Amber Archive Mar 2024: by date

Thursday, 29 February 2024
- Re: [AMBER] Constant pH replica exchange Dulal Mondal via AMBER
Friday, 1 March 2024
- [AMBER] Metadynamics question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Metadynamics question Carlos Simmerling via AMBER
- Re: [AMBER] Constant pH replica exchange Carlos Simmerling via AMBER
- [AMBER] Using PLUMED to Calculate Collective Variables and GaMD Reweighting in Amber Munazzah Fatima Ansari via AMBER
- Re: [AMBER] Constant pH replica exchange Carlos Simmerling via AMBER
- Re: [AMBER] Error building Amber22 with cuda Dhariwal, Rohit via AMBER
- [AMBER] Unable to compile with CUDA Weatherby,Gerard via AMBER
- Re: [AMBER] uncertainty in atomic positional fluctuations Duggan, Brendan via AMBER
- Re: [AMBER] Please remove my email from mailing list. Thank you David A Case via AMBER
- Re: [AMBER] Sander.mpi haults at 999 steps David A Case via AMBER
- Re: [AMBER] make install error related to pmemd xray & MKL David A Case via AMBER
- Re: [AMBER] Renumber residues (Error: No change type specified) - AMBER MD 18 David A Case via AMBER
- Re: [AMBER] Unable to compile with CUDA David A Case via AMBER
- [AMBER] amber18 compilation for cuda.MPI Dulal Mondal via AMBER
Saturday, 2 March 2024
- Re: [AMBER] Sander.mpi haults at 999 steps Carlos Simmerling via AMBER
- [AMBER] CUDA version installation error: undefined reference to 'gpu_aoint_' Abdelaty, Mohamed via AMBER
- Re: [AMBER] Error building Amber22 with cuda Goetz, Andreas via AMBER
- Re: [AMBER] CUDA version installation error: undefined reference to 'gpu_aoint_' Goetz, Andreas via AMBER
Sunday, 3 March 2024
- Re: [AMBER] amber18 compilation for cuda.MPI Dulal Mondal via AMBER
- Re: [AMBER] amber18 compilation for cuda.MPI Hector A. Baldoni via AMBER
Monday, 4 March 2024
- [AMBER] ir6 restraint with pmemd.cuda problem Niklas Halbwedl via AMBER
- [AMBER] MMGBSA Calculation Warning Robert Palmere via AMBER
- [AMBER] MMGBSA Analysis Joshi, Keya via AMBER
- Re: [AMBER] MMGBSA Analysis Todd Minehardt via AMBER
- Re: [AMBER] Sander.mpi haults at 999 steps Montalvillo, Fernando via AMBER
- Re: [AMBER] Sander.mpi haults at 999 steps Carlos Simmerling via AMBER
- Re: [AMBER] Metadynamics question Carlos Simmerling via AMBER
- Re: [AMBER] MMGBSA Calculation Warning Bill Miller III via AMBER
- Re: [AMBER] using 12_6_4 ion parameters with OPC water model Carlos Simmerling via AMBER
- Re: [AMBER] Sander.mpi haults at 999 steps Montalvillo, Fernando via AMBER
- [AMBER] NPT run prior to REMD Liyanage, Risi \(MU-Student\) via AMBER
- [AMBER] Suitable water model for solvent-exposed structures? Sasha Buzko via AMBER
- Re: [AMBER] Suitable water model for solvent-exposed structures? Carlos Simmerling via AMBER
- Re: [AMBER] amber18 compilation for cuda.MPI Dulal Mondal via AMBER
Tuesday, 5 March 2024
- [AMBER] Issue with ANTECHAMBER library file generation Sayan Poddar via AMBER
- [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Goetz, Andreas via AMBER
Wednesday, 6 March 2024
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
- [AMBER] ESANDER output question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] ESANDER output question Carlos Simmerling via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
- [AMBER] How to reduce the standard deviation of MMPBSA Yang Wei via AMBER
- Re: [AMBER] How to reduce the standard deviation of MMPBSA Adrian Roitberg via AMBER
- Re: [AMBER] How to reduce the standard deviation of MMPBSA Todd Minehardt via AMBER
- Re: [AMBER] Issue with ANTECHAMBER library file generation David A Case via AMBER
- Re: [AMBER] How to reduce the standard deviation of MMPBSA David A Case via AMBER
Thursday, 7 March 2024
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Goetz, Andreas via AMBER
- [AMBER] Gaussian imput error in QM/MM with external user template Claire Claire via AMBER
- [AMBER] MM-GBSA Entropy Calculation Error Robert Palmere via AMBER
- [AMBER] Generate prmtop file using parmed. Dulal Mondal via AMBER
- [AMBER] How to add KCl cellular concentration. Sayan Poddar via AMBER
- Re: [AMBER] How to add KCl cellular concentration. Maria Nagan via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
- Re: [AMBER] Generate prmtop file using parmed. He, Amy via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Hector A. Baldoni via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
Friday, 8 March 2024
- [AMBER] cpptraj.mpi for multi-frame pdb trajectory Enrico Martinez via AMBER
- Re: [AMBER] ir6 restraint with pmemd.cuda problem Niklas Halbwedl via AMBER
- [AMBER] Adding extra solvent molecules to a membrane-protein system Bhattacharjee, Sinjini via AMBER
- Re: [AMBER] Adding extra solvent molecules to a membrane-protein system Stephan Schott via AMBER
- Re: [AMBER] ir6 restraint with pmemd.cuda problem Niklas Halbwedl via AMBER
- [AMBER] AMBER error vlimit exceed for step VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
- Re: [AMBER] Adding extra solvent molecules to a membrane-protein system Todd Minehardt via AMBER
- [AMBER] Partial charge calculation from gaussian ESP calculation Intravaia, Lauren E via AMBER
- Re: [AMBER] Partial charge calculation from gaussian ESP calculation Carlos Simmerling via AMBER
- Re: [AMBER] No restraint defined when using torsional restraints Carlos Simmerling via AMBER
- Re: [AMBER] AMBER error vlimit exceed for step He, Amy via AMBER
Saturday, 9 March 2024
- [AMBER] Any news on AMBER24 release? Cenk Andac via AMBER
Sunday, 10 March 2024
- Re: [AMBER] MM-GBSA Entropy Calculation Error Daniel Roe via AMBER
- Re: [AMBER] imaging membrane system Daniel Roe via AMBER
Monday, 11 March 2024
- [AMBER] Simulation not running on more than one MPI process with 12-6-4 parameters Markowska
- [AMBER] Running TI calculations VERONICA MARTIN HERNANDEZ via AMBER
- [AMBER] New cpptraj processing issue with oligomeric system Enrico Martinez via AMBER
- 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
Wednesday, 13 March 2024
- [AMBER] Modelling missing residues VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Modelling missing residues Charo del Genio via AMBER
- [AMBER] Hamiltonian REMD simulation Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] Modelling missing residues Steinbrecher, Thomas via AMBER
- [AMBER] Peptide linked to a protein: force field limitations? Sasha Buzko via AMBER
- Re: [AMBER] Error building Amber22 with cuda Dhariwal, Rohit via AMBER
- Re: [AMBER] Hamiltonian REMD simulation He, Amy via AMBER
- Re: [AMBER] amber18 compilation for cuda.MPI David A Case via AMBER
- Re: [AMBER] AMBER error vlimit exceed for step David A Case via AMBER
- Re: [AMBER] Peptide linked to a protein: force field limitations? Carlos Simmerling via AMBER
- Re: [AMBER] Peptide linked to a protein: force field limitations? Carlos Simmerling via AMBER
Thursday, 14 March 2024
- [AMBER] Boost Error in MoFT - metatwist Lorenzo Cupellini via AMBER
- [AMBER] Fw: Cpptraj Question Mariam Ibrahim via AMBER
- Re: [AMBER] Boost Error in MoFT - metatwist Stephan Schott via AMBER
- Re: [AMBER] Fw: Cpptraj Question Daniel Roe via AMBER
- [AMBER] RMSD Calculation Advice Kaleem Arshad via AMBER
- [AMBER] Amber FF simulations with lipids not in LIPID21 Derek M Shore via AMBER
- Re: [AMBER] Amber FF simulations with lipids not in LIPID21 Stephan Schott via AMBER
- Re: [AMBER] Amber FF simulations with lipids not in LIPID21 Derek M Shore via AMBER
- [AMBER] cpptraj error with Test_SPAM Hirosuke Hotta \(Fujitsu\) via AMBER
Friday, 15 March 2024
- Re: [AMBER] cpptraj error with Test_SPAM Daniel Roe via AMBER
- [AMBER] mpirun error for thermodynamic integration Dulal Mondal via AMBER
- [AMBER] cpptraj nastruct defined base-pairing Slavnikova Pavlina via AMBER
- Re: [AMBER] Boost Error in MoFT - metatwist Lorenzo Cupellini via AMBER
- Re: [AMBER] Boost Error in MoFT - metatwist Stephan Schott via AMBER
- [AMBER] (UNKNOWN ATOM TYPE: c5) Trevor Kramer via AMBER
- [AMBER] Multiple trajectory MMPBSA Yang Wei via AMBER
Saturday, 16 March 2024
- Re: [AMBER] mpirun error for thermodynamic integration David A Case via AMBER
- Re: [AMBER] cpptraj nastruct defined base-pairing David A Case via AMBER
- Re: [AMBER] (UNKNOWN ATOM TYPE: c5) David A Case via AMBER
- Re: [AMBER] Multiple trajectory MMPBSA David A Case via AMBER
- [AMBER] Minimization fails with a larger solvent box Sasha Buzko via AMBER
- [AMBER] 回复: NaN error during heating in building 12-6-4 LJ multisite Mg2+ model of DNA gyrase. 郭家藩 via AMBER
Sunday, 17 March 2024
- [AMBER] Antechamber Error SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- [AMBER] Maximum coordination exceeded on metal ions 杨镇岳 via AMBER
- [AMBER] 回复: Maximum coordination exceeded on metal ions 郭家藩 via AMBER
- Re: [AMBER] Minimization fails with a larger solvent box Carlos Simmerling via AMBER
- Re: [AMBER] Antechamber Error David A Case via AMBER
Monday, 18 March 2024
- Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step VERONICA MARTIN HERNANDEZ via AMBER
Tuesday, 19 March 2024
- [AMBER] Unable to reproduce the results from Amber RISM tutorial with Amber22 Markowska
- [AMBER] Compressing/Expanding Monolayer Systems Amanda Ferrante via AMBER
Wednesday, 20 March 2024
- Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step VERONICA MARTIN HERNANDEZ via AMBER
- [AMBER] Possible bug in PMEMD (appearence of synchronization artifacts between parallel tasks) Charo del Genio via AMBER
- [AMBER] MM-PBSA for membrane protein system Bhattacharjee, Sinjini via AMBER
- Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step David A Case via AMBER
- Re: [AMBER] MM-PBSA for membrane protein system Ray Luo via AMBER
- Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step He, Amy via AMBER
Thursday, 21 March 2024
- Re: [AMBER] AMBER error vlimit exceed for step Téletchéa Stéphane via AMBER
- Re: [AMBER] GAMESS QM optimization protocols James Kress via AMBER
- Re: [AMBER] GAMESS QM optimization protocols Debarati DasGupta via AMBER
- Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step He, Amy via AMBER
- [AMBER] Non-Standard Parametrization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- Re: [AMBER] Non-Standard Parametrization Issue He, Amy via AMBER
- Re: [AMBER] Non-Standard Parametrization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- Re: [AMBER] Non-Standard Parametrization Issue He, Amy via AMBER
Friday, 22 March 2024
- [AMBER] Issue with glycam nomenclature SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- Re: [AMBER] Issue with glycam nomenclature Daniel Roe via AMBER
- [AMBER] Protein Binding Question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Protein Binding Question Carlos Simmerling via AMBER
- Re: [AMBER] Protein Binding Question Matthew Guberman-Pfeffer via AMBER
- [AMBER] Parametrization of a system with missed loop fragments Enrico Martinez via AMBER
Saturday, 23 March 2024
- [AMBER] Query regarding amber20 ambertools23 installation Sayan Poddar via AMBER
- Re: [AMBER] Query regarding amber20 ambertools23 installation David Case via AMBER
- [AMBER] amber20 installation issue Sayan Poddar via AMBER
Sunday, 24 March 2024
- [AMBER] generate prmtop and inpcrd file Dulal Mondal via AMBER
- Re: [AMBER] amber20 installation issue David A Case via AMBER
- Re: [AMBER] generate prmtop and inpcrd file David A Case via AMBER
- Re: [AMBER] amber20 installation issue David A Case via AMBER
- [AMBER] error_install_run_cmake_Amber22 ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] error_install_run_cmake_Amber22 Daniel Roe via AMBER
- Re: [AMBER] Error - Amber 22 Installation David A Case via AMBER
- Re: [AMBER] error_install_run_cmake_Amber22 David A Case via AMBER
Monday, 25 March 2024
- Re: [AMBER] Unable to reproduce the results from Amber RISM tutorial with Amber22 Markowska
- Re: [AMBER] Protein Binding Question Carlos Simmerling via AMBER
- Re: [AMBER] error_install_run_cmake_Amber22 David A Case via AMBER
- [AMBER] Error_install_run_cmake_Amber22 ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Error_install_run_cmake_Amber22 David A Case via AMBER
- [AMBER] LJ Energy Mismatch William Livernois via AMBER
- Re: [AMBER] LJ Energy Mismatch Carlos Simmerling via AMBER
- Re: [AMBER] LJ Energy Mismatch Carlos Simmerling via AMBER
Tuesday, 26 March 2024
- Re: [AMBER] Parametrization of a system with missed loop fragments Enrico Martinez via AMBER
- [AMBER] Information about number of water molecules found in .out files Maria Bzówka via AMBER
- Re: [AMBER] Issue with glycam nomenclature Daniel Roe via AMBER
- [AMBER] Error with Amber22 test.serial Sayan Poddar via AMBER
- [AMBER] Dpeaks Clustering Algorithm Joshi, Keya via AMBER
- Re: [AMBER] Information about number of water molecules found in .out files David A Case via AMBER
Wednesday, 27 March 2024
- [AMBER] Install Amber22 CUDA_12.0 ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Dpeaks Clustering Algorithm Daniel Roe via AMBER
- [AMBER] native contacts calculation using cpptraj Prithviraj Nandigrami via AMBER
Thursday, 28 March 2024
- [AMBER] make-install amber22_cuda ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Quick QM/MM fails with GPUs but not with CPUs Montalvillo, Fernando via AMBER
- Re: [AMBER] make-install amber22_cuda David A Case via AMBER
- [AMBER] Regarding MMPBSA calculation: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Regarding MMPBSA calculation: Ray Luo via AMBER
Friday, 29 March 2024
- Re: [AMBER] Parametrization of a system with missed loop fragments Enrico Martinez via AMBER
- [AMBER] Minimization with pmemd.cuda Enrico Martinez via AMBER
- Re: [AMBER] Possible bug in PMEMD (appearence of synchronization artifacts between parallel tasks) Adrian Roitberg via AMBER
- Re: [AMBER] make-install amber22_cuda David A Case via AMBER
- Re: [AMBER] Error with Amber22 test.serial David A Case via AMBER
- Re: [AMBER] Minimization with pmemd.cuda Enrico Martinez via AMBER
- [AMBER] RMSD of protein with domain insertion Colin Pierce via AMBER
- Re: [AMBER] RMSD of protein with domain insertion Carlos Simmerling via AMBER
- Re: [AMBER] RMSD of protein with domain insertion Carlos Simmerling via AMBER
- Re: [AMBER] Error with Amber22 test.serial David A Case via AMBER
- Re: [AMBER] Error with Amber22 test.serial Todd Minehardt via AMBER

Last message date: Fri Mar 29 2024 - 15:30:02 PDT
Archived on: Wed May 08 2024 - 05:56:06 PDT

Amber Archive Mar 2024 by date