Amber Archive Nov 2022: by date

Monday, 31 October 2022
- Re: [AMBER] Amber22 GPU installation fails while building NVCC object `pmemd_xray_cuda_generated_BulkMaskGPU.cu.o` Nitin Kulhar via AMBER
Tuesday, 1 November 2022
- [AMBER] Free Energy Calculation using TI Suguna Sakkiah via AMBER
- [AMBER] Query regarding AMBER tutorial Replica Exchange Munazzah Fatima Ansari via AMBER
Wednesday, 2 November 2022
- [AMBER] Do RTX 3080Ti video cards supported by the amber20? Wei Jiao via AMBER
- Re: [AMBER] Query regarding AMBER tutorial Replica Exchange David A Case via AMBER
- [AMBER] Compiling Amber on Apple Silicon M2? David A Case via AMBER
- [AMBER] counting number of ions within cutoff region angad sharma via AMBER
- [AMBER] about mmgbsa method laura zhang via AMBER
- Re: [AMBER] about mmgbsa method Dr. Anselm Horn via AMBER
- Re: [AMBER] about mmgbsa method laura zhang via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
- Re: [AMBER] AMBER20 GPU error Thomas Cheatham via AMBER
Thursday, 3 November 2022
- [AMBER] question on mmgbsa energy calculation laura zhang via AMBER
- Re: [AMBER] question on mmgbsa energy calculation Bill Miller III via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
- [AMBER] Settings for CHAMM FF? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Settings for CHAMM FF? Carlos Simmerling via AMBER
- Re: [AMBER] AMBER20 GPU error Thomas Cheatham via AMBER
- [AMBER] Installation of amber18 on on parallel CPU Dulal Mondal via AMBER
Friday, 4 November 2022
- Re: [AMBER] about mmgbsa method Dr. Anselm Horn via AMBER
- Re: [AMBER] Installation of amber18 on on parallel CPU David A Case via AMBER
- Re: [AMBER] Do RTX 3080Ti video cards supported by the amber20? David A Case via AMBER
- [AMBER] Do RTX 3080Ti video cards supported by the amber20? Alessandro Contini via AMBER
- [AMBER] compile AMBER 22 with non-default gcc Vlad Cojocaru via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
- Re: [AMBER] AMBER20 GPU error Thomas Cheatham via AMBER
- [AMBER] Metal center created with MCPB.py collapses on MD start? Gustavo Seabra via AMBER
- [AMBER] Problem with topology file generation Tanmoy Paul via AMBER
- Re: [AMBER] compile AMBER 22 with non-default gcc Scott Brozell via AMBER
Saturday, 5 November 2022
- Re: [AMBER] Problem with topology file generation Gustavo Seabra via AMBER
- Re: [AMBER] compile AMBER 22 with non-default gcc David A Case via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
- Re: [AMBER] compile AMBER 22 with non-default gcc Vlad Cojocaru via AMBER
- Re: [AMBER] Problem with topology file generation Tanmoy Paul via AMBER
- [AMBER] Installation problem on amber18 with parallel CPU in linux Dulal Mondal via AMBER
Sunday, 6 November 2022
- Re: [AMBER] Problem with topology file generation Tanmoy Paul via AMBER
- Re: [AMBER] Installation problem on amber18 with parallel CPU in linux David A Case via AMBER
- Re: [AMBER] Problem with topology file generation David A Case via AMBER
- Re: [AMBER] Problem with topology file generation Tanmoy Paul via AMBER
Monday, 7 November 2022
- [AMBER] AMBER-TI running error Hwang, Sunny via AMBER
- Re: [AMBER] {SPAM?} AMBER-TI running error Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] AMBER-TI running error Kevin Hauser via AMBER
- Re: [AMBER] AMBER-TI running error David A Case via AMBER
- [AMBER] unbalanced usage of GPU cards in Replica Exchange MD kurisaki2013--- via AMBER
Tuesday, 8 November 2022
- Re: [AMBER] Alchemical gti keyword questions accuratefreeenergy--- via AMBER
- [AMBER] installation Nitin Kulhar via AMBER
- [AMBER] Reimaging issues Damiano Spadoni via AMBER
- [AMBER] What is the "right" number of unit cells for simulating protein crystals? Reim, Thorben via AMBER
- Re: [AMBER] Metal center created with MCPB.py collapses on MD start? Clorice Reinhardt via AMBER
- [AMBER] Autoimage cannot find topology information Hunter Wilson via AMBER
- Re: [AMBER] Autoimage cannot find topology information Clorice Reinhardt via AMBER
- Re: [AMBER] Autoimage cannot find topology information Daniel Roe via AMBER
- Re: [AMBER] Metal center created with MCPB.py collapses on MD start? Gustavo Seabra via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
Wednesday, 9 November 2022
- [AMBER] Query regarding AMBER tutorial Munazzah Fatima Ansari via AMBER
- Re: [AMBER] installation David A Case via AMBER
- Re: [AMBER] What is the "right" number of unit cells for simulating protein crystals? David A Case via AMBER
- Re: [AMBER] AMBER20 GPU error David A Case via AMBER
- [AMBER] Installation Problem Matthew Guberman-Pfeffer via AMBER
- [AMBER] Fwd: Aluminum parameters, URGENT Nour Alkhatib via AMBER
- [AMBER] LJ parameters for AL3+ Nour Alkhatib via AMBER
- Re: [AMBER] AMBER20 GPU error Thomas Cheatham via AMBER
- Re: [AMBER] Installation Problem Scott Brozell via AMBER
Thursday, 10 November 2022
- Re: [AMBER] Installation Problem Matthew Guberman-Pfeffer via AMBER
- [AMBER] Announcement: Atomic Simulation Center Symposium 2022, Nov 28/29 Dr. Anselm Horn via AMBER
- Re: [AMBER] Installation Problem David A Case via AMBER
- Re: [AMBER] Installation Problem Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Fwd: Aluminum parameters, URGENT David A Case via AMBER
- [AMBER] Trouble reproducing solvateOct output from Tutorial 1.4 Kerry Woolnough via AMBER
- Re: [AMBER] Fwd: Aluminum parameters, URGENT Nour Alkhatib via AMBER
- [AMBER] Changing CUDA toolkits - need recompile? James Kress via AMBER
- Re: [AMBER] installation Nitin Kulhar via AMBER
- Re: [AMBER] Fwd: Aluminum parameters, URGENT Dr. Anselm Horn via AMBER
- Re: [AMBER] Changing CUDA toolkits - need recompile? Scott Brozell via AMBER
- [AMBER] Simulating a Protein - cyclic peptide complex - question Suchetana Gupta via AMBER
- Re: [AMBER] Simulating a Protein - cyclic peptide complex - question Carol Pacheco via AMBER
- [AMBER] Generating parameters for unnatural amino acids Suchetana Gupta via AMBER
- Re: [AMBER] Generating parameters for unnatural amino acids Suchetana Gupta via AMBER
Friday, 11 November 2022
- Re: [AMBER] Simulating a Protein - cyclic peptide complex - question Dr. Anselm Horn via AMBER
- Re: [AMBER] Generating parameters for unnatural amino acids Dr. Anselm Horn via AMBER
- Re: [AMBER] {SPAM?} Re: Installation Problem Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Installation Problem David A Case via AMBER
- Re: [AMBER] Simulating a Protein - cyclic peptide complex - question David A Case via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
- Re: [AMBER] Simulating a Protein - cyclic peptide complex - question Suchetana Gupta via AMBER
- Re: [AMBER] Generating parameters for unnatural amino acids Suchetana Gupta via AMBER
- Re: [AMBER] AMBER20 GPU error Carlos Simmerling via AMBER
- Re: [AMBER] AMBER20 GPU error Thomas Cheatham via AMBER
- [AMBER] Installation of amber18 on on parallel CPU Dulal Mondal via AMBER
- [AMBER] Installation of amber18 (MPI version) with CPU and intel mpi Dulal Mondal via AMBER
Saturday, 12 November 2022
- Re: [AMBER] {SPAM?} Re: Alchemical gti keyword questions accuratefreeenergy--- via AMBER
- Re: [AMBER] Installation of amber18 (MPI version) with CPU and intel mpi David A Case via AMBER
- Re: [AMBER] AMBER20 GPU error David A Case via AMBER
- Re: [AMBER] Simulation of ssDNA folding Jiaan Zhu via AMBER
Sunday, 13 November 2022
- [AMBER] Testing suite for openMP James Kress via AMBER
Monday, 14 November 2022
- [AMBER] Postdoc and PhD position at IPB Halle (Germany) Mehdi D. Davari via AMBER
- Re: [AMBER] Installation of amber18 (MPI version) with CPU and intel mpi Dulal Mondal via AMBER
Tuesday, 15 November 2022
- [AMBER] Query regarding RMS in minimization of explicit solvent Nitin Kulhar via AMBER
- [AMBER] Installation of Amber19 SATYAJIT KHATUA via AMBER
- Re: [AMBER] Installation of Amber19 David A Case via AMBER
- Re: [AMBER] Query regarding RMS in minimization of explicit solvent David A Case via AMBER
- Re: [AMBER] Testing suite for openMP David A Case via AMBER
- [AMBER] Unable to access xleap software! Swapnil Singh via AMBER
- Re: [AMBER] Unable to access xleap software! David A Case via AMBER
- Re: [AMBER] Testing suite for openMP James Kress via AMBER
- Re: [AMBER] Unable to access xleap software! Swapnil Singh via AMBER
- Re: [AMBER] Unable to access xleap software! Suchetana Gupta via AMBER
- [AMBER] Force filed for non-specific residue CAS Jelena Tosovic via AMBER
- [AMBER] 你好amber@ambermd.org 3163490855--- via AMBER
- Re: [AMBER] {SPAM?} Force filed for non-specific residue CAS Matthew Guberman-Pfeffer via AMBER
Wednesday, 16 November 2022
- [AMBER] How to use MCPB.py to deal with the oxygen atom Fe=O of CpdⅠ 张恒炜 via AMBER
- [AMBER] Position restraints in NPT Miroslav Suruzhon via AMBER
- Re: [AMBER] Installation of amber18 (MPI version) with CPU and intel mpi Dulal Mondal via AMBER
- Re: [AMBER] {SPAM?} Force filed for non-specific residue CAS Carlos Simmerling via AMBER
Thursday, 17 November 2022
- [AMBER] Gradual heating: Linear response pressure? Hocine EL KHAOUDI ENYOURY via AMBER
- [AMBER] Temperature drop while switching from NVT to NPT during equilibration Reim, Thorben via AMBER
- Re: [AMBER] Position restraints in NPT Franz Waibl via AMBER
- Re: [AMBER] Installation of amber18 (MPI version) with CPU and intel mpi David A Case via AMBER
- [AMBER] amber tools2016 sxl18235290334--- via AMBER
- Re: [AMBER] amber tools2016 Dr. Anselm Horn via AMBER
- Re: [AMBER] Temperature drop while switching from NVT to NPT during equilibration Carlos Simmerling via AMBER
- Re: [AMBER] Query regarding AMBER tutorial Carlos Simmerling via AMBER
- Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms Carlos Simmerling via AMBER
- [AMBER] Restart and Topology Files Contain Different Numbers of Atoms Kerry Woolnough via AMBER
- Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms Kerry Woolnough via AMBER
- Re: [AMBER] Temperature drop while switching from NVT to NPT during equilibration David A Case via AMBER
- Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms David A Case via AMBER
Friday, 18 November 2022
- Re: [AMBER] Gradual heating: Linear response pressure? David A Case via AMBER
- Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms Kerry Woolnough via AMBER
- Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms Carlos Simmerling via AMBER
- [AMBER] Extract all frame from a nc file using cpptraj Dulal Mondal via AMBER
- Re: [AMBER] Extract all frame from a nc file using cpptraj Carlos Simmerling via AMBER
- Re: [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
- [AMBER] gmx_MMPBSA installation error please help İmren Bayıl via AMBER
Saturday, 19 November 2022
- [AMBER] gmx_MMPBSA installation error İmren Bayıl via AMBER
- Re: [AMBER] gmx_MMPBSA installation error please help David A Case via AMBER
- Re: [AMBER] gmx_MMPBSA installation error please help İmren Bayıl via AMBER
- [AMBER] Missing GaMD restart file Matthew Guberman-Pfeffer via AMBER
Sunday, 20 November 2022
- [AMBER] Vacuum simulation problem Matthew Guberman-Pfeffer via AMBER
- [AMBER] MM/PBSA & MM/GBSA and three trajectories Ibrahim Said via AMBER
- Re: [AMBER] Vacuum simulation problem James Kress via AMBER
- Re: [AMBER] {SPAM?} Re: Vacuum simulation problem Matthew Guberman-Pfeffer via AMBER
Monday, 21 November 2022
- Re: [AMBER] Gradual heating: Linear response pressure? Hocine EL KHAOUDI ENYOURY via AMBER
- [AMBER] OPC3-pol Piia Bartos via AMBER
- Re: [AMBER] Vacuum simulation problem David A Case via AMBER
- Re: [AMBER] {SPAM?} Re: Vacuum simulation problem Matthew Guberman-Pfeffer via AMBER
- [AMBER] Generation of CPIN in CpHMD simulations Divya Rai via AMBER
- Re: [AMBER] Generation of CPIN in CpHMD simulations Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] OPC3-pol Carlos Simmerling via AMBER
- Re: [AMBER] Gradual heating: Linear response pressure? Carlos Simmerling via AMBER
- [AMBER] Questions about refinement of dihedral parameters by QM calculations He, Amy via AMBER
- Re: [AMBER] Questions about refinement of dihedral parameters by QM calculations Carlos Simmerling via AMBER
- Re: [AMBER] Lambda-Scheduling, what is TypeGen? accuratefreeenergy--- via AMBER
Tuesday, 22 November 2022
- Re: [AMBER] Generation of CPIN in CpHMD simulations Divya Rai via AMBER
- Re: [AMBER] Position restraints in NPT Miroslav Suruzhon via AMBER
- [AMBER] the mmgbsa output laura zhang via AMBER
- Re: [AMBER] MCPB.py (Error: the charges and atom numbers are mismatch) Saranya vasudevan via AMBER
- [AMBER] Messages not getting through to the Amber Mailing List? Gert Kruger via AMBER
- Re: [AMBER] Messages not getting through to the Amber Mailing List? Suchetana Gupta via AMBER
- Re: [AMBER] the mmgbsa output Bill Miller III via AMBER
- Re: [AMBER] Messages not getting through to the Amber Mailing List? David A Case via AMBER
Wednesday, 23 November 2022
- Re: [AMBER] Messages not getting through to the Amber Mailing List? Dr. Anselm Horn via AMBER
- Re: [AMBER] Position restraints in NPT Franz Waibl via AMBER
- Re: [AMBER] Gradual heating: Linear response pressure? Carlos Simmerling via AMBER
- Re: [AMBER] Gradual heating: Linear response pressure? David A Case via AMBER
Thursday, 24 November 2022
- [AMBER] TIP4P/Ice (2005) water model in AMBER? Surajit Kalita via AMBER
- Re: [AMBER] Position restraints in NPT Miroslav Suruzhon via AMBER
- [AMBER] Error - Amber 22 Installation with Cuda Gert Kruger via AMBER
- [AMBER] Applying position restraint on ligand Enrico Martinez via AMBER
- Re: [AMBER] Applying position restraint on ligand Gustavo Seabra via AMBER
- [AMBER] Antechamber and py_resp qout format Евгений Кадцын via AMBER
- [AMBER] Cpptraj for loops and dataset operations Pietro ARONICA via AMBER
Friday, 25 November 2022
- Re: [AMBER] Applying position restraint on ligand Enrico Martinez via AMBER
- Re: [AMBER] Applying position restraint on ligand Enrico Martinez via AMBER
- [AMBER] Questions about reading the right LJ_Acoef values in *.prmtop file ChenXin via AMBER
Saturday, 26 November 2022
- Re: [AMBER] OPC3-pol Piia Bartos via AMBER
- Re: [AMBER] Questions about reading the right LJ_Acoef values in *.prmtop file Carlos Simmerling via AMBER
Sunday, 27 November 2022
- [AMBER] Inconsistent GPU Results Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] {SPAM?} Inconsistent GPU Results Matthew Guberman-Pfeffer via AMBER
Monday, 28 November 2022
- [AMBER] Reimaging issues Damiano Spadoni via AMBER
- Re: [AMBER] Error - Amber 22 Installation with Cuda David A Case via AMBER
- Re: [AMBER] Inconsistent GPU Results David A Case via AMBER
- Re: [AMBER] gti_cut vs. gti_cut_sc accuratefreeenergy--- via AMBER
- Re: [AMBER] {SPAM?} scbeta, wrong default? accuratefreeenergy--- via AMBER
- Re: [AMBER] {SPAM?} Re: Inconsistent GPU Results Matthew Guberman-Pfeffer via AMBER
- [AMBER] Missing parameters while Simulating a Zn containing protein in Amber Suchetana Gupta via AMBER
- Re: [AMBER] Simulating a Protein - cyclic peptide complex - question Suchetana Gupta via AMBER
- Re: [AMBER] Antechamber and py_resp qout format Shiji Zhao via AMBER
Tuesday, 29 November 2022
- Re: [AMBER] OPC3-pol Piia Bartos via AMBER
- Re: [AMBER] Simulating a Protein - cyclic peptide complex - question Dr. Anselm Horn via AMBER
- [AMBER] Detect vacuum bubbles Hocine EL KHAOUDI ENYOURY via AMBER
- Re: [AMBER] {SPAM?} scbeta, wrong default? accuratefreeenergy--- via AMBER
- Re: [AMBER] Detect vacuum bubbles Carlos Simmerling via AMBER
- [AMBER] Only three atoms in water molecules instead of four Dmitry Suplatov via AMBER
- [AMBER] test FAILURE in ired.vec.diff Martin Juhás via AMBER
- Re: [AMBER] Only three atoms in water molecules instead of four Dmitry Suplatov via AMBER
- Re: [AMBER] test FAILURE in ired.vec.diff Daniel Roe via AMBER
Wednesday, 30 November 2022
- [AMBER] monovalent ions in methanol Antonija Tomić via AMBER
- Re: [AMBER] Cpptraj for loops and dataset operations Daniel Roe via AMBER
- Re: [AMBER] Cpptraj for loops and dataset operations Daniel Roe via AMBER
- [AMBER] Updates to mdinfo with amber 22 Greenberg, Jerry via AMBER
- Re: [AMBER] Cpptraj for loops and dataset operations James Kress via AMBER
- Re: [AMBER] Cpptraj for loops and dataset operations Carlos Simmerling via AMBER

Last message date: Wed Nov 30 2022 - 15:00:02 PST
Archived on: Wed Dec 25 2024 - 05:56:13 PST

Amber Archive Nov 2022 by date