Amber Archive Mar 2024 by thread
- Re: [AMBER] Constant pH replica exchange Dulal Mondal via AMBER (Thu Feb 29 2024 - 23:08:16 PST)
- [AMBER] Metadynamics question Matthew Guberman-Pfeffer via AMBER (Fri Mar 01 2024 - 04:11:14 PST)
- [AMBER] Using PLUMED to Calculate Collective Variables and GaMD Reweighting in Amber Munazzah Fatima Ansari via AMBER (Fri Mar 01 2024 - 05:35:14 PST)
- Re: [AMBER] Error building Amber22 with cuda Dhariwal, Rohit via AMBER (Fri Mar 01 2024 - 08:35:06 PST)
- [AMBER] Unable to compile with CUDA Weatherby,Gerard via AMBER (Fri Mar 01 2024 - 10:53:40 PST)
- Re: [AMBER] uncertainty in atomic positional fluctuations Duggan, Brendan via AMBER (Fri Mar 01 2024 - 11:36:16 PST)
- Re: [AMBER] Please remove my email from mailing list. Thank you David A Case via AMBER (Fri Mar 01 2024 - 17:31:56 PST)
- Re: [AMBER] Sander.mpi haults at 999 steps David A Case via AMBER (Fri Mar 01 2024 - 17:29:59 PST)
- Re: [AMBER] make install error related to pmemd xray & MKL David A Case via AMBER (Fri Mar 01 2024 - 17:36:08 PST)
- Re: [AMBER] Renumber residues (Error: No change type specified) - AMBER MD 18 David A Case via AMBER (Fri Mar 01 2024 - 17:39:17 PST)
- [AMBER] amber18 compilation for cuda.MPI Dulal Mondal via AMBER (Fri Mar 01 2024 - 22:59:15 PST)
- [AMBER] CUDA version installation error: undefined reference to 'gpu_aoint_' Abdelaty, Mohamed via AMBER (Sat Mar 02 2024 - 11:28:59 PST)
- [AMBER] ir6 restraint with pmemd.cuda problem Niklas Halbwedl via AMBER (Mon Mar 04 2024 - 00:54:45 PST)
- [AMBER] MMGBSA Calculation Warning Robert Palmere via AMBER (Mon Mar 04 2024 - 06:07:39 PST)
- [AMBER] MMGBSA Analysis Joshi, Keya via AMBER (Mon Mar 04 2024 - 07:35:25 PST)
- Re: [AMBER] using 12_6_4 ion parameters with OPC water model Carlos Simmerling via AMBER (Mon Mar 04 2024 - 09:54:33 PST)
- [AMBER] NPT run prior to REMD Liyanage, Risi \(MU-Student\) via AMBER (Mon Mar 04 2024 - 13:36:17 PST)
- [AMBER] Suitable water model for solvent-exposed structures? Sasha Buzko via AMBER (Mon Mar 04 2024 - 17:30:39 PST)
- [AMBER] Issue with ANTECHAMBER library file generation Sayan Poddar via AMBER (Tue Mar 05 2024 - 06:37:59 PST)
- [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER (Tue Mar 05 2024 - 11:58:05 PST)
- [AMBER] ESANDER output question Matthew Guberman-Pfeffer via AMBER (Wed Mar 06 2024 - 13:48:54 PST)
- [AMBER] How to reduce the standard deviation of MMPBSA Yang Wei via AMBER (Wed Mar 06 2024 - 16:13:45 PST)
- [AMBER] Gaussian imput error in QM/MM with external user template Claire Claire via AMBER (Thu Mar 07 2024 - 05:24:53 PST)
- [AMBER] MM-GBSA Entropy Calculation Error Robert Palmere via AMBER (Thu Mar 07 2024 - 06:59:03 PST)
- [AMBER] Generate prmtop file using parmed. Dulal Mondal via AMBER (Thu Mar 07 2024 - 07:21:16 PST)
- [AMBER] How to add KCl cellular concentration. Sayan Poddar via AMBER (Thu Mar 07 2024 - 07:50:31 PST)
- [AMBER] cpptraj.mpi for multi-frame pdb trajectory Enrico Martinez via AMBER (Fri Mar 08 2024 - 00:59:02 PST)
- [AMBER] Adding extra solvent molecules to a membrane-protein system Bhattacharjee, Sinjini via AMBER (Fri Mar 08 2024 - 06:05:35 PST)
- [AMBER] AMBER error vlimit exceed for step VERONICA MARTIN HERNANDEZ via AMBER (Fri Mar 08 2024 - 08:20:24 PST)
- [AMBER] Partial charge calculation from gaussian ESP calculation Intravaia, Lauren E via AMBER (Fri Mar 08 2024 - 13:14:04 PST)
- Re: [AMBER] No restraint defined when using torsional restraints Carlos Simmerling via AMBER (Fri Mar 08 2024 - 14:33:53 PST)
- [AMBER] Any news on AMBER24 release? Cenk Andac via AMBER (Sat Mar 09 2024 - 14:38:59 PST)
- Re: [AMBER] imaging membrane system Daniel Roe via AMBER (Sun Mar 10 2024 - 09:46:06 PDT)
- [AMBER] Simulation not running on more than one MPI process with 12-6-4 parameters Markowska (Mon Mar 11 2024 - 00:10:17 PDT)
- [AMBER] Running TI calculations VERONICA MARTIN HERNANDEZ via AMBER (Mon Mar 11 2024 - 00:57:40 PDT)
- [AMBER] New cpptraj processing issue with oligomeric system Enrico Martinez via AMBER (Mon Mar 11 2024 - 06:55:31 PDT)
- Re: [AMBER] [Sender Not Verified] Re: Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER (Mon Mar 11 2024 - 11:24:59 PDT)
- [AMBER] Modelling missing residues VERONICA MARTIN HERNANDEZ via AMBER (Wed Mar 13 2024 - 01:31:19 PDT)
- [AMBER] Hamiltonian REMD simulation Dulal Mondal via AMBER (Wed Mar 13 2024 - 01:58:07 PDT)
- [AMBER] Peptide linked to a protein: force field limitations? Sasha Buzko via AMBER (Wed Mar 13 2024 - 07:56:27 PDT)
- [AMBER] Boost Error in MoFT - metatwist Lorenzo Cupellini via AMBER (Thu Mar 14 2024 - 07:19:30 PDT)
- [AMBER] Fw: Cpptraj Question Mariam Ibrahim via AMBER (Thu Mar 14 2024 - 08:32:06 PDT)
- [AMBER] RMSD Calculation Advice Kaleem Arshad via AMBER (Thu Mar 14 2024 - 11:02:04 PDT)
- [AMBER] Amber FF simulations with lipids not in LIPID21 Derek M Shore via AMBER (Thu Mar 14 2024 - 15:15:53 PDT)
- [AMBER] cpptraj error with Test_SPAM Hirosuke Hotta \(Fujitsu\) via AMBER (Thu Mar 14 2024 - 23:13:44 PDT)
- [AMBER] mpirun error for thermodynamic integration Dulal Mondal via AMBER (Fri Mar 15 2024 - 06:31:01 PDT)
- [AMBER] cpptraj nastruct defined base-pairing Slavnikova Pavlina via AMBER (Fri Mar 15 2024 - 08:07:11 PDT)
- [AMBER] (UNKNOWN ATOM TYPE: c5) Trevor Kramer via AMBER (Fri Mar 15 2024 - 12:43:41 PDT)
- [AMBER] Multiple trajectory MMPBSA Yang Wei via AMBER (Fri Mar 15 2024 - 13:37:06 PDT)
- [AMBER] Minimization fails with a larger solvent box Sasha Buzko via AMBER (Sat Mar 16 2024 - 19:54:34 PDT)
- [AMBER] 回复: NaN error during heating in building 12-6-4 LJ multisite Mg2+ model of DNA gyrase. 郭 家藩 via AMBER (Sat Mar 16 2024 - 21:57:41 PDT)
- [AMBER] Antechamber Error SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Sun Mar 17 2024 - 03:32:14 PDT)
- [AMBER] Maximum coordination exceeded on metal ions 杨镇岳 via AMBER (Sun Mar 17 2024 - 04:03:37 PDT)
- Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step VERONICA MARTIN HERNANDEZ via AMBER (Mon Mar 18 2024 - 07:37:16 PDT)
- [AMBER] Unable to reproduce the results from Amber RISM tutorial with Amber22 Markowska (Tue Mar 19 2024 - 10:13:02 PDT)
- [AMBER] Compressing/Expanding Monolayer Systems Amanda Ferrante via AMBER (Tue Mar 19 2024 - 16:02:53 PDT)
- [AMBER] Possible bug in PMEMD (appearence of synchronization artifacts between parallel tasks) Charo del Genio via AMBER (Wed Mar 20 2024 - 04:28:21 PDT)
- [AMBER] MM-PBSA for membrane protein system Bhattacharjee, Sinjini via AMBER (Wed Mar 20 2024 - 05:45:31 PDT)
- Re: [AMBER] GAMESS QM optimization protocols James Kress via AMBER (Thu Mar 21 2024 - 12:36:51 PDT)
- [AMBER] Non-Standard Parametrization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER (Thu Mar 21 2024 - 22:38:42 PDT)
- [AMBER] Issue with glycam nomenclature SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Fri Mar 22 2024 - 03:46:04 PDT)
- [AMBER] Protein Binding Question Matthew Guberman-Pfeffer via AMBER (Fri Mar 22 2024 - 05:40:07 PDT)
- [AMBER] Parametrization of a system with missed loop fragments Enrico Martinez via AMBER (Fri Mar 22 2024 - 08:31:09 PDT)
- [AMBER] Query regarding amber20 ambertools23 installation Sayan Poddar via AMBER (Sat Mar 23 2024 - 09:56:09 PDT)
- [AMBER] amber20 installation issue Sayan Poddar via AMBER (Sat Mar 23 2024 - 23:00:49 PDT)
- [AMBER] generate prmtop and inpcrd file Dulal Mondal via AMBER (Sun Mar 24 2024 - 06:39:24 PDT)
- [AMBER] error_install_run_cmake_Amber22 ABDELATIF MESSAOUDI via AMBER (Sun Mar 24 2024 - 10:35:59 PDT)
- Re: [AMBER] Error - Amber 22 Installation David A Case via AMBER (Sun Mar 24 2024 - 11:34:14 PDT)
- [AMBER] Error_install_run_cmake_Amber22 ABDELATIF MESSAOUDI via AMBER (Mon Mar 25 2024 - 11:07:07 PDT)
- [AMBER] LJ Energy Mismatch William Livernois via AMBER (Mon Mar 25 2024 - 13:24:20 PDT)
- [AMBER] Information about number of water molecules found in .out files Maria Bzówka via AMBER (Tue Mar 26 2024 - 06:40:09 PDT)
- [AMBER] Error with Amber22 test.serial Sayan Poddar via AMBER (Tue Mar 26 2024 - 10:55:45 PDT)
- [AMBER] Dpeaks Clustering Algorithm Joshi, Keya via AMBER (Tue Mar 26 2024 - 11:00:01 PDT)
- [AMBER] Install Amber22 CUDA_12.0 ABDELATIF MESSAOUDI via AMBER (Wed Mar 27 2024 - 02:53:49 PDT)
- [AMBER] native contacts calculation using cpptraj Prithviraj Nandigrami via AMBER (Wed Mar 27 2024 - 16:15:02 PDT)
- [AMBER] make-install amber22_cuda ABDELATIF MESSAOUDI via AMBER (Thu Mar 28 2024 - 03:18:57 PDT)
- [AMBER] Regarding MMPBSA calculation: Kankana Bhattacharjee via AMBER (Thu Mar 28 2024 - 21:50:25 PDT)
- [AMBER] Minimization with pmemd.cuda Enrico Martinez via AMBER (Fri Mar 29 2024 - 07:33:48 PDT)
- [AMBER] RMSD of protein with domain insertion Colin Pierce via AMBER (Fri Mar 29 2024 - 09:38:16 PDT)
- Last message date: Fri Mar 29 2024 - 15:30:02 PDT
- Archived on: Wed Dec 11 2024 - 05:56:09 PST
