Amber Archive Jan 2021 by thread
- [AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory assawin daducale (Fri Jan 01 2021 - 11:07:25 PST)
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Mohd Farid Ismail (Fri Jan 01 2021 - 16:54:56 PST)
- [AMBER] doubt frames simulation MYRIAN TORRES RICO (Sat Jan 02 2021 - 05:00:50 PST)
- [AMBER] Problem with PB calculation CAVALLARO MATTIA (Sat Jan 02 2021 - 06:24:20 PST)
- [AMBER] Generating LJ paramters of divalent copper ions angad sharma (Sat Jan 02 2021 - 10:15:43 PST)
- [AMBER] do you know Gordon Richard Chalmers (Sun Jan 03 2021 - 04:57:50 PST)
- [AMBER] error... MYRIAN TORRES RICO (Sun Jan 03 2021 - 09:19:00 PST)
- [AMBER] SMD & MULTI_RMSD Fabian Glaser (Sun Jan 03 2021 - 09:47:21 PST)
- [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer (Sun Jan 03 2021 - 12:37:09 PST)
- [AMBER] How to apply GLYCAM Parameters Matthew Guberman-Pfeffer (Sun Jan 03 2021 - 12:45:07 PST)
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Mon Jan 04 2021 - 00:56:57 PST)
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Li,Haoxi (Mon Jan 04 2021 - 09:13:32 PST)
- [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes (Mon Jan 04 2021 - 13:20:26 PST)
- [AMBER] Error in the apr.py code - steered MD simulation Eduardo R. Almeida (Mon Jan 04 2021 - 19:29:23 PST)
- [AMBER] cif to pdb Pinky Mazumder (Mon Jan 04 2021 - 20:19:22 PST)
- [AMBER] Energy Evaluations Matthew Guberman-Pfeffer (Mon Jan 04 2021 - 20:51:42 PST)
- [AMBER] tinker_to_amber Юлия Беляева (Tue Jan 05 2021 - 11:16:01 PST)
- [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Tue Jan 05 2021 - 16:55:17 PST)
- [AMBER] pytraj in python 3.9 Abdul-Rashid III Sampaco (Tue Jan 05 2021 - 20:54:53 PST)
- [AMBER] Sander code doesn’t output trajectory files K Jan (Wed Jan 06 2021 - 04:58:23 PST)
- [AMBER] Fwd: copper RISM angad sharma (Wed Jan 06 2021 - 06:13:38 PST)
- [AMBER] GB pairwise decomposition - Salt Bridge Tarsis (Wed Jan 06 2021 - 06:28:57 PST)
- [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom Mateusz Bieniek (Wed Jan 06 2021 - 06:40:28 PST)
- [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 15:15:55 PST)
- [AMBER] RMSD analysis K Jan (Thu Jan 07 2021 - 14:34:51 PST)
- [AMBER] MD GPU Scaling Performance Jatin Kashyap (Thu Jan 07 2021 - 14:38:26 PST)
- [AMBER] CPPTRAJ error while Clustering Maghsoud, Yazdan (Fri Jan 08 2021 - 08:08:27 PST)
- [AMBER] Error in xleap: water molecules Eduardo R. Almeida (Fri Jan 08 2021 - 15:39:20 PST)
- [AMBER] how to pull group of atoms towards a fixed molecule using Steered molecular dynamics simulation Pinky Mazumder (Fri Jan 08 2021 - 17:11:43 PST)
- [AMBER] How to apply shear loading on carbohydrates Pinky Mazumder (Fri Jan 08 2021 - 21:11:18 PST)
- [AMBER] Domain distances using cpptraj Athena N (Fri Jan 08 2021 - 23:19:12 PST)
- [AMBER] How to pull/push group of atoms Pinky Mazumder (Sat Jan 09 2021 - 21:06:06 PST)
- [AMBER] Probmlems compiling under macOS Gustaf Olsson (Sun Jan 10 2021 - 00:13:00 PST)
- [AMBER] Error searching for compatible GPU Hongwei Tan (Sun Jan 10 2021 - 00:29:22 PST)
- [AMBER] Issue about the generaton of rst files 辛志宏 (Sun Jan 10 2021 - 06:41:11 PST)
- [AMBER] TI simulation blowing up with pmemd.CUDA Delwakkada Liyanage, Senal Dinuka (Sun Jan 10 2021 - 10:07:39 PST)
- [AMBER] Preparation of input file for RAMD (Geng Dong) 东庚 (Sun Jan 10 2021 - 20:11:12 PST)
- [AMBER] Lateral movement of membrane bound protein during MD simulation in Amber Biplab Ghosh (Sun Jan 10 2021 - 21:27:36 PST)
- [AMBER] How to use AM1 for Ti atom in Amber? 孙天宇 (Sun Jan 10 2021 - 21:28:23 PST)
- [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Vaibhav Dixit (Sun Jan 10 2021 - 22:59:49 PST)
- [AMBER] Cpptraj v13 command is not working fixatomorder Ana Ziad (Sun Jan 10 2021 - 23:01:44 PST)
- [AMBER] Problem in running cmake Airy Sanjeev (Sun Jan 10 2021 - 23:17:00 PST)
- [AMBER] error job MYRIAN TORRES RICO (Mon Jan 11 2021 - 03:09:58 PST)
- [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Mon Jan 11 2021 - 03:45:14 PST)
- [AMBER] US or SMD for torsion angle steering? Fabian Glaser (Mon Jan 11 2021 - 06:31:08 PST)
- [AMBER] Pull group of atoms together Pinky Mazumder (Mon Jan 11 2021 - 10:34:11 PST)
- [AMBER] Spam purewater keyword Debarati DasGupta (Mon Jan 11 2021 - 12:49:02 PST)
- [AMBER] Fwd: Creating a bond in leap Victoria E Hill (Mon Jan 11 2021 - 13:37:33 PST)
- [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Amanda Buyan (Mon Jan 11 2021 - 19:24:58 PST)
- [AMBER] Issue about the generaton of rst files 辛志宏 (Tue Jan 12 2021 - 04:33:44 PST)
- [AMBER] ff15ipq-m force field for protein mimetics Lillian Chong (Tue Jan 12 2021 - 05:46:41 PST)
- [AMBER] Problems when running make test.parallel Beatriz Gomes Guimaraes (Tue Jan 12 2021 - 06:35:36 PST)
- [AMBER] abfQMMM with Terachem Eugen Hruska (Tue Jan 12 2021 - 10:21:06 PST)
- [AMBER] Non-integer/zero charges from RESP fitting? Kenneth Huang (Tue Jan 12 2021 - 11:18:04 PST)
- Re: [AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Goetz, Andreas (Tue Jan 12 2021 - 16:15:54 PST)
- [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach (Wed Jan 13 2021 - 01:43:07 PST)
- [AMBER] Errors whilst installing GPU Amber20 Victoria E Hill (Wed Jan 13 2021 - 03:58:43 PST)
- [AMBER] gaff/parm MYRIAN TORRES RICO (Thu Jan 14 2021 - 01:36:10 PST)
- [AMBER] PROTEIN-DNA RMSD plots Syeda Amna Arshi (Thu Jan 14 2021 - 03:14:05 PST)
- [AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com (Thu Jan 14 2021 - 05:03:45 PST)
- [AMBER] Number of na, cl ions Женя Елизарова (Thu Jan 14 2021 - 08:10:11 PST)
- [AMBER] DNA-ligand simulation Kehinde Idowu (Thu Jan 14 2021 - 16:33:20 PST)
- [AMBER] Question of targeted molecular dynamics simulation 吴晓东 (Thu Jan 14 2021 - 18:37:16 PST)
- [AMBER] Typo in update.13 for AmberTools20 Hashemi, Mohtadin (Fri Jan 15 2021 - 12:28:26 PST)
- [AMBER] How to use GLYCAM_06j-1 in LAMMPS Pinky Mazumder (Fri Jan 15 2021 - 15:43:05 PST)
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Fri Jan 15 2021 - 18:01:53 PST)
- [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected Loki (Sat Jan 16 2021 - 03:54:54 PST)
- [AMBER] Langevin thermostat different gamma_ln giving systematically different energies? Liao (Sat Jan 16 2021 - 17:44:16 PST)
- [AMBER] How to apply Compressive loading on wood Pinky Mazumder (Sat Jan 16 2021 - 18:55:54 PST)
- Re: [AMBER] lj1264 in vacuum Pengfei Li (Sat Jan 16 2021 - 19:21:56 PST)
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Sat Jan 16 2021 - 19:29:17 PST)
- [AMBER] antechamber assigns DU as atom type for nitrogen nguerin (Sat Jan 16 2021 - 19:47:04 PST)
- [AMBER] working with mmpbsa with protein and three ligands in same complex Sadaf Rani (Sun Jan 17 2021 - 02:36:31 PST)
- [AMBER] Distance of every c alpha in a protein to every other c alpha Jenny 148 (Sun Jan 17 2021 - 21:50:28 PST)
- [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 15:17:02 PST)
- [AMBER] Extending DNA structure Airy Sanjeev (Mon Jan 18 2021 - 19:57:16 PST)
- [AMBER] vlimit exceeded for step 0; vmax = 50.6241 Pinky Mazumder (Tue Jan 19 2021 - 13:50:09 PST)
- [AMBER] Creating input files using tleap Nicy yadav (Tue Jan 19 2021 - 14:27:00 PST)
- [AMBER] makedepend for sander Antoine MARION (Wed Jan 20 2021 - 03:26:06 PST)
- [AMBER] combining crashed trajectories Ayesha Fatima (Wed Jan 20 2021 - 05:58:19 PST)
- [AMBER] The long and winding STSM Luis Simon (Wed Jan 20 2021 - 07:56:33 PST)
- [AMBER] Major Cpptraj Update (GitHub) Daniel Roe (Wed Jan 20 2021 - 11:54:44 PST)
- [AMBER] ZAFF force field Tabassum Khair Barbhuiya (Wed Jan 20 2021 - 17:09:11 PST)
- [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani (Wed Jan 20 2021 - 21:13:09 PST)
- [AMBER] Fwd: Error during amber16 installation spss4.iacs.res.in (Thu Jan 21 2021 - 02:29:46 PST)
- [AMBER] question MYRIAN TORRES RICO (Thu Jan 21 2021 - 03:05:45 PST)
- [AMBER] Cpptraj Stejskal, Lenka (Thu Jan 21 2021 - 07:14:43 PST)
- [AMBER] Nvidia RTX 3080/3090 Servers mish (Thu Jan 21 2021 - 18:48:54 PST)
- [AMBER] Energy minimization script raissa.conceicao.bol.com.br (Fri Jan 22 2021 - 05:45:00 PST)
- [AMBER] How to extract restart file with velocity from a trajectory file? 辛志宏 (Fri Jan 22 2021 - 06:19:42 PST)
- [AMBER] Understanding File Format Specifications nguerin (Fri Jan 22 2021 - 12:48:45 PST)
- [AMBER] How to pull two group of atoms in two different direction? Pinky Mazumder (Sun Jan 24 2021 - 16:23:33 PST)
- [AMBER] Running simulations richa anand (Sun Jan 24 2021 - 22:41:53 PST)
- [AMBER] Amber 16/cpptraj diffusion command Pau Mayorga Delgado (Mon Jan 25 2021 - 00:37:48 PST)
- [AMBER] DNA protein simulation protocol Airy Sanjeev (Mon Jan 25 2021 - 01:04:14 PST)
- [AMBER] pdb4amber error Nicy yadav (Mon Jan 25 2021 - 08:24:33 PST)
- [AMBER] overall and internal correlation function Mani Radh (Mon Jan 25 2021 - 09:48:12 PST)
- [AMBER] OPC monovalent ion parameters Sebastian Oleksy (Mon Jan 25 2021 - 10:07:26 PST)
- [AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION" Luis Simon (Mon Jan 25 2021 - 13:03:43 PST)
- [AMBER] Help to generate prmtop and .crd files from a PDB trajectory Devlina Chakravarty (Mon Jan 25 2021 - 17:46:03 PST)
- [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Renato Araujo (Mon Jan 25 2021 - 17:49:58 PST)
- [AMBER] how to get amber 18 tools Sadaf Rani (Wed Jan 27 2021 - 04:25:11 PST)
- [AMBER] technical problems with installing amber20 Игорь Злотников (Wed Jan 27 2021 - 04:59:02 PST)
- [AMBER] rotdif analysis in cpptraj Adeleh Mokhles Gerami (Wed Jan 27 2021 - 06:41:02 PST)
- [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder (Wed Jan 27 2021 - 13:49:22 PST)
- [AMBER] How to fix the issue of generating restart file from a trajectory? 辛志宏 (Wed Jan 27 2021 - 20:00:04 PST)
- [AMBER] Error in minimization Kehinde Idowu (Thu Jan 28 2021 - 13:06:05 PST)
- [AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files? Debarati DasGupta (Fri Jan 29 2021 - 06:36:40 PST)
- [AMBER] in chimera, which one should I use for carbohydrates Pinky Mazumder (Fri Jan 29 2021 - 07:38:28 PST)
- [AMBER] Potential energy discrepancy in RXSGLD Charo del Genio (Fri Jan 29 2021 - 08:28:51 PST)
- [AMBER] Suggestions on crossing energy barrier to break strong HBs Amit Sharma (Asstt. Prof., MCARS) (Fri Jan 29 2021 - 15:40:35 PST)
- [AMBER] Bug when using RESPA in REMD runs Charo del Genio (Sat Jan 30 2021 - 03:23:41 PST)
- [AMBER] Can't restart a RXSGLD run (possible bug) Charo del Genio (Sun Jan 31 2021 - 02:13:41 PST)
- [AMBER] Non zero ligand warning Ayesha Fatima (Sun Jan 31 2021 - 05:10:51 PST)
- [AMBER] Patches to fix the replica exchange restart bug Charo del Genio (Sun Jan 31 2021 - 12:11:59 PST)
- Last message date: Sun Jan 31 2021 - 12:30:02 PST
- Archived on: Fri Dec 20 2024 - 05:56:05 PST
