Amber Archive Jan 2022: by author

A R
- [AMBER] Distorted average pdb structure from 10 ns trajectory !!! (Sun Jan 23 2022 - 06:03:06 PST)
Aashish Bhatt
- Re: [AMBER] QM / MM module query (Wed Jan 19 2022 - 10:19:02 PST)
- [AMBER] QM / MM module query (Thu Jan 13 2022 - 02:56:32 PST)
ABDUL BASIT
- [AMBER] MCPB.py error in GAMESS-US calculations (Sat Jan 08 2022 - 05:51:00 PST)
- [AMBER] 1D-RISM Convergence (Tue Jan 04 2022 - 06:34:50 PST)
Alan
- Re: [AMBER] Protein + DNA, which FF? (Mon Jan 17 2022 - 02:05:26 PST)
- [AMBER] Protein + DNA, which FF? (Mon Jan 17 2022 - 01:50:18 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Fri Jan 14 2022 - 03:42:17 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Fri Jan 14 2022 - 03:31:07 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Thu Jan 13 2022 - 08:16:13 PST)
- [AMBER] Single Point Energy: sander x python sander (Thu Jan 13 2022 - 01:26:51 PST)
- Re: [AMBER] sqm performance: does it run in parallel? (Sat Jan 01 2022 - 02:51:57 PST)
Alexis Azucena
- Re: [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM (Mon Jan 17 2022 - 17:33:07 PST)
- [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM (Sun Jan 16 2022 - 22:42:17 PST)
Antonio Frances Monerris
- Re: [AMBER] ?==?utf-8?q? Distorted water molecules in QM partition (possible?==?utf-8?q? bug) (Tue Jan 18 2022 - 08:26:31 PST)
- [AMBER] Distorted water molecules in QM partition (possible bug) (Mon Jan 17 2022 - 07:56:26 PST)
- [AMBER] Amber21/Orca5.0?==?utf-8?q? QM/MM simulations (Mon Jan 10 2022 - 11:22:07 PST)
Arooma Maryam
- [AMBER] About the drug charge _antechamber (Wed Jan 12 2022 - 10:21:36 PST)
- [AMBER] Help in ligand preparation_antechamber (Mon Jan 10 2022 - 10:59:19 PST)
Björn Karlsson
- Re: [AMBER] NETCDF problem (Fri Jan 14 2022 - 09:51:52 PST)
- Re: [AMBER] NETCDF problem (Fri Jan 14 2022 - 05:27:46 PST)
- [AMBER] NETCDF problem (Fri Jan 14 2022 - 01:28:00 PST)
Burns Casamayor, Violeta
- [AMBER] CMAP and NBFIX Charmm36 in amber (Thu Jan 13 2022 - 10:31:56 PST)
Carlos Simmerling
- Re: [AMBER] dihedral restraints slowing down simulation (Fri Jan 28 2022 - 09:30:46 PST)
- Re: [AMBER] Calculating energies per residue pair, rather than per residue (Fri Jan 28 2022 - 02:09:14 PST)
- Re: [AMBER] Regarding targeted md (Thu Jan 27 2022 - 03:50:43 PST)
- Re: [AMBER] dihedral restraints slowing down simulation (Thu Jan 27 2022 - 03:43:40 PST)
- Re: [AMBER] dihedral restraints slowing down simulation (Wed Jan 26 2022 - 13:41:43 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Tue Jan 25 2022 - 07:26:00 PST)
- Re: [AMBER] Regarding targeted md (Tue Jan 25 2022 - 04:17:16 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Mon Jan 24 2022 - 13:46:26 PST)
- Re: [AMBER] Distorted average pdb structure from 10 ns trajectory !!! (Sun Jan 23 2022 - 06:11:04 PST)
- Re: [AMBER] Comparing trajectories (Wed Jan 19 2022 - 13:16:36 PST)
- Re: [AMBER] low-water system, bad NPT and NVT (Mon Jan 17 2022 - 16:38:29 PST)
- Re: [AMBER] Need help with SMD (Mon Jan 17 2022 - 09:41:31 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable (Sat Jan 08 2022 - 06:07:27 PST)
- Re: [AMBER] lipid modification to a nucleic acid base (Wed Jan 05 2022 - 04:49:09 PST)
Casalini Tommaso
- [AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers? (Sun Jan 09 2022 - 23:51:49 PST)
Cenk Andac
- Re: [AMBER] Torsion parameters (Fri Jan 28 2022 - 06:13:33 PST)
- [AMBER] Torsion parameters (Fri Jan 28 2022 - 04:30:26 PST)
Chris Lee
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file (Sun Jan 09 2022 - 08:43:03 PST)
Christina Bergonzo
- Re: [AMBER] attaching a residue to DNA (Mon Jan 10 2022 - 06:04:23 PST)
Damiano Spadoni
- Re: [AMBER] Li salt parameterisation issue (Mon Jan 03 2022 - 08:05:31 PST)
Daniel Burns
- Re: [AMBER] Restraint removal doesn't seem to be happening (Sat Jan 15 2022 - 09:44:28 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening (Sat Jan 15 2022 - 06:17:42 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening (Fri Jan 14 2022 - 16:29:10 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening (Thu Jan 13 2022 - 07:30:04 PST)
- [AMBER] Restraint removal doesn't seem to be happening (Wed Jan 12 2022 - 13:42:04 PST)
Daniel Fowles
- [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files (Wed Jan 19 2022 - 04:26:45 PST)
- [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files (Tue Jan 18 2022 - 02:25:44 PST)
Daniel Konstantinovsky
- [AMBER] adding ions to half the water box (Tue Jan 25 2022 - 08:54:53 PST)
- Re: [AMBER] MEOHBOX/CHCL3BOX not working (Mon Jan 24 2022 - 14:17:54 PST)
- [AMBER] MEOHBOX/CHCL3BOX not working (Mon Jan 24 2022 - 13:41:54 PST)
- [AMBER] low-water system, bad NPT and NVT (Mon Jan 17 2022 - 15:01:09 PST)
- [AMBER] RESP giving ridiculous charges (Tue Jan 11 2022 - 11:59:43 PST)
- Re: [AMBER] how to stop making terminal residue (Tue Jan 11 2022 - 07:08:54 PST)
- [AMBER] how to stop making terminal residue (Mon Jan 10 2022 - 08:34:03 PST)
- [AMBER] attaching a residue to DNA (Sun Jan 09 2022 - 05:37:22 PST)
- Re: [AMBER] tleap error: "expected 'default'" (Fri Jan 07 2022 - 14:17:07 PST)
- Re: [AMBER] RESP doesn't incorporate charge constraint (Fri Jan 07 2022 - 11:12:25 PST)
- [AMBER] RESP doesn't incorporate charge constraint (Fri Jan 07 2022 - 09:54:42 PST)
- [AMBER] lipid modification to a nucleic acid base (Tue Jan 04 2022 - 11:54:21 PST)
Daniel Roe
- Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets (Fri Jan 21 2022 - 15:46:28 PST)
- Re: [AMBER] Aligning a dimer for PCA analysis (Fri Jan 21 2022 - 11:23:25 PST)
- [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets (Tue Jan 18 2022 - 17:21:12 PST)
- Re: [AMBER] number of waters near a mask (K+) cpptraj (Thu Jan 13 2022 - 05:43:03 PST)
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file (Mon Jan 10 2022 - 07:42:17 PST)
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file (Sun Jan 09 2022 - 14:13:49 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable (Sat Jan 08 2022 - 06:42:14 PST)
- Re: [AMBER] Hydrogen Bonding Analysis (Wed Jan 05 2022 - 06:21:18 PST)
David A Case
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points (Mon Jan 31 2022 - 18:17:32 PST)
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points (Mon Jan 31 2022 - 10:23:18 PST)
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Wed Jan 26 2022 - 12:34:53 PST)
- Re: [AMBER] dihedral restraints slowing down simulation (Wed Jan 26 2022 - 12:13:51 PST)
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Wed Jan 26 2022 - 07:08:27 PST)
- Re: [AMBER] adding ions to half the water box (Tue Jan 25 2022 - 10:19:28 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Tue Jan 25 2022 - 10:11:24 PST)
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Tue Jan 25 2022 - 06:22:07 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Tue Jan 25 2022 - 06:06:04 PST)
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Mon Jan 24 2022 - 13:43:22 PST)
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Mon Jan 24 2022 - 06:47:41 PST)
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Mon Jan 24 2022 - 06:27:00 PST)
- Re: [AMBER] Installing amber20 in conda (Thu Jan 20 2022 - 04:07:37 PST)
- Re: [AMBER] Parameterize SO4 (Thu Jan 20 2022 - 04:05:09 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening (Wed Jan 19 2022 - 05:06:27 PST)
- Re: [AMBER] Distorted water molecules in QM partition (possible bug) (Tue Jan 18 2022 - 04:42:33 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening (Fri Jan 14 2022 - 18:55:11 PST)
- Re: [AMBER] NETCDF problem (Fri Jan 14 2022 - 08:38:28 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Fri Jan 14 2022 - 05:20:38 PST)
- Re: [AMBER] NETCDF problem (Fri Jan 14 2022 - 05:13:34 PST)
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? (Thu Jan 13 2022 - 18:13:45 PST)
- Re: [AMBER] CMAP and NBFIX Charmm36 in amber (Thu Jan 13 2022 - 12:34:57 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Thu Jan 13 2022 - 09:37:01 PST)
- Re: [AMBER] QM / MM module query (Thu Jan 13 2022 - 06:27:40 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Thu Jan 13 2022 - 06:25:52 PST)
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory (Thu Jan 13 2022 - 06:18:26 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening (Thu Jan 13 2022 - 06:02:57 PST)
- Re: [AMBER] About the drug charge _antechamber (Wed Jan 12 2022 - 17:51:46 PST)
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory (Wed Jan 12 2022 - 06:05:41 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 (Tue Jan 11 2022 - 18:15:54 PST)
- Re: [AMBER] regading no tortion terms (Tue Jan 11 2022 - 18:07:56 PST)
- Re: [AMBER] how to stop making terminal residue (Tue Jan 11 2022 - 08:06:20 PST)
- Re: [AMBER] Help in ligand preparation_antechamber (Tue Jan 11 2022 - 07:20:00 PST)
- Re: [AMBER] how to stop making terminal residue (Tue Jan 11 2022 - 06:18:46 PST)
- Re: [AMBER] regading no tortion terms (Tue Jan 11 2022 - 06:15:37 PST)
- Re: [AMBER] regading no tortion terms (Mon Jan 10 2022 - 06:14:12 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable (Sat Jan 08 2022 - 05:43:00 PST)
- [AMBER] Problem with reading a mol2 file into tleap (Fri Jan 07 2022 - 18:04:45 PST)
- Re: [AMBER] Heating only a region of the system (Fri Jan 07 2022 - 09:20:29 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Tue Jan 04 2022 - 13:10:10 PST)
- Re: [AMBER] regading no tortion terms (Tue Jan 04 2022 - 06:04:37 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Mon Jan 03 2022 - 13:08:23 PST)
- Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] (Mon Jan 03 2022 - 07:27:33 PST)
- Re: [AMBER] TIP4PD water box error (Sun Jan 02 2022 - 10:08:23 PST)
- Re: [AMBER] DE Shaw RNA parameters error (Sun Jan 02 2022 - 10:03:30 PST)
David Cerutti
- Re: [AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers? (Mon Jan 10 2022 - 09:43:51 PST)
Dr. Anselm Horn
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Wed Jan 26 2022 - 03:15:06 PST)
- Re: [AMBER] Aligning a dimer for PCA analysis (Mon Jan 24 2022 - 01:33:09 PST)
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks (Wed Jan 19 2022 - 02:23:28 PST)
- Re: [AMBER] RESP giving ridiculous charges (Wed Jan 12 2022 - 02:23:25 PST)
- Re: [AMBER] how to stop making terminal residue (Wed Jan 12 2022 - 01:01:00 PST)
- Re: [AMBER] regading no tortion terms (Mon Jan 10 2022 - 06:15:41 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group (Thu Jan 06 2022 - 23:14:43 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group (Wed Jan 05 2022 - 04:40:06 PST)
Erdem Yeler
- Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] (Fri Jan 07 2022 - 16:28:52 PST)
- [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] (Sat Jan 01 2022 - 14:38:15 PST)
Feng Pan
- Re: [AMBER] CV_type (Fri Jan 07 2022 - 08:05:47 PST)
Gerald Monard
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Sun Jan 23 2022 - 03:39:06 PST)
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Sun Jan 23 2022 - 03:31:05 PST)
- Re: [AMBER] Reg: PLP - LYS parameters (Mon Jan 10 2022 - 16:42:43 PST)
Gian Marco ELISI
- [AMBER] Thermodynamic integration equilibration (Wed Jan 12 2022 - 03:23:01 PST)
Guessregen, Stefan /DE
- [AMBER] GCC and EuroSAMPL Satellite Workshop 2022 - Submission deadline extension (Wed Jan 05 2022 - 09:50:50 PST)
Hai Nguyen
- Re: [AMBER] adding ions to half the water box (Tue Jan 25 2022 - 18:04:42 PST)
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks (Wed Jan 19 2022 - 12:31:06 PST)
Huimin Tian
- [AMBER] [MCPB] The force field parameter problem of the MCPB (Fri Jan 14 2022 - 05:30:34 PST)
Jacopo Sgrignani
- [AMBER] SMD (Wed Jan 12 2022 - 00:37:45 PST)
- [AMBER] SMD negative distance (Mon Jan 10 2022 - 07:17:02 PST)
James Kress
- [AMBER] hydrogen mass repartitioning with accelerated MD (Sun Jan 23 2022 - 11:05:32 PST)
- Re: [AMBER] Archive page (Fri Jan 21 2022 - 15:48:27 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 (Tue Jan 11 2022 - 19:34:47 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 (Tue Jan 11 2022 - 15:57:03 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 (Tue Jan 11 2022 - 12:14:55 PST)
- [AMBER] Multi-GPU Bug in Amber20 (Tue Jan 11 2022 - 10:51:51 PST)
- [AMBER] Multi-GPU oddity (Sun Jan 09 2022 - 15:30:11 PST)
Jason Swails
- Re: [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files (Thu Jan 20 2022 - 06:23:31 PST)
- Re: [AMBER] Extending constant pH to additional titratable groups (Mon Jan 03 2022 - 09:12:30 PST)
Jiang, Yaoyukun
- [AMBER] Issue concerning the AMBER/TeraChem interface (Thu Jan 27 2022 - 19:56:00 PST)
John Chodera
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Tue Jan 25 2022 - 14:06:35 PST)
- [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Sun Jan 23 2022 - 18:58:51 PST)
Jordi Bujons
- Re: [AMBER] ghost pmemd.cuda process ? (Tue Jan 25 2022 - 07:52:59 PST)
- [AMBER] ghost pmemd.cuda process ? (Sat Jan 22 2022 - 13:02:53 PST)
Karl Kirschner
- Re: [AMBER] Torsion parameters (Fri Jan 28 2022 - 04:59:23 PST)
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Mon Jan 24 2022 - 00:20:57 PST)
Kellon Belfon
- Re: [AMBER] dihedral restraints slowing down simulation (Thu Jan 27 2022 - 05:09:15 PST)
- Re: [AMBER] dihedral restraints slowing down simulation (Thu Jan 27 2022 - 04:48:34 PST)
- Re: [AMBER] dihedral restraints slowing down simulation (Thu Jan 27 2022 - 00:46:42 PST)
Kenneth Huang
- [AMBER] Adding on terminal hydrogen/phosphate to nucleosides in ff86? (Thu Jan 20 2022 - 11:03:01 PST)
King Wu
- [AMBER] CPPTRAJ for Buried SA (Tue Jan 25 2022 - 16:16:53 PST)
Kodituwakku,Dimuthu Nirmani
- [AMBER] Aligning a dimer for PCA analysis (Fri Jan 21 2022 - 08:19:36 PST)
Lara rajam
- [AMBER] Reg: PLP - LYS parameters (Mon Jan 10 2022 - 11:47:14 PST)
Li,Haoxi
- [AMBER] GaMD error: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Fri Jan 21 2022 - 08:37:26 PST)
Liao
- [AMBER] Heating only a region of the system (Wed Jan 05 2022 - 12:05:15 PST)
Manuel Fernandez Merino
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory (Thu Jan 13 2022 - 06:54:46 PST)
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory (Thu Jan 13 2022 - 01:23:50 PST)
- [AMBER] Running AmberTools21 on HPC cluster using distributed memory (Wed Jan 12 2022 - 01:28:56 PST)
Mark Dixon
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Wed Jan 05 2022 - 07:02:02 PST)
Matthew Guberman-Pfeffer
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points (Mon Jan 31 2022 - 11:16:36 PST)
- Re: [AMBER] Calculating energies per residue pair, rather than per residue (Thu Jan 27 2022 - 19:34:24 PST)
- Re: [AMBER] MEOHBOX/CHCL3BOX not working (Mon Jan 24 2022 - 14:21:49 PST)
- Re: [AMBER] MEOHBOX/CHCL3BOX not working (Mon Jan 24 2022 - 13:59:32 PST)
- Re: [AMBER] Parameterize SO4 (Thu Jan 20 2022 - 21:57:57 PST)
- Re: [AMBER] Parameterize SO4 (Thu Jan 20 2022 - 04:50:00 PST)
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks (Tue Jan 18 2022 - 19:12:31 PST)
- [AMBER] Request for Extra Points Functionality (Thu Jan 13 2022 - 22:01:04 PST)
- [AMBER] MCPB, atom mismatch and naming problem (Tue Jan 11 2022 - 08:42:53 PST)
- Re: [AMBER] tleap error: "expected 'default'" (Fri Jan 07 2022 - 16:41:03 PST)
- Re: [AMBER] tleap error: "expected 'default'" (Fri Jan 07 2022 - 13:50:30 PST)
- Re: [AMBER] RESP doesn't incorporate charge constraint (Fri Jan 07 2022 - 11:18:02 PST)
- Re: [AMBER] RESP doesn't incorporate charge constraint (Fri Jan 07 2022 - 10:42:28 PST)
- Re: [AMBER] Non-standard residue parameterization questions (Sat Jan 01 2022 - 09:39:09 PST)
Michael Coleman
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Mon Jan 24 2022 - 15:51:36 PST)
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Sun Jan 23 2022 - 13:42:39 PST)
- [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) (Fri Jan 21 2022 - 21:05:14 PST)
Ming Tang
- [AMBER] Installing amber20 in conda (Wed Jan 19 2022 - 22:02:10 PST)
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks (Wed Jan 19 2022 - 21:35:31 PST)
- [AMBER] how to obtain index of atoms based on residue and atom masks (Tue Jan 18 2022 - 17:01:41 PST)
- [AMBER] CV_type (Thu Jan 06 2022 - 18:40:55 PST)
MIRA JHAWAR
- Re: [AMBER] regading no tortion terms (Tue Jan 11 2022 - 20:12:23 PST)
- Re: [AMBER] regading no tortion terms (Tue Jan 11 2022 - 07:30:52 PST)
- Re: [AMBER] regading no tortion terms (Tue Jan 11 2022 - 06:20:52 PST)
- Re: [AMBER] regading no tortion terms (Tue Jan 11 2022 - 04:03:43 PST)
- Re: [AMBER] regading no tortion terms (Mon Jan 10 2022 - 08:03:14 PST)
- Re: [AMBER] regading no tortion terms (Mon Jan 10 2022 - 06:29:42 PST)
- Re: [AMBER] regading no tortion terms (Mon Jan 10 2022 - 04:08:02 PST)
- Re: [AMBER] regading no tortion terms (Sun Jan 09 2022 - 22:12:35 PST)
- Re: [AMBER] regading no tortion terms (Sun Jan 09 2022 - 22:08:55 PST)
- [AMBER] regading no tortion terms (Tue Jan 04 2022 - 03:22:34 PST)
- [AMBER] Fw: regarding no tortion terms (Tue Jan 04 2022 - 03:17:26 PST)
Mohamed Aboelnga
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? (Thu Jan 13 2022 - 16:56:45 PST)
Nagar, Hemant
- [AMBER] RESP VS ESP charge fitting (Sat Jan 08 2022 - 17:39:22 PST)
natalia francisca rodriguez cabello
- [AMBER] Need help with SMD (Mon Jan 17 2022 - 08:33:31 PST)
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? (Fri Jan 14 2022 - 04:24:07 PST)
- [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? (Thu Jan 13 2022 - 13:16:07 PST)
Naveen Kumar Vasudevan
- [AMBER] LIE calculation with distance-based mask - reg. (Wed Jan 26 2022 - 17:25:52 PST)
Piotr Cieplak
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark (Mon Jan 24 2022 - 12:39:44 PST)
Pranabesh Mandal (PhD, Bioinformatics August-2019)
- Re: [AMBER] Regarding targeted md (Wed Jan 26 2022 - 23:27:37 PST)
- [AMBER] Regarding targeted md (Mon Jan 24 2022 - 20:30:36 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group (Fri Jan 07 2022 - 21:04:28 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group (Thu Jan 06 2022 - 21:18:18 PST)
- [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group (Wed Jan 05 2022 - 03:49:37 PST)
Prithviraj Nandigrami
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Tue Jan 25 2022 - 07:16:34 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Mon Jan 24 2022 - 14:24:21 PST)
- [AMBER] Restraint file for amber20 with pmemd.cuda implementation (Mon Jan 24 2022 - 13:31:04 PST)
Rafał Madaj
- Re: [AMBER] Restraint removal doesn't seem to be happening (Fri Jan 14 2022 - 01:24:22 PST)
Rakesh Roy
- [AMBER] Problem in mmpbsa calculation (Sun Jan 09 2022 - 21:46:47 PST)
Ray Luo
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points (Mon Jan 31 2022 - 10:59:52 PST)
- Re: [AMBER] Single Point Energy: sander x python sander (Thu Jan 13 2022 - 09:06:18 PST)
Renato Araujo
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Tue Jan 04 2022 - 09:42:54 PST)
Reza Khayat
- Re: [AMBER] Comparing trajectories (Wed Jan 19 2022 - 13:30:11 PST)
- [AMBER] Comparing trajectories (Wed Jan 19 2022 - 13:04:17 PST)
Richard Kullmann
- Re: [AMBER] dihedral restraints slowing down simulation (Thu Jan 27 2022 - 06:28:19 PST)
- Re: [AMBER] dihedral restraints slowing down simulation (Thu Jan 27 2022 - 01:57:40 PST)
- [AMBER] dihedral restraints slowing down simulation (Wed Jan 26 2022 - 06:22:50 PST)
Robert Molt
- Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets (Tue Jan 18 2022 - 17:22:14 PST)
Rodrigo Galindo-Murillo
- Re: [AMBER] Comparing trajectories (Wed Jan 19 2022 - 13:45:14 PST)
Ross Walker
- Re: [AMBER] ghost pmemd.cuda process ? (Mon Jan 24 2022 - 06:45:16 PST)
- [AMBER] A4500 Benchmarks (Tue Jan 18 2022 - 06:50:49 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 (Tue Jan 11 2022 - 11:22:57 PST)
Scott Boesch
- Re: [AMBER] [External] How to calculate multipole moment？ (Wed Jan 12 2022 - 04:57:49 PST)
- Re: [AMBER] [External] How to calculate multipole moment？ (Wed Jan 12 2022 - 04:55:59 PST)
Sruthi Sudhakar
- Re: [AMBER] Error in MMPBSA calculation (Fri Jan 14 2022 - 23:25:20 PST)
- [AMBER] Error in MMPBSA calculation (Fri Jan 14 2022 - 13:54:15 PST)
Suchetana Gupta
- [AMBER] Question on REMD on GPU/CPU (Tue Jan 11 2022 - 20:22:02 PST)
Thomas Cheatham
- Re: [AMBER] Archive page (Fri Jan 21 2022 - 15:29:52 PST)
- Re: [AMBER] Comparing trajectories (Wed Jan 19 2022 - 13:16:26 PST)
tluchko
- Re: [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM (Mon Jan 17 2022 - 11:02:34 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Tue Jan 04 2022 - 13:46:08 PST)
- Re: [AMBER] 1D-RISM Convergence (Tue Jan 04 2022 - 12:04:14 PST)
Tue
- [AMBER] Calculating energies per residue pair, rather than per residue (Thu Jan 27 2022 - 18:09:32 PST)
Vaibhav Dixit
- Re: [AMBER] number of waters near a mask (K+) cpptraj (Thu Jan 13 2022 - 06:32:58 PST)
- [AMBER] number of waters near a mask (K+) cpptraj (Wed Jan 12 2022 - 22:38:55 PST)
Vinicius Wilian Cruzeiro
- Re: [AMBER] Issue concerning the AMBER/TeraChem interface (Thu Jan 27 2022 - 20:40:31 PST)
- Re: [AMBER] Question on REMD on GPU/CPU (Tue Jan 11 2022 - 21:01:49 PST)
Volkan Findik
- [AMBER] Umbrella Sampling Collective Variable (Wed Jan 26 2022 - 23:25:09 PST)
xiangyu
- [AMBER] FEP calculation in tutorial 9 (Sat Jan 08 2022 - 08:12:13 PST)
Xinheng He
- [AMBER] The application of QM/MMGBSA in the evaluation of protein stability, is it reasonable? (Thu Jan 13 2022 - 22:32:49 PST)
Yi Ren
- [AMBER] Bad atom type error and invalid periodicity error in MMPBSA.py (Mon Jan 17 2022 - 00:13:37 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable (Sat Jan 08 2022 - 16:59:24 PST)
- [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable (Fri Jan 07 2022 - 19:01:01 PST)
zz sheng
- [AMBER] The effect of water box size for TI free energy calculation (Wed Jan 26 2022 - 21:17:57 PST)
- Re: [AMBER] Parameterize SO4 (Fri Jan 21 2022 - 05:48:25 PST)
- Re: [AMBER] Parameterize SO4 (Thu Jan 20 2022 - 19:24:20 PST)
- [AMBER] Parameterize SO4 (Wed Jan 19 2022 - 21:37:41 PST)
王世玉
- [AMBER] How to compute MM/PB(GB)SA with Extra Points (Wed Jan 19 2022 - 05:56:30 PST)

Amber Archive Jan 2022 by author