari (Tue Jul 27 2021 - 23:03:37 CDT)
- MMGBSA binding free energy by MolAICal and NAMD molaical (Tue Jul 27 2021 - 12:20:38 CDT)
- Query in running NAMD Ruturaj warake (Mon Jul 26 2021 - 11:27:59 CDT)
- Error in running simulation Ruturaj warake (Mon Jul 26 2021 - 08:29:30 CDT)
- Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? zeynab hosseini (Sun Jul 25 2021 - 14:07:42 CDT)
- namd-I: Request for help in error fixing Dr. Anupama Tiwari (Sun Jul 25 2021 - 09:07:10 CDT)
- About Meta dynamics Vidhya Sankar (Thu Jul 22 2021 - 08:18:34 CDT)
- Request for help on error fixing Amir Zeb (Thu Jul 22 2021 - 01:10:49 CDT)
- NAMD download form unavailable? Renfro, Michael (Wed Jul 21 2021 - 15:18:31 CDT)
- Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Ryan Woltz (Tue Jul 20 2021 - 18:14:31 CDT)
- difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Ryan Woltz (Tue Jul 20 2021 - 18:06:14 CDT)
- Constraints required for alpha helix secondary structure Diship Srivastava (Fri Jul 16 2021 - 05:51:56 CDT)
- wrap is On to Diffusion phenomena ? Ropon-Palacios G. (Thu Jul 15 2021 - 17:45:26 CDT)
- MMGBSA binding free energy by MolAICal and NAMD Mi Yang (Wed Jul 14 2021 - 13:42:09 CDT)
- simulations space partitioning parameters Nancy Singh (Wed Jul 14 2021 - 06:45:55 CDT)
- Protein-ligand complex is coming out of the water box Nancy Singh (Wed Jul 14 2021 - 06:16:58 CDT)
- question about free energy calculation through FEP method in NAMD M. A (Wed Jul 14 2021 - 01:35:05 CDT)
- question about free energy calculation through FEP method in NAMD M. A (Tue Jul 13 2021 - 08:41:10 CDT)
- Temperature accelerated MD with Colvar or TclForces Ropon-Palacios G. (Fri Jul 09 2021 - 18:49:40 CDT)
- Binding free energy analysis at specific time interval during MD trajectory Mi Yang (Thu Jul 08 2021 - 13:48:20 CDT)
- Simulation of protein-lipid complex by NAMD with OPLS3e ff? Amir Zeb (Tue Jul 06 2021 - 22:04:42 CDT)
- Membrane Protein Flipping in ABF Ishaan Roy (Wed Jun 30 2021 - 20:44:23 CDT)
- Inquiry about NAMD beta Sandeep Dash (Wed Jun 30 2021 - 10:48:36 CDT)
- Constant ph md Diship Srivastava (Mon Jun 28 2021 - 08:02:29 CDT)
- NAMD jobs in SLURM environment, not entering queueing system Prathit Chatterjee (Mon Jun 28 2021 - 03:54:22 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system René Hafner TUK (Mon Jun 28 2021 - 04:03:46 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system René Hafner TUK (Mon Jun 28 2021 - 04:27:06 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system Prathit Chatterjee (Mon Jun 28 2021 - 04:32:05 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system Natalia Ostrowska (Mon Jun 28 2021 - 04:37:25 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system Prathit Chatterjee (Thu Jul 01 2021 - 06:45:44 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system Prathit Chatterjee (Thu Jul 01 2021 - 10:41:31 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system René Hafner TUK (Mon Jun 28 2021 - 04:27:06 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system René Hafner TUK (Mon Jun 28 2021 - 04:03:46 CDT)
- Potential NAMD Update Bug Shiv Seshan (Fri Jun 25 2021 - 15:17:43 CDT)
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- Re: Jarzynski calculate ROPĂ“N-PALACIOS G. (Fri Jun 18 2021 - 14:20:07 CDT)
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- PSF file format Maximilian Ebert (Fri Jun 04 2021 - 12:10:00 CDT)
- Re: PSF file format Josh Vermaas (Fri Jun 04 2021 - 12:48:41 CDT)
- Re: PSF file format Axel Kohlmeyer (Fri Jun 04 2021 - 12:59:48 CDT)
- Re: PSF file format Maximilian Ebert (Fri Jun 04 2021 - 13:51:49 CDT)
- Re: PSF file format Giacomo Fiorin (Fri Jun 04 2021 - 13:56:06 CDT)
- Re: PSF file format Maximilian Ebert (Fri Jun 04 2021 - 16:38:03 CDT)
- Re: PSF file format Vermaas, Josh (Sat Jun 05 2021 - 04:54:48 CDT)
- Re: PSF file format Maximilian Ebert (Sat Jun 05 2021 - 07:55:19 CDT)
- Re: PSF file format Axel Kohlmeyer (Sat Jun 05 2021 - 08:57:07 CDT)
- Re: PSF file format Axel Kohlmeyer (Fri Jun 04 2021 - 12:59:48 CDT)
- Re: PSF file format Josh Vermaas (Fri Jun 04 2021 - 12:48:41 CDT)
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- Re: Re: Re-center membrane protein Ropon-Palacios G. (Fri May 14 2021 - 12:21:20 CDT)
- Re-center membrane protein Ropon-Palacios G. (Fri May 14 2021 - 12:02:34 CDT)
- newby in NAMD joseph pareti (Fri May 14 2021 - 11:12:45 CDT)
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- Mail about Alchemify error Vidhya Sankar (Wed May 05 2021 - 08:36:17 CDT)
- Mail about error in Alchemify programme in namd Vidhya Sankar (Tue May 04 2021 - 07:30:53 CDT)
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- Error Analysis in Metadynamics Diship Srivastava (Tue Apr 20 2021 - 01:39:25 CDT)
- Re: Error Analysis in Metadynamics Miro Astore (Tue Apr 20 2021 - 02:35:11 CDT)
- Re: Error Analysis in Metadynamics Giacomo Fiorin (Fri Apr 23 2021 - 10:57:34 CDT)
- Re: Error Analysis in Metadynamics René Hafner TUK (Fri Apr 23 2021 - 11:40:05 CDT)
- Re: Error Analysis in Metadynamics Giacomo Fiorin (Fri Apr 23 2021 - 18:49:14 CDT)
- Re: Error Analysis in Metadynamics Diship Srivastava (Sun Apr 25 2021 - 12:39:05 CDT)
- Re: Error Analysis in Metadynamics Giacomo Fiorin (Wed Apr 28 2021 - 10:34:17 CDT)
- Re: Error Analysis in Metadynamics Giacomo Fiorin (Fri Apr 23 2021 - 10:57:34 CDT)
- Re: Error Analysis in Metadynamics Miro Astore (Tue Apr 20 2021 - 02:35:11 CDT)
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- Re: Multi-node-gpu NAMD Vermaas, Josh (Wed Apr 14 2021 - 15:41:07 CDT)
- Multi-node-gpu NAMD Ropon-Palacios G. (Wed Apr 14 2021 - 13:22:03 CDT)
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- (no subject) soumadwip ghosh (Thu Mar 25 2021 - 11:25:58 CDT)
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- Re: Lipid into sphere Mike McCallum (Thu Mar 18 2021 - 17:13:26 CDT)
- Re: Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 17:18:34 CDT)
- RE: Lipid into sphere Jeffrey Potoff (Thu Mar 18 2021 - 17:27:10 CDT)
- Re: Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 17:47:33 CDT)
- RE: Lipid into sphere Jeffrey Potoff (Thu Mar 18 2021 - 17:51:24 CDT)
- Re: Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 18:08:32 CDT)
- RE: Lipid into sphere Jeffrey Potoff (Thu Mar 18 2021 - 18:12:21 CDT)
- Re: Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 18:25:02 CDT)
- Re: Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 17:18:34 CDT)
- Re: Lipid into sphere Mike McCallum (Thu Mar 18 2021 - 17:13:26 CDT)
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- Rule of thumb for choosing time step in MD Mi Yang (Tue Mar 16 2021 - 15:12:08 CDT)
- AMBER99bsc1 force field for NAMD Almeida-Hernández, Yasser, Dr. (Tue Mar 16 2021 - 05:06:25 CDT)
- Lone pair disconnected after minimization Rabiul Gazi (Mon Mar 15 2021 - 04:36:13 CDT)
- Add repulsive potential with dummy atom Ropon-Palacios G. (Fri Mar 12 2021 - 14:54:01 CST)
- Avoiding unfavorable interactions during Docking with Vina Mi Yang (Fri Mar 12 2021 - 13:05:23 CST)
- Ligand concentration Ropon-Palacios G. (Thu Mar 11 2021 - 21:09:31 CST)
- Ligand concentration Ropon-Palacios G. (Thu Mar 11 2021 - 20:50:28 CST)
- 3.0alpha9 CUDA version Michael Von Domaros (Thu Mar 11 2021 - 18:42:23 CST)
- Re: 3.0alpha9 CUDA version Vermaas, Josh (Thu Mar 11 2021 - 19:27:53 CST)
- Axis Definition in Metadynamics Sodiq Waheed (Wed Mar 10 2021 - 12:56:17 CST)
- Lone pair disconnected after minimization Rabiul Gazi (Mon Mar 08 2021 - 03:03:44 CST)
- NAMD and VMD on AMAZON instances Ropon-Palacios G. (Sun Mar 07 2021 - 23:33:10 CST)
- N-glycosylation bond not view after patching Ropon-Palacios G. (Sun Mar 07 2021 - 17:15:26 CST)
- NAMD3 Alpha7 MultiGPU errors Raman Preet Singh (Sun Mar 07 2021 - 07:01:04 CST)
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- (no subject) soumadwip ghosh (Sat Mar 06 2021 - 02:12:11 CST)
- Placed random molecules into Box Ropon-Palacios G. (Fri Mar 05 2021 - 16:05:22 CST)
- simulations under a periodic electric field - possible bug Oleksii Zdorevskyi (Fri Mar 05 2021 - 11:11:29 CST)
- Re: Compile NAMD with AMD GPU Vermaas, Josh (Wed Mar 03 2021 - 15:33:43 CST)
- Compile NAMD with AMD GPU Ropon-Palacios G. (Wed Mar 03 2021 - 15:12:23 CST)
- Negative current in open pore simulation soumadwip ghosh (Wed Mar 03 2021 - 00:32:20 CST)
- Dual topology questions Randall Hall (Mon Mar 01 2021 - 20:01:52 CST)
- NAMD 3.0 FEP Atoms moving too fast error Michael Joseph Robertson (Fri Feb 26 2021 - 04:22:32 CST)
- Re: CHARMM Parameter question Ramon Mendoza Uriarte (Thu Feb 25 2021 - 15:26:33 CST)
- Namd-3 alpha 7 error Dr. Eddie (Tue Feb 23 2021 - 11:49:01 CST)
- Small molecule simulation error NAMD Chathuranga Siriwardhana (Mon Feb 22 2021 - 17:28:35 CST)
- Re: Small molecule simulation error NAMD Jeff Comer (Mon Feb 22 2021 - 17:34:17 CST)
- Re: Small molecule simulation error NAMD Chathuranga Siriwardhana (Mon Feb 22 2021 - 17:41:42 CST)
- Re: Small molecule simulation error NAMD David Hardy (Mon Feb 22 2021 - 18:49:25 CST)
- Re: Small molecule simulation error NAMD Gumbart, JC (Mon Feb 22 2021 - 20:12:06 CST)
- Re: Small molecule simulation error NAMD Gumbart, JC (Mon Feb 22 2021 - 20:41:20 CST)
- Re: Small molecule simulation error NAMD JosĂ© VillalaĂn (Wed Feb 24 2021 - 01:59:49 CST)
- Re: Small molecule simulation error NAMD Jeff Comer (Mon Feb 22 2021 - 17:34:17 CST)
- NAMD3 multiGPU: invalid device function error Lorenzo Casalino (Fri Feb 19 2021 - 21:24:19 CST)
- Error in calculation dihedral angle jiali wang (Fri Feb 12 2021 - 23:54:43 CST)
- Question about merging MW-eABF René Hafner TUK (Fri Feb 12 2021 - 07:08:21 CST)
- Problem with running NAMD config file Tiglath Moradkhan (Wed Feb 10 2021 - 19:01:22 CST)
- the centers value in colvar.in file for binding free energy (BFEE) M. A (Fri Feb 05 2021 - 05:26:01 CST)
- Issue about replica exchange molecular dynamics 辛志宏 (Thu Feb 04 2021 - 06:04:53 CST)
- Mail about error in namd Vidhya Sankar (Thu Feb 04 2021 - 02:21:28 CST)
- NAMD3 Multiple Instances Raman Preet Singh (Wed Feb 03 2021 - 11:50:04 CST)
- Dealing with lone pairs Seke Keretsu (Wed Feb 03 2021 - 02:51:29 CST)
- Re: NAMD CUDA Vermaas, Josh (Mon Feb 01 2021 - 14:12:51 CST)
- NAMD CUDA Seibold, Steve Allan (Mon Feb 01 2021 - 13:50:11 CST)
- Convert mmCIF to PDB Ropon-Palacios G. (Mon Feb 01 2021 - 12:02:56 CST)
- output results to phenix Ming Sun (Mon Feb 01 2021 - 11:26:59 CST)
- Problem with FEP simulations Luba Simhaev (Mon Feb 01 2021 - 02:48:14 CST)
- Dealing with lone pairs (LP) during simulation Seke Keretsu (Sat Jan 30 2021 - 01:05:09 CST)
- Re: Improve performance Vermaas, Josh (Thu Jan 28 2021 - 18:45:52 CST)
- Improve performance Ropon-Palacios G. (Thu Jan 28 2021 - 18:08:39 CST)
- Implementing decaying potential (non-linear potential) Athreya, Nagendra Bala Murali (Thu Jan 28 2021 - 14:14:26 CST)
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- Protein RMSF in replica exchange simulations Victor Zhao (Mon Jan 25 2021 - 15:50:03 CST)
- Supervised MD using NAMD Dr. Eddie (Mon Jan 25 2021 - 07:27:32 CST)
- NAMD speed and Scaling raghav singh (Mon Jan 25 2021 - 06:02:52 CST)
- Infrared spectrum prediction Raman Preet Singh (Mon Jan 18 2021 - 12:21:23 CST)
- Re: Infrared spectrum prediction Raman Preet Singh (Fri Feb 12 2021 - 04:34:16 CST)
- Maximum and minimum box size Raman Preet Singh (Mon Jan 18 2021 - 12:16:42 CST)
- NAMD QMMM Scheme nikolaev_at_spbau.ru (Sun Jan 17 2021 - 11:20:54 CST)
- Judging Convergence on Free Energy Calculations Ethan Croitoru (Fri Jan 15 2021 - 13:45:40 CST)
- FATAL ERROR: patch has 127043 atoms, maximum allowed is 65535 Paula Mihaljevic-Juric (Fri Jan 15 2021 - 11:51:37 CST)
- NAMD qm/mm: QM charge not integer Chunli Yan (Thu Jan 14 2021 - 11:58:24 CST)
- Problems Building Circular DNA Sebastian S (Mon Jan 11 2021 - 19:42:36 CST)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Thu Jan 07 2021 - 21:56:25 CST)
- An running issue in eABF-replica calculations hua hao (Mon Jan 04 2021 - 10:59:56 CST)
- Re: An running issue in eABF-replica calculations René Hafner TUK (Mon Mar 01 2021 - 02:28:52 CST)
- Re: An running issue in eABF-replica calculations Abhishek Acharya (Mon Mar 01 2021 - 06:50:20 CST)
- Re: An running issue in eABF-replica calculations hua hao (Mon Mar 01 2021 - 09:21:29 CST)
- Re: An running issue in eABF-replica calculations JĂ©rĂ´me HĂ©nin (Mon Mar 08 2021 - 16:41:24 CST)
- Re: An running issue in eABF-replica calculations René Hafner TUK (Mon Mar 08 2021 - 17:21:02 CST)
- Re: An running issue in eABF-replica calculations JĂ©rĂ´me HĂ©nin (Wed Mar 17 2021 - 08:52:57 CDT)
- Re: An running issue in eABF-replica calculations René Hafner TUK (Fri Apr 09 2021 - 06:20:59 CDT)
- Re: An running issue in eABF-replica calculations JĂ©rĂ´me HĂ©nin (Mon Apr 12 2021 - 08:53:14 CDT)
- Re: An running issue in eABF-replica calculations hua hao (Mon Mar 01 2021 - 09:21:29 CST)
- namdEnergy empy output file Khoualdi Asma Feriel (Thu Dec 31 2020 - 22:29:18 CST)
- FEP calculations - membrane protein Luba Simhaev (Thu Dec 31 2020 - 02:45:38 CST)
- namdEnergy execution issue -path for namd2 in server Khoualdi Asma Feriel (Wed Dec 30 2020 - 23:23:08 CST)
- about geometrical restrain protein on membrane Liqun Zhang (Wed Dec 30 2020 - 21:30:37 CST)
- [NAMD] Example of submission script on Comet/Stampede GPUs Sebastian S (Mon Dec 28 2020 - 12:58:27 CST)
- Force Field Parametrization Ramon Mendoza Uriarte (Sun Dec 27 2020 - 19:08:44 CST)
- Charmm hybrid topology ROPĂ“N-PALACIOS G. (Sat Dec 26 2020 - 15:32:44 CST)
- Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Thu Dec 24 2020 - 13:02:23 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Mon Dec 28 2020 - 23:44:34 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 01:27:03 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF varun dewaker (Wed Dec 30 2020 - 01:45:49 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 08:04:13 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 11:17:23 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Wed Dec 30 2020 - 12:52:19 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 01:27:03 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Mon Dec 28 2020 - 23:44:34 CST)
- Question about Radius of hexagon; Seke Keretsu (Thu Dec 24 2020 - 00:33:17 CST)
- Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 14:39:15 CST)
- SMD on Intermembrane Helices Ethan Croitoru (Tue Dec 22 2020 - 11:15:45 CST)
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- ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Mi Yang (Sat Dec 19 2020 - 08:07:11 CST)
- path CV Stefano Guglielmo (Fri Dec 18 2020 - 08:48:27 CST)
- Assessing total time of run in NAMD Mi Yang (Thu Dec 17 2020 - 12:50:33 CST)
- Force field for Li-ion batteries electrolytes based on ionic liquids Mauro Sgroi (Thu Dec 17 2020 - 03:46:32 CST)
- Installation with tcl Arturo Fernandez (Wed Dec 16 2020 - 16:22:33 CST)
- Water wrapping in the QMMM simulations Alex Balaeff (Mon Dec 14 2020 - 17:27:11 CST)
- I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Prince, Chandler (Mon Dec 14 2020 - 08:20:48 CST)
- NAMD QM/MM multi nodes performance bad Chunli Yan (Sun Dec 13 2020 - 20:47:15 CST)
- Question Colvar o tclforces ROPĂ“N-PALACIOS G. (Sat Dec 12 2020 - 13:15:23 CST)
- Centre of mass distance in ABF Aashish Bhatt (Sat Dec 12 2020 - 02:15:46 CST)
- About the well-tempered metadynamics convergence.. zeynab hosseini (Thu Dec 10 2020 - 12:49:14 CST)
- NAMD3: how to get the best performance in one gpu node? Siyoung Kim (Wed Dec 09 2020 - 03:00:02 CST)
- Fep setup membrane protein-Drug complex ROPĂ“N-PALACIOS G. (Tue Dec 08 2020 - 13:20:41 CST)
- namd QM/MM on oak ridge ANDES cluster Chunli Yan (Sun Dec 06 2020 - 19:14:06 CST)
- Free Energy Pertubation simulation set-up alli suliat (Sun Dec 06 2020 - 18:19:23 CST)
- NAMD3 segfault while writing restart files David Sept (Sat Dec 05 2020 - 11:09:55 CST)
- Membrana-protein-lig protocol ROPĂ“N-PALACIOS G. (Fri Dec 04 2020 - 12:42:24 CST)
- Hydrogen Mass Repartitioning McGuire, Kelly (Thu Dec 03 2020 - 21:04:50 CST)
- RE: Hydrogen Mass Repartitioning Mohammed umar Sheriff (Thu Dec 03 2020 - 21:35:10 CST)
- Re: Hydrogen Mass Repartitioning Gumbart, JC (Thu Dec 03 2020 - 21:57:23 CST)
- AW: Hydrogen Mass Repartitioning Norman Geist (Fri Dec 04 2020 - 03:00:59 CST)
- RE: Hydrogen Mass Repartitioning James Kress (Fri Dec 04 2020 - 17:32:44 CST)
- Re: Hydrogen Mass Repartitioning Rafael Bernardi (Sat Dec 05 2020 - 14:27:45 CST)
- RE: Hydrogen Mass Repartitioning James Kress (Sat Dec 05 2020 - 15:43:49 CST)
- Re: Hydrogen Mass Repartitioning René Hafner TUK (Mon Apr 12 2021 - 05:33:10 CDT)
- Re: Hydrogen Mass Repartitioning Axel Kohlmeyer (Mon Apr 12 2021 - 06:52:34 CDT)
- Re: Hydrogen Mass Repartitioning Gumbart, JC (Mon Apr 12 2021 - 07:01:08 CDT)
- Re: Hydrogen Mass Repartitioning René Hafner TUK (Mon Apr 12 2021 - 07:37:38 CDT)
- Re: Hydrogen Mass Repartitioning Gumbart, JC (Thu Dec 03 2020 - 21:57:23 CST)
- RE: Hydrogen Mass Repartitioning Mohammed umar Sheriff (Thu Dec 03 2020 - 21:35:10 CST)
- CPU vs GPU Question McGuire, Kelly (Wed Dec 02 2020 - 16:51:37 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 02 2020 - 17:05:50 CST)
- Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 03 2020 - 21:05:05 CST)
- Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 01:14:47 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 09 2020 - 10:21:54 CST)
- Re: Re: CPU vs GPU Question Gumbart, JC (Wed Dec 09 2020 - 14:56:23 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:15:28 CST)
- Re: Re: CPU vs GPU Question Gumbart, JC (Wed Dec 09 2020 - 16:19:41 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:27:36 CST)
- Re: Re: CPU vs GPU Question Rafael Bernardi (Wed Dec 09 2020 - 23:26:20 CST)
- Re: Re: CPU vs GPU Question Bennion, Brian (Wed Dec 09 2020 - 23:35:11 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:36:06 CST)
- Re: Re: CPU vs GPU Question vermaasj (Wed Dec 09 2020 - 18:23:32 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 10 2020 - 19:27:16 CST)
- Re: Re: CPU vs GPU Question Rafael Bernardi (Thu Dec 10 2020 - 19:35:32 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 10 2020 - 19:40:46 CST)
- Re: Re: CPU vs GPU Question Rafael Bernardi (Thu Dec 10 2020 - 21:39:48 CST)
- Re: CPU vs GPU Question Mohammed umar Sheriff (Sat Dec 05 2020 - 05:33:54 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 02 2020 - 17:05:50 CST)
- Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 13:43:17 CST)
- Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 18:11:37 CST)
- Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 19:35:52 CST)
- Re: Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 19:48:32 CST)
- Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 20:07:58 CST)
- Re: Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Thu Dec 03 2020 - 13:40:23 CST)
- Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 19:35:52 CST)
- Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 18:11:37 CST)
- Advice for Protein Mutation FEP Calculations Matthew Guberman-Pfeffer (Tue Dec 01 2020 - 10:27:43 CST)
- NamdEnergy Nonbonded H-bonds Francesco Pietra (Mon Nov 30 2020 - 11:06:52 CST)
- not getting NAMD multicopy simulation started René Hafner TUK (Mon Nov 23 2020 - 07:22:36 CST)
- Implicit MD is slower than explcit MD! Krishna Vkm (Mon Nov 23 2020 - 05:18:51 CST)
- Cavernous Depressions in Water Box Oscar Bastidas (Sat Nov 21 2020 - 19:22:14 CST)
- regarding constant PH simulation zahra nabavi (Thu Nov 19 2020 - 21:07:35 CST)
- Restarting QMMM Francesco Pietra (Thu Nov 19 2020 - 05:13:41 CST)
- performing SMD in Z using colvar module RopĂłn-Palacios G. (Mon Nov 16 2020 - 16:16:33 CST)
- Exit code 127 with QMMM Francesco Pietra (Mon Nov 16 2020 - 10:58:30 CST)
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- Adding bias potential Peter Rosenquist (Thu Nov 12 2020 - 15:00:38 CST)
- Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Wed Nov 11 2020 - 13:04:29 CST)
- FEP/λ-REMD Simulation error Alao, John-Paul (Mon Nov 09 2020 - 11:01:26 CST)
- psf generation for multiple trehalose molecules Ritu Arora (Sun Nov 08 2020 - 18:24:15 CST)
- Setting up QM-MM with homotrimer Francesco Pietra (Thu Nov 05 2020 - 10:52:27 CST)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Wed Nov 04 2020 - 10:47:22 CST)
- Rmsd calculation Asmi Mahmood (Tue Nov 03 2020 - 00:22:54 CST)
- rmsd Asmi Mahmood (Mon Nov 02 2020 - 04:41:35 CST)
- rmsd colvar Stefano Guglielmo (Sun Nov 01 2020 - 10:17:10 CST)
- NPT then NVT simulation in a single config file for water box? Tanooj Shah (Fri Oct 30 2020 - 21:52:19 CDT)
- restart file Constantin Gunkel (Fri Oct 30 2020 - 09:45:17 CDT)
- Problem Constantin Gunkel (Wed Oct 28 2020 - 20:15:43 CDT)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Wed Oct 28 2020 - 09:44:24 CDT)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Tue Oct 27 2020 - 10:04:49 CDT)
- Compile NAMD with PLUMED Jiali Wang (Mon Oct 26 2020 - 22:15:28 CDT)
- Can Namd 2.14 and genpsf 2.0 process halogen bonds? Nan Li (Mon Oct 26 2020 - 17:15:06 CDT)
- (no subject) Mersch, Kacey (Mon Oct 26 2020 - 16:33:00 CDT)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Mon Oct 26 2020 - 12:50:33 CDT)
- Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Mon Oct 26 2020 - 07:33:11 CDT)
- Re: Running multiple walker metadynamics replicas as a bundle Josh Vermaas (Mon Oct 26 2020 - 11:04:02 CDT)
- Repulsive wall potential or spherical boundry conditions Almeida-Hernández, Yasser, Dr. (Fri Oct 23 2020 - 05:13:55 CDT)
- How to Selectively Scale Interactions Matthew Guberman-Pfeffer (Thu Oct 22 2020 - 23:30:47 CDT)
- Velocity MAP calculation in VMD Abhijit Gogoi (Wed Oct 21 2020 - 03:59:13 CDT)
- Protein:ligand standard binding free energies clarification question Ethan Croitoru (Tue Oct 20 2020 - 21:14:53 CDT)
- NAMD 2.14 fatal error executing tcl script Alsaloum, Matthew (Sun Oct 18 2020 - 21:06:58 CDT)
- well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Fri Oct 16 2020 - 03:44:27 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Fri Oct 16 2020 - 09:10:26 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Mon Oct 19 2020 - 12:36:07 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Tue Oct 20 2020 - 15:33:10 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Tue Oct 20 2020 - 16:01:43 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Wed Oct 21 2020 - 09:47:29 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Wed Oct 21 2020 - 09:59:40 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Wed Oct 21 2020 - 10:26:15 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Wed Oct 21 2020 - 13:03:28 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Wed Oct 21 2020 - 14:08:35 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Thu Oct 22 2020 - 03:10:38 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Thu Oct 22 2020 - 15:45:17 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Fri Oct 23 2020 - 04:21:33 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Fri Oct 16 2020 - 09:10:26 CDT)
- GPU Acceleration and Drude Simulations Michael Robinson (Fri Oct 16 2020 - 01:23:57 CDT)
- MM/QM with namd Asmi Mahmood (Thu Oct 15 2020 - 08:04:32 CDT)
- NAMD QM/MM simulations jing liang (Thu Oct 15 2020 - 03:18:48 CDT)
- Targeted MD in NAMD 3.0? Smith, Harper E. (Tue Oct 13 2020 - 11:18:03 CDT)
- A home PC to run NAMD simulations Harish Srinivasan (Sun Oct 11 2020 - 02:02:27 CDT)
- Question about PBC and RMSD alli suliat (Sat Oct 10 2020 - 00:31:11 CDT)
- Formation of nanoparticle ligand complex Yuvam Bhateja (Fri Oct 09 2020 - 14:09:30 CDT)
- Quary resgading Adaptive biasing force Aashish Bhatt (Thu Oct 08 2020 - 08:43:44 CDT)
- Transition State Search BY NAMD 辛志宏 (Wed Oct 07 2020 - 02:26:58 CDT)
- amber force field divyabharathi korlepara (Tue Oct 06 2020 - 23:51:49 CDT)
- COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics Chythra J N (Tue Oct 06 2020 - 21:57:46 CDT)
- shifting of ions from -z to +z in a single frame(1ps) Basanta Acharya (Tue Oct 06 2020 - 21:54:07 CDT)
- Ligand coated Silver Nanoparticle. Yuvam Bhateja (Tue Oct 06 2020 - 11:19:02 CDT)
- CHARMM36 to Drude conversion for NAMD Almeida-Hernández, Yasser, Dr. (Tue Oct 06 2020 - 03:37:32 CDT)
- Optimum time for md run in i3 laptop achchirangeebi (Tue Oct 06 2020 - 01:30:55 CDT)
- NAMD doesn't use my CUDA enabled GPU Rimon Riju (Tue Oct 06 2020 - 01:17:45 CDT)
- Regarding "lossiness" of namd on GPUs Bassam Haddad (Mon Oct 05 2020 - 16:19:26 CDT)
- psf generation divyabharathi korlepara (Mon Oct 05 2020 - 10:13:35 CDT)
- Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:08:48 CDT)
- How to determine the residue of qmLSSRef in QwikMD? 辛志宏 (Sun Oct 04 2020 - 20:28:28 CDT)
- Incorrect restarting velocities Kodituwakku,Dimuthu Nirmani (Fri Oct 02 2020 - 09:53:02 CDT)
- QwikMD--ERROR) Unable to ascertain relative endianness of remote machine 辛志宏 (Fri Oct 02 2020 - 03:18:39 CDT)
- TMD questions - refined Nadia Elghobashi-Meinhardt (Thu Oct 01 2020 - 08:59:18 CDT)
- renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Wed Sep 30 2020 - 10:30:25 CDT)
- REUS Ashkan Shekaari (Mon Sep 28 2020 - 11:37:29 CDT)
- WHAM Ashkan Shekaari (Mon Sep 28 2020 - 08:40:02 CDT)
- TMD config parameters Nadia Elghobashi-Meinhardt (Fri Sep 25 2020 - 02:48:06 CDT)
- VMD nc file problem Seibold, Steve Allan (Thu Sep 24 2020 - 09:20:51 CDT)
- NAMD trajectory with MMPBSA.py Asmi Mahmood (Wed Sep 23 2020 - 09:36:52 CDT)
- REMD Problem Anup Prasad (Wed Sep 23 2020 - 05:47:08 CDT)
- Getting high performance on multi-copy (replica) GPU simulations Victor Zhao (Tue Sep 22 2020 - 11:12:58 CDT)
- Regarding to the parameters of QwikMD 辛志宏 (Tue Sep 22 2020 - 09:42:12 CDT)
- Error running command for QM forces calculation 辛志宏 (Mon Sep 21 2020 - 01:21:20 CDT)
- Farnesylated Cysteine Xu, Shenyuan (Sun Sep 20 2020 - 10:55:46 CDT)
- namd3 on centos 6 Boyan Bonev (Sat Sep 19 2020 - 07:49:07 CDT)
- (no subject) shyam sharma (Fri Sep 18 2020 - 04:20:27 CDT)
- (no subject) shyam sharma (Fri Sep 18 2020 - 03:58:41 CDT)
- Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 10:07:35 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 10:40:50 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 13:20:05 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 14:42:53 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 16:07:10 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 16:48:19 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 13:20:05 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 10:40:50 CDT)
- Atom outside of the MSM grid in NVT simulation - Semiperiodic boundaries Guna Mandava (Wed Sep 16 2020 - 21:20:28 CDT)
- MD simulation of a molecule with a halogen Federico Rui (Wed Sep 16 2020 - 11:22:17 CDT)
- simulated annealing Stefano Guglielmo (Wed Sep 16 2020 - 10:53:09 CDT)
- Convert solvated CHARMM PDB + PSF to Amber Gianluca Interlandi (Tue Sep 15 2020 - 20:34:44 CDT)
- Parameters and topology files regarding arsorite(ASO3 - - -) Basanta Acharya (Tue Sep 15 2020 - 07:29:51 CDT)
- (no subject) Basanta Acharya (Tue Sep 15 2020 - 07:27:03 CDT)
- AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 00:53:42 CDT)
- NAN in output of aMD Ritu Arora (Mon Sep 14 2020 - 09:33:03 CDT)
- Hybrid Coarse Grain/ all atom simulation in NAMD Shadi Rahnama (Sun Sep 13 2020 - 14:18:26 CDT)
- Post processing NAMD trajectory Kodituwakku,Dimuthu Nirmani (Sun Sep 13 2020 - 13:08:14 CDT)
- Equilibration of a solvated CNT using C36 zeynab hosseini (Sun Sep 13 2020 - 09:01:52 CDT)
- FATAL ERROR: Error running command for QM forces calculation 辛志宏 (Sun Sep 13 2020 - 07:52:13 CDT)
- toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Tue Sep 01 2020 - 13:29:11 CDT)
- ERROR: Atoms moving too fast; simulation has become unstable 辛志宏 (Wed Sep 09 2020 - 23:03:53 CDT)
- DRMS Colvar Ethan Croitoru (Wed Sep 09 2020 - 14:25:33 CDT)
- Basics of MD Raman Preet Singh (Tue Sep 08 2020 - 05:10:10 CDT)
- How to treat electrostatics in crystal lattice MD simulation Matthew Guberman-Pfeffer (Mon Sep 07 2020 - 07:02:17 CDT)
- Issue regarding to the speed of QM/MM 辛志宏 (Mon Sep 07 2020 - 03:40:03 CDT)
- Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Mon Sep 07 2020 - 13:11:07 CDT)
- << Setting the simulation time parameters >> I. Camps (Sat Sep 05 2020 - 13:44:17 CDT)
- << Conformational sampling with NAMD >> I. Camps (Sat Sep 05 2020 - 12:54:13 CDT)
- Support for drudeNbthole on CUDA version of NAMD HEMANTH H (Sat Sep 05 2020 - 02:15:51 CDT)
- xMDFF Error Joey Farrell (Thu Sep 03 2020 - 23:19:47 CDT)
- ABF Not Sampling Whole Window Ethan Croitoru (Thu Sep 03 2020 - 18:35:15 CDT)
- Replica exchange problem Julian David Baquero Contreras (Wed Sep 02 2020 - 13:13:59 CDT)
- Colvars Harmonic Bias Force Direction Mortimer Hemmit (Wed Sep 02 2020 - 07:28:03 CDT)
- Wrong number of basis-sets stored! 辛志宏 (Tue Sep 01 2020 - 21:10:17 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 00:10:54 CDT)
- Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 09:48:38 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 13:45:48 CDT)
- Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 19:32:23 CDT)
- Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Wed Sep 02 2020 - 20:17:40 CDT)
- Re:Re: Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 21:25:09 CDT)
- Re: Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Wed Sep 02 2020 - 22:08:03 CDT)
- Re:Re: Re: Re:Re: Wrong number of basis-sets stored! 辛志宏 (Thu Sep 03 2020 - 02:41:43 CDT)
- Re: Re:Re: Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Thu Sep 03 2020 - 11:31:51 CDT)
- Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 09:48:38 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 00:10:54 CDT)
- PME in PairInteraction Calculations Matthew Guberman-Pfeffer (Tue Sep 01 2020 - 00:01:51 CDT)
- Problems in sharing of replicas in REMD Anup Prasad (Mon Aug 31 2020 - 18:03:59 CDT)
- Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sat Aug 29 2020 - 18:36:01 CDT)
- Re: Error when using namdplot Peter Freddolino (Sat Aug 29 2020 - 22:26:08 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:18:40 CDT)
- Re: Error when using namdplot Peter Freddolino (Sun Aug 30 2020 - 11:55:03 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 11:58:07 CDT)
- Re: Error when using namdplot Peter Freddolino (Sun Aug 30 2020 - 23:38:09 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Mon Aug 31 2020 - 07:34:00 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:18:40 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:33:47 CDT)
- Re: Error when using namdplot Peter Freddolino (Sat Aug 29 2020 - 22:26:08 CDT)
- QM atom cannot be fixed in space 辛志宏 (Sat Aug 29 2020 - 07:51:21 CDT)
- Re: : Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Aug 28 2020 - 18:21:18 CDT)
- Problem with BEUS in NAMD 2.14 David Tang (Mon Aug 24 2020 - 14:29:10 CDT)
- Re: namd-l digest V1 #2927 Raman Preet Singh (Mon Aug 24 2020 - 01:45:58 CDT)
- Running NAMD - 2.14 - SMP - Verbs - CUDA Bassam Haddad (Wed Aug 19 2020 - 20:56:19 CDT)
- Simulation Crash SMD Coarse-Grained Ethan Croitoru (Wed Aug 19 2020 - 15:24:01 CDT)
- JS plugin issues when constructing large systems Cavalleri A. (Mon Aug 17 2020 - 13:37:22 CDT)
- Error in fftk during bond opt using VMD 1.9.3 Faisal, H M Nasrullah (Mon Aug 17 2020 - 10:08:00 CDT)
- Re: namd-l digest V1 #2923 Raman Preet Singh (Mon Aug 17 2020 - 01:47:09 CDT)
- Low simulation speed with 24 processors Asmi Mahmood (Sun Aug 16 2020 - 12:39:26 CDT)
- Hi Asmi Mahmood (Sun Aug 16 2020 - 12:38:21 CDT)
- Re: vmd-l: PME boolean HEMANTH H (Fri Aug 14 2020 - 03:20:48 CDT)
- Resuming / Resubmitting RAMD simulations on a HPC Gerald Keller (Thu Aug 13 2020 - 02:51:37 CDT)
- Annealing stepin QwikMD of VMD soodabeh ghaffari (Wed Aug 12 2020 - 17:50:01 CDT)
- Re: ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 12:44:55 CDT)
- ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 11:13:53 CDT)
- Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 11 2020 - 19:50:48 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 25 2020 - 15:06:12 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions JC Gumbart (Tue Aug 25 2020 - 19:27:34 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions David Hardy (Thu Aug 27 2020 - 10:16:22 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Wed Sep 02 2020 - 21:35:55 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 25 2020 - 15:06:12 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 CDT)
- POSTDOCTORAL POSITION at CFM/MPC (Donostia, San Sebastian - SPAIN) Aritz Leonardo Liceranzu (Mon Aug 10 2020 - 17:04:46 CDT)
- Cuboid water box issues Raman Preet Singh (Fri Aug 07 2020 - 13:29:06 CDT)
- Postdoctoral opening at MSU Josh Vermaas (Thu Aug 06 2020 - 09:46:56 CDT)
- QM/MM simulations with live solvent Oleksii Zdorevskyi (Thu Aug 06 2020 - 05:15:26 CDT)
- Extra frame at start of each trajectory Ethan Croitoru (Wed Aug 05 2020 - 14:23:47 CDT)
- Possible issue with NAMD_2.13_Linux-x86_64-multicore-CUDA version for Drude support HEMANTH H (Wed Aug 05 2020 - 10:11:08 CDT)
- Alchemical Transformation for calculation of standard binding free energies Cameron Grant (Wed Aug 05 2020 - 04:44:58 CDT)
- Senior Investigator/ Investigator Position (Molecular Dynamics) at Silicon Therapeutics Joao Ribeiro (Mon Aug 03 2020 - 12:51:52 CDT)
- Senior Investigator/ Investigator Position (Quantum Mechanics) at Silicon Therapeutics Joao Ribeiro (Mon Aug 03 2020 - 07:50:06 CDT)
- Parameters for molecular N2 Raman Preet Singh (Fri Jul 31 2020 - 13:29:47 CDT)
- [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Thu Jul 30 2020 - 18:43:15 CDT)
- Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. yjcoshc (Thu Jul 30 2020 - 20:17:40 CDT)
- Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Fri Jul 31 2020 - 11:01:46 CDT)
- Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Mon Aug 03 2020 - 18:39:14 CDT)
- Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. yjcoshc (Thu Jul 30 2020 - 20:17:40 CDT)
- CUDA Error Roshan Shrestha (Wed Jul 29 2020 - 13:22:36 CDT)
- Slow performance over multi-core processor and CUDA build Roshan Shrestha (Tue Jul 28 2020 - 05:01:14 CDT)
- Re: Slow performance over multi-core processor and CUDA build Ashkan Shekaari (Tue Jul 28 2020 - 07:25:29 CDT)
- AW: Slow performance over multi-core processor and CUDA build Norman Geist (Tue Jul 28 2020 - 07:36:02 CDT)
- Re: Slow performance over multi-core processor and CUDA build Giacomo Fiorin (Tue Jul 28 2020 - 08:04:52 CDT)
- Re: Slow performance over multi-core processor and CUDA build Roshan Shrestha (Tue Jul 28 2020 - 11:36:36 CDT)
- Re: Slow performance over multi-core processor and CUDA build Josh Vermaas (Tue Jul 28 2020 - 14:28:59 CDT)
- Re: Slow performance over multi-core processor and CUDA build Joseph Farran (Tue Jul 28 2020 - 12:41:18 CDT)
- Re: Slow performance over multi-core processor and CUDA build Josh Vermaas (Tue Jul 28 2020 - 20:32:26 CDT)
- AW: Slow performance over multi-core processor and CUDA build Norman Geist (Tue Jul 28 2020 - 07:36:02 CDT)
- Re: Slow performance over multi-core processor and CUDA build Ashkan Shekaari (Tue Jul 28 2020 - 07:25:29 CDT)
- NAMD on 24 threads Asmi Mahmood (Mon Jul 27 2020 - 04:06:28 CDT)
- error with namd2_ti.pl script Qasim Pars (Sat Jul 25 2020 - 23:42:22 CDT)
- NAMD CUDA specification Asmi Mahmood (Sat Jul 25 2020 - 01:33:55 CDT)
- Missing frames in DCD header when continue from segment without DCD output Maximilian Ebert (Fri Jul 24 2020 - 15:30:32 CDT)
- PhD Position In Computational Structural Biology Of Membrane Proteins Marawan Hussien (Thu Jul 23 2020 - 17:49:08 CDT)
- FATAL ERROR: EOF ENCOUNTERED WHILE READING BONDS FROM PSF FILE Jose Correa (Thu Jul 23 2020 - 12:28:07 CDT)
- FATAL ERROR: must have same number of LP hosts as lone pairs Selemon Bekele (Wed Jul 22 2020 - 16:33:33 CDT)
- TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Mateusz Bieniek (Sat Jul 18 2020 - 09:30:33 CDT)
- Free-energy of association of transmembrane helices Ethan Croitoru (Fri Jul 17 2020 - 20:05:40 CDT)
- issues with QMMM and parameters Francesco Pietra (Wed Jul 15 2020 - 02:23:43 CDT)
- obtaining the viscosity of mixture from NAMD output file Kosar Khajeh (Wed Jul 15 2020 - 02:21:23 CDT)
- NAMD overestimates the hydration free energy with Drude force field Qasim Pars (Tue Jul 14 2020 - 12:10:01 CDT)
- Degrees of Freedom in REST2 Alex Hummels (Sun Jul 12 2020 - 13:31:49 CDT)
- Dcd file abnormal termination please help Kushal Roy (Sun Jul 12 2020 - 06:43:28 CDT)
- Restarting aborted NAMD run Raman Preet Singh (Sun Jul 12 2020 - 03:56:22 CDT)
- Dynamic switching GPU/CPU minimization Maximilian Ebert (Sat Jul 11 2020 - 08:49:50 CDT)
- Pair interaction calculations of the QM/MM system Alex Balaeff (Tue Jul 07 2020 - 18:44:21 CDT)
- Re: scripts to generate initial boxes of solvents Josh Vermaas (Sun Jul 05 2020 - 14:51:48 CDT)
- Equilibrated boxes of organic solvents Francesco Pietra (Sat Jul 04 2020 - 11:46:15 CDT)
- MOPAC output file analysis M. A (Fri Jul 03 2020 - 14:53:05 CDT)
- The HIP version of NAMD gets wrong results when computing on more than one node ĺĽ é©ć´˛ (Fri Jul 03 2020 - 04:58:16 CDT)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 05:54:33 CDT)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node ĺĽ é©ć´˛ (Fri Jul 03 2020 - 06:36:12 CDT)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 10:33:14 CDT)
- Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node ĺĽ é©ć´˛ (Fri Jul 03 2020 - 23:03:54 CDT)
- Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 23:17:09 CDT)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node ĺĽ é©ć´˛ (Fri Jul 03 2020 - 06:36:12 CDT)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 05:54:33 CDT)
- Questions about soluteScalingFactor in REST2 Alex Hummels (Thu Jul 02 2020 - 17:19:11 CDT)
- CpHMD: Warning when building atom of unknown mass (psfgen) Aalap Parikh (Tue Jun 30 2020 - 15:35:37 CDT)
- RAMD seed number Aashish Bhatt (Mon Jun 29 2020 - 08:31:10 CDT)
- NAMD configuration file error Ratnika Sharma (Sun Jun 28 2020 - 15:45:27 CDT)
- Patch bond not formed Kodituwakku,Dimuthu Nirmani (Sun Jun 28 2020 - 00:58:56 CDT)
- How to best use GPUs Itamar Kass (Thu Jun 25 2020 - 05:06:46 CDT)
- How to restart a FEP simulation Qasim Pars (Thu Jun 25 2020 - 02:37:46 CDT)
- npt simulation where only one of the dimensions is fixed Oleksii Zdorevskyi (Wed Jun 24 2020 - 01:29:50 CDT)
- Protein-ligand complex Raman Preet Singh (Tue Jun 23 2020 - 08:47:56 CDT)
- how does NAMD know which residue to (de)couple Qasim Pars (Sun Jun 21 2020 - 17:28:19 CDT)
- Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ............... Indrajit Deb (Wed Jun 17 2020 - 00:03:18 CDT)
- Re: Transforming ORCA data to CHARMM format GIUSEPPE LEONARDO LICARI (Thu Jun 11 2020 - 08:58:22 CDT)
- Transforming ORCA data to CHARMM format Peter Mawanga (Thu Jun 11 2020 - 06:32:40 CDT)
- how to run flexible fitting for structure with helical symmetry Zhang Yan (Thu Jun 11 2020 - 03:24:31 CDT)
- how to disable the periodic condition tracking two atom distance Jiali Wang (Wed Jun 10 2020 - 12:54:51 CDT)
- Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Wed Jun 10 2020 - 15:10:35 CDT)
- Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Thu Jun 11 2020 - 11:49:54 CDT)
- Re: [External Email] Re: how to disable the periodic condition tracking two atom distance JĂ©rĂ´me HĂ©nin (Fri Jun 12 2020 - 12:42:26 CDT)
- Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Fri Jun 12 2020 - 13:10:20 CDT)
- Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Fri Jun 12 2020 - 13:41:22 CDT)
- Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Fri Jun 12 2020 - 13:42:29 CDT)
- Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Thu Jun 11 2020 - 11:49:54 CDT)
- Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Wed Jun 10 2020 - 15:10:35 CDT)
- ERROR: Atoms (still) moving too fast Justine Raymond (Wed Jun 10 2020 - 09:23:34 CDT)
- CPU/GPU Distribution Youssef Elmougy (Tue Jun 09 2020 - 16:44:59 CDT)
- (no subject) shyam sharma (Mon Jun 08 2020 - 04:29:00 CDT)
- How can I analyse QMMM log file? M. A (Sun Jun 07 2020 - 02:43:55 CDT)
- Psfgen, Disulfide Linkages, and the Drude Polarizable Force Field Michael Robinson (Fri Jun 05 2020 - 03:31:05 CDT)
- Re: Error during simulation shyam sharma (Thu Jun 04 2020 - 22:54:10 CDT)
- Bond between custom ligand and protein sidechain McGuire, Kelly (Thu Jun 04 2020 - 20:05:51 CDT)
- Non-SLI GPUs in NAMD Raman Preet Singh (Thu Jun 04 2020 - 12:56:58 CDT)
- Comparison of electric field between MD simulation and Experiments Mani Kandan (Sun May 31 2020 - 11:47:55 CDT)
- Question about QMMM simulation M. A (Sun May 31 2020 - 06:31:38 CDT)
- Drude polarizable force field Nicolás Marcelo Rozas Castro (Sun May 31 2020 - 04:13:43 CDT)
- Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 00:20:07 CDT)
- System Drifts Along Z-Axis Bassam Haddad (Fri May 29 2020 - 14:36:49 CDT)
- error: minimizer slowly moving xxx atoms with bad contacts downhill Ceren Ciraci (Tue May 26 2020 - 10:45:45 CDT)
- Specifying a pull direction with COLVARS Selemon Bekele (Mon May 25 2020 - 23:52:47 CDT)
- Setting up / Running NAMD on HPC Gerald Keller (Mon May 25 2020 - 03:56:34 CDT)
- Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Mon May 25 2020 - 00:35:20 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Josh Vermaas (Mon May 25 2020 - 17:35:40 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Tue May 26 2020 - 14:44:22 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Giacomo Fiorin (Tue May 26 2020 - 15:14:19 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Wed May 27 2020 - 13:09:41 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Josh Vermaas (Wed May 27 2020 - 16:00:44 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Wed May 27 2020 - 19:11:32 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Tue May 26 2020 - 14:44:22 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Josh Vermaas (Mon May 25 2020 - 17:35:40 CDT)
- Negative Forces in SMD Simulations Souvik Dey (Fri May 22 2020 - 16:40:25 CDT)
- Re: Negative Forces in SMD Simulations Gumbart, JC (Tue May 26 2020 - 13:17:03 CDT)
- Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 13:21:19 CDT)
- Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 13:30:11 CDT)
- Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 15:22:19 CDT)
- Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 15:42:59 CDT)
- Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 19:05:54 CDT)
- Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 19:24:35 CDT)
- Re: Negative Forces in SMD Simulations Josh Vermaas (Tue May 26 2020 - 19:27:23 CDT)
- Re: Negative Forces in SMD Simulations Pratik Narain Srivastava (Tue May 26 2020 - 13:34:55 CDT)
- Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 15:25:04 CDT)
- Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 13:21:19 CDT)
- Re: Negative Forces in SMD Simulations Gumbart, JC (Tue May 26 2020 - 13:17:03 CDT)
- Dcdfreq Variable Value Question Oscar Bastidas (Fri May 22 2020 - 15:23:45 CDT)
- NAMD 3.0 alpha, operating system requirements Nicholas M. Glykos (Fri May 22 2020 - 13:19:02 CDT)
- solvation with SWM4 water model Qasim Pars (Thu May 21 2020 - 19:37:21 CDT)
- Negative Forces in SMD Simulations Souvik Dey (Thu May 21 2020 - 16:45:28 CDT)
- Format of 'dcdfreq' field in conf file Oscar Bastidas (Thu May 21 2020 - 01:09:00 CDT)
- Fwd: Inquiry regarding benchmark simulations David Hardy (Wed May 20 2020 - 17:15:38 CDT)
- Issue in reading the soluteScalingFile for REST2 GILLET Natacha (Sat May 16 2020 - 01:56:52 CDT)
- how to set the input file for the free energy calculations with CHARMM Drude force field Qasim Pars (Fri May 15 2020 - 17:36:33 CDT)
- Re: FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 15:01:49 CDT)
- Replica exchange on GPU with OPA network and Slurm Thibaut Very (Mon May 11 2020 - 03:20:50 CDT)
- FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 01:43:20 CDT)
- Re: Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 10:19:43 CDT)
- Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 06:12:57 CDT)
- Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 02:49:55 CDT)
- Langevin dynamics and random seeds Morgan Packer (Tue May 05 2020 - 17:30:54 CDT)
- NAMD job takes long time to finish 1 ns equilibration Khoualdi Asma Feriel (Tue May 05 2020 - 14:57:27 CDT)
- Re: Rattle algorithm error: when to minimise Khoualdi Asma Feriel (Tue May 05 2020 - 14:49:42 CDT)
- Parametrization of zinc ion (+2) in using CHARMM force field. varun dewaker (Tue May 05 2020 - 00:26:12 CDT)
- pbc correction for nve unwrap trajectory aiming calculation of diffusion coefficient Santanu Santra (Mon May 04 2020 - 23:54:19 CDT)
- actual production MD L- (Mon May 04 2020 - 20:01:10 CDT)
- Box of Water L- (Mon May 04 2020 - 19:12:03 CDT)
- DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 05:08:10 CDT)
- When to use a semicolon in a *.conf file? Oscar Bastidas (Wed Apr 29 2020 - 23:14:07 CDT)
- Run NAMD without GPU L- (Sun Apr 26 2020 - 06:33:50 CDT)
- qmmm simulation and question for md analysis M. A (Mon Apr 20 2020 - 03:59:45 CDT)
- Patch grid too small error in first production run Khoualdi Asma Feriel (Sun Apr 19 2020 - 14:29:06 CDT)
- Receptor-ligand binding energy from QMMM Francesco Pietra (Sat Apr 18 2020 - 03:52:40 CDT)
- Re: FATAL ERROR: Error running command for QM forces calculation. M. A (Fri Apr 17 2020 - 11:53:08 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:42:25 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 11:52:28 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 12:29:46 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Tue Apr 28 2020 - 12:06:01 CDT)
- Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:09:36 CDT)
- Issue about replica-exchangeumbrella sampling by 16 threads 辛志宏 (Thu Apr 16 2020 - 04:12:37 CDT)
- Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... zeynab hosseini (Wed Apr 15 2020 - 00:07:27 CDT)
- Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... Giacomo Fiorin (Thu Apr 16 2020 - 09:13:14 CDT)
- Issues with vdW for non existing atom Francesco Pietra (Wed Apr 15 2020 - 10:29:14 CDT)
- (no subject) ROPĂ“N-PALACIOS G. (Tue Apr 14 2020 - 21:25:41 CDT)
- minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 09:37:29 CDT)
- Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:16:35 CDT)
- Re: minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 12:24:18 CDT)
- Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:42:24 CDT)
- Re: minimise in restarting first equilibration step Giacomo Fiorin (Mon Apr 13 2020 - 12:54:03 CDT)
- Re: minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 13:50:03 CDT)
- Re: minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 12:24:18 CDT)
- Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:16:35 CDT)
- Compile NAMD on Windows 64 bit; nocuda, multicore Mortimer Hemmit (Sun Apr 12 2020 - 17:36:46 CDT)
- QwikMD Error: child killed: unknown signal Frank Lam (Sun Apr 12 2020 - 13:29:06 CDT)
- rmsd colvars atom definition Francesco Pietra (Fri Apr 10 2020 - 01:44:55 CDT)
- .coor and .vel output files not generated Khoualdi Asma Feriel (Thu Apr 09 2020 - 21:32:20 CDT)
- Forces in QM/MM calculations nikolaev_at_spbau.ru (Wed Apr 08 2020 - 12:57:07 CDT)
- FATAL ERROR: Error running command for QM forces calculation. M. A (Tue Apr 07 2020 - 10:31:12 CDT)
- PSF for Cyclic-Branched Peptides Hendrik Schröder (Sun Apr 05 2020 - 17:20:18 CDT)
- Error generating files with QwikMD Marcos Verissimo Alves (Sun Apr 05 2020 - 00:33:57 CDT)
- Fwd: fatal error: error in qm-mm bond assignment mariano spivak (Sat Apr 04 2020 - 11:40:19 CDT)
- difference between numsteps and run in step4_equilibration.inp soodabeh ghaffari (Thu Apr 02 2020 - 14:39:05 CDT)
- converting gromacs topology file to namd Hadi Rahmaninejad (Wed Apr 01 2020 - 17:11:40 CDT)
- how i can utilize 4 GPU in simulation with poor performance L- (Wed Apr 01 2020 - 11:30:13 CDT)
- MDFF chirality restrain error - measure imprp: empty atom index Indrajit Deb (Wed Apr 01 2020 - 11:15:57 CDT)
- QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 05:49:53 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 09:57:44 CDT)
- Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 11:09:29 CDT)
- Fwd: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 12:46:17 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 13:15:37 CDT)
- Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 16:16:42 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 17:05:32 CDT)
- Re: QMMM param issue Francesco Pietra (Thu Apr 02 2020 - 03:30:27 CDT)
- Re: QMMM param issue Josh Vermaas (Thu Apr 02 2020 - 11:41:22 CDT)
- Re: QMMM param issue Francesco Pietra (Fri Apr 03 2020 - 12:48:50 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Sat Apr 04 2020 - 11:25:27 CDT)
- Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 11:09:29 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 09:57:44 CDT)
- using an Amber topology with OPC water model in NAMD Vlad Cojocaru (Tue Mar 31 2020 - 13:38:42 CDT)
- Collaboration offer Raman Preet Singh (Mon Mar 30 2020 - 08:01:54 CDT)
- Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 04:42:43 CDT)
- Unpredictably Crashes upon Restarting Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 16:56:43 CDT)
- Lipids generated by VMD could not use "coordpdb" to read jiali wang (Thu Mar 26 2020 - 23:42:27 CDT)
- How to avoid producing a huge DCD file? 辛志宏 (Mon Mar 23 2020 - 22:15:53 CDT)
- How to fix mutex error Matthew Guberman-Pfeffer (Sat Mar 21 2020 - 22:51:27 CDT)
- acetylene Mikhail Suyetin (Wed Mar 18 2020 - 06:56:47 CDT)
- NGRP NST2 Selemon Bekele (Tue Mar 17 2020 - 12:13:20 CDT)
- Technical specifications for the V100 and GTX gpu cards Souvik Sinha (Tue Mar 17 2020 - 03:26:28 CDT)
- Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 12:10:53 CDT)
- NAMD error : alloc_mempool_block: posix_memalign failed Himanshu Joshi (Fri Mar 13 2020 - 15:51:51 CDT)
- Does NAMD have unit tests or how can I confirm the correctness of the simulation results of NAMD? ĺĽ é©ć´˛ (Tue Mar 10 2020 - 20:29:34 CDT)
- Stability issues with POPC membrane using Drude force field Batuhan Kav (Tue Mar 10 2020 - 05:08:14 CDT)
- Error Restarting Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 12:46:34 CDT)
- Different Velocity or Margin Errors for Restarted Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 09:08:14 CDT)
- NAMD performance Stefano Guglielmo (Thu Mar 05 2020 - 09:05:31 CST)
- MD with 3-site CO model Nadia Elghobashi-Meinhardt (Wed Mar 04 2020 - 08:24:51 CST)
- adding peptide constraint in NAMD configuration file soodabeh ghaffari (Tue Mar 03 2020 - 22:49:20 CST)
- A question about the code in CudaPmeSolverUtilKernel.cu ĺĽ é©ć´˛ (Tue Mar 03 2020 - 01:04:07 CST)
- question to run namd2 with multiple CPUs Yu, Tao (Fri Feb 28 2020 - 16:10:20 CST)
- Re: question to run namd2 with multiple CPUs Josh Vermaas (Fri Feb 28 2020 - 16:29:09 CST)
- Re: question to run namd2 with multiple CPUs Yu, Tao (Mon Mar 02 2020 - 15:08:04 CST)
- Re: question to run namd2 with multiple CPUs Josh Vermaas (Mon Mar 02 2020 - 15:30:03 CST)
- Re: question to run namd2 with multiple CPUs Renfro, Michael (Thu Mar 05 2020 - 10:25:21 CST)
- Re: question to run namd2 with multiple CPUs Yu, Tao (Thu Mar 05 2020 - 10:46:41 CST)
- Re: question to run namd2 with multiple CPUs Renfro, Michael (Thu Mar 05 2020 - 14:26:22 CST)
- Re: question to run namd2 with multiple CPUs Yu, Tao (Mon Mar 02 2020 - 15:08:04 CST)
- Re: question to run namd2 with multiple CPUs Victor Kwan (Thu Mar 05 2020 - 18:33:23 CST)
- Re: question to run namd2 with multiple CPUs Josh Vermaas (Fri Feb 28 2020 - 16:29:09 CST)
- bad angle error!! ROPĂ“N-PALACIOS G. (Thu Feb 27 2020 - 21:10:45 CST)
- Re: Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 14:28:19 CST)
- Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 12:32:58 CST)
- QM/MM error in the charges Aashish Bhatt (Thu Feb 27 2020 - 04:14:45 CST)
- AW: vmd-l: How to increase the number of core Norman Geist (Wed Feb 26 2020 - 01:59:33 CST)
- Swarms of Trajectrories MPI NAMD Run Ebru Çetin (Tue Feb 25 2020 - 10:15:37 CST)
- Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Tue Feb 25 2020 - 04:23:19 CST)
- The best initial structure of Protein-Protein complex Alireza Mansouri (Mon Feb 24 2020 - 03:54:21 CST)
- Protocol share Ribosome ROPĂ“N-PALACIOS G. (Fri Feb 21 2020 - 09:05:33 CST)
- Can NAMD 2.13 be build on Charm++ with UCX backend? ĺĽ é©ć´˛ (Fri Feb 21 2020 - 03:55:25 CST)
- Bad global bond count! Francesco Pietra (Tue Feb 18 2020 - 15:07:46 CST)
- (no subject) Francesco Pietra (Tue Feb 18 2020 - 15:05:34 CST)
- FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sat Feb 15 2020 - 23:45:11 CST)
- Conformation Sampling tutorial: factor of 2 in monitor.sh Alexander Adams (Tue Feb 11 2020 - 13:24:21 CST)
- Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 14:34:38 CST)
- Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 05 2020 - 12:12:29 CST)
- Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Wed Feb 05 2020 - 12:51:05 CST)
- Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 05 2020 - 13:34:38 CST)
- Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Mon Feb 10 2020 - 06:14:11 CST)
- Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Mon Feb 10 2020 - 20:41:47 CST)
- Re: Flat-bottom harmonic position restraints using colvars David Hardy (Tue Feb 11 2020 - 15:57:40 CST)
- Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Tue Feb 11 2020 - 16:12:12 CST)
- Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 12 2020 - 19:24:22 CST)
- Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Wed Feb 05 2020 - 12:51:05 CST)
- mail about cuda exculssion count Vidhya Sankar (Wed Feb 05 2020 - 06:28:37 CST)
- How are the virial related variables passed from GPU to CPU memory? ĺĽ é©ć´˛ (Tue Feb 04 2020 - 04:13:21 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Mon Feb 03 2020 - 09:50:27 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Mon Feb 03 2020 - 10:07:57 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Tue Feb 04 2020 - 09:02:41 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Wed Feb 05 2020 - 08:10:34 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Wed Feb 05 2020 - 09:18:50 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Thu Feb 06 2020 - 00:28:01 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Wed Feb 05 2020 - 08:10:34 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Thu Feb 06 2020 - 09:50:39 CST)
- FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Sun Feb 02 2020 - 22:00:48 CST)
- Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 08:32:52 CST)
- Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 09:22:02 CST)
- Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:14:59 CST)
- Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 10:18:48 CST)
- Re: [External Email] Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:30:02 CST)
- Re: [External Email] Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 10:35:02 CST)
- Re: [External Email] Re: [External Email] Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:36:51 CST)
- Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:14:59 CST)
- Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 09:22:02 CST)
- problem with TIP4P on nightly version Laura Lopes (Fri Jan 31 2020 - 04:22:42 CST)
- Solvent Heating with Rigid Bonds ben estimated.com (Sun Jan 26 2020 - 22:07:34 CST)
- Why very large force reported at the starting point of constant velocity SMD run in NAMD log file? Shadi Rahnama (Sat Jan 25 2020 - 14:56:57 CST)
- Topology and parameter files for flavonoid compounds Shruthi M (116011752017) Res/Bio-Tech (Fri Jan 24 2020 - 00:42:52 CST)
- Re: vmd-l: NAMD and VMD Armv8-A Giacomo Fiorin (Thu Jan 23 2020 - 09:37:59 CST)
- GaMD with nucleotides Francesco Pietra (Thu Jan 23 2020 - 09:30:57 CST)
- Analysis of force applied to a certain atom nikolaev_at_spbau.ru (Thu Jan 23 2020 - 09:12:27 CST)
- Amber14 in NAMD 2.13 nikolaev_at_spbau.ru (Thu Jan 23 2020 - 08:57:23 CST)
- spontaneous binding pathway with PMF calculation? Jiali Wang (Mon Jan 20 2020 - 21:42:47 CST)
- GaMD config file Francesco Pietra (Mon Jan 20 2020 - 15:43:10 CST)
- Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru (Fri Jan 17 2020 - 03:33:13 CST)
- modelling an aqueous solution of protein+hydrogen peroxide Artur Hermano (Wed Jan 15 2020 - 17:50:41 CST)
- log file Alexei Rossokhin (Tue Jan 14 2020 - 08:36:53 CST)
- harmonic-restraints/colvars Francesco Pietra (Tue Jan 14 2020 - 03:44:06 CST)
- How to protonate GLU Kaique Gracia De Sá Billotta (Fri Jan 10 2020 - 11:56:05 CST)
- Unable to calculate SMD for amber topology Aashish Bhatt (Fri Jan 10 2020 - 08:33:10 CST)
- Measuring Kinetic Energy of Solvent ben estimated.com (Tue Jan 07 2020 - 17:00:00 CST)
- Order of Minimizing/Heating/Equilibrating ben estimated.com (Tue Jan 07 2020 - 16:33:51 CST)
- LIE protocol in QM/MM Shahar Keinan (Fri Jan 03 2020 - 07:25:04 CST)
Last message date: Thu Dec 30 2021 - 09:20:14 CST
Archived on: Fri Dec 31 2021 - 23:17:12 CST
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