July 2019 Archives by thread

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Starting: Mon Jul 1 02:09:10 CEST 2019
Ending: Wed Jul 31 21:22:14 CEST 2019
Messages: 287

[gmx-users] interrupt of gmx mdrun Dallas Warren
[gmx-users] Error in creating parameter files using SwissParam GAYATHRI S
- [gmx-users] Error in creating parameter files using SwissParam Dallas Warren
[gmx-users] Error on scaling the charges Apramita Chand
- [gmx-users] Error on scaling the charges Justin Lemkul
[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis? Vikas Dubey
[gmx-users] How to install gromacs on cpu cluster sunyeping
- [gmx-users] How to install gromacs on cpu cluster Benson Muite
  - [gmx-users] How to install gromacs on cpu cluster sunyeping
[gmx-users] missing prepare-qmmm.py Dhr. D.W. Sjoerdsma (d.w.sjoerdsma)
- [gmx-users] missing prepare-qmmm.py Benson Muite
  - [gmx-users] missing prepare-qmmm.py Dhr. D.W. Sjoerdsma (d.w.sjoerdsma)
    - [gmx-users] missing prepare-qmmm.py Benson Muite
[gmx-users] a99SB-disp forcefield Joe Greener
- [gmx-users] a99SB-disp forcefield João Henriques
[gmx-users] simulation of water gradient across membrane protein Phuong Tran
- [gmx-users] simulation of water gradient across membrane protein Kutzner, Carsten
  - [gmx-users] simulation of water gradient across membrane protein Phuong Tran
[gmx-users] Help with generating Arginine topology for Amber FF Pandya, Akash
[gmx-users] No compatible domain decomposition Daniel Bauer
- [gmx-users] No compatible domain decomposition Mark Abraham
[gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells Carlos Navarro
- [gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells Mark Abraham
  - [gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells Carlos Navarro
[gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash) ABEL Stephane
- [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash) Pandya, Akash
  - [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash) Justin Lemkul
[gmx-users] clustering of ions during NPT simulation Justin Lemkul
- [gmx-users] clustering of ions during NPT simulation Netaly Khazanov
[gmx-users] how to visualize gromacs trajectory Sun Yeping
- [gmx-users] how to visualize gromacs trajectory Stephani Macalino
  - [gmx-users] how to visualize gromacs trajectory atb files
  - [gmx-users] how to visualize gromacs trajectory sunyeping
    - [gmx-users] how to visualize gromacs trajectory Justin Lemkul
    - [gmx-users] how to visualize gromacs trajectory sunyeping
    - [gmx-users] how to visualize gromacs trajectory Stephani Macalino
[gmx-users] a99SB-disp forcefield Timofey Tyugashev
- [gmx-users] a99SB-disp forcefield João Henriques
[gmx-users] How to do proper NVE simulation using Gromacs atb files
[gmx-users] About ligands and metals in specbond.dat Bakary N'tji Diallo
- [gmx-users] About ligands and metals in specbond.dat Justin Lemkul
[gmx-users] carbon dioxide model does not provide valid ideal-gas pressure Amin Rouy
- [gmx-users] carbon dioxide model does not provide valid ideal-gas pressure Amin Rouy
[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis? Vikas Dubey
- [gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis? atb files
- [gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis? atb files
[gmx-users] how to visualize gromacs trajectory sunyeping
[gmx-users] GPU support on macOS 10.14 Falk Hoffmann
- [gmx-users] GPU support on macOS 10.14 Mark Abraham
  - [gmx-users] GPU support on macOS 10.14 Michael Williams
    - [gmx-users] GPU support on macOS 10.14 Falk Hoffmann
    - [gmx-users] GPU support on macOS 10.14 Falk Hoffmann
    - [gmx-users] GPU support on macOS 10.14 Falk Hoffmann
    - [gmx-users] GPU support on macOS 10.14 Szilárd Páll
    - [gmx-users] GPU support on macOS 10.14 Szilárd Páll
[gmx-users] How to generate topology file of cyclodextrin for gromacs? jsPARK
- [gmx-users] How to generate topology file of cyclodextrin for gromacs? atb files
[gmx-users] Relative constraint deviation after LINCS: Dilip.H.N
- [gmx-users] Relative constraint deviation after LINCS: Mark Abraham
[gmx-users] Install on Windows 10 with AMD GPU James Burchfield
- [gmx-users] Install on Windows 10 with AMD GPU Szilárd Páll
  - [gmx-users] Install on Windows 10 with AMD GPU James Burchfield
    - [gmx-users] Install on Windows 10 with AMD GPU Szilárd Páll
    - [gmx-users] Install on Windows 10 with AMD GPU James Burchfield
    - [gmx-users] Install on Windows 10 with AMD GPU James Burchfield
    - [gmx-users] Install on Windows 10 with AMD GPU Szilárd Páll
    - [gmx-users] Install on Windows 10 with AMD GPU James Burchfield
[gmx-users] gromacs pullcode zhaox
- [gmx-users] gromacs pullcode Justin Lemkul
[gmx-users] NVT ensemble for simulating of carbon nanotube (as drug delivery) afsaneh maleki
- [gmx-users] NVT ensemble for simulating of carbon nanotube (as drug delivery) Justin Lemkul
[gmx-users] About 2019 GMX manual Alan
- [gmx-users] About 2019 GMX manual Benson Muite
  - [gmx-users] About 2019 GMX manual Paul bauer
    - [gmx-users] About 2019 GMX manual Alan
[gmx-users] protein-ligand simulation problem Prabir Khatua
[gmx-users] Self-interaction across periodic boundaries Salman Zarrini
- [gmx-users] Self-interaction across periodic boundaries Mark Abraham
  - [gmx-users] Self-interaction across periodic boundaries Salman Zarrini
    - [gmx-users] Self-interaction across periodic boundaries Paul Buscemi
[gmx-users] rigid body motion Morteza Chehel Amirani
- [gmx-users] rigid body motion Justin Lemkul
[gmx-users] Repeat Simulation n times Neena Susan Eappen
- [gmx-users] Repeat Simulation n times Justin Lemkul
[gmx-users] POPC Berger lipids parameters for AMBER99sb Carlos Navarro
- [gmx-users] POPC Berger lipids parameters for AMBER99sb Justin Lemkul
  - [gmx-users] POPC Berger lipids parameters for AMBER99sb Carlos Navarro
    - [gmx-users] POPC Berger lipids parameters for AMBER99sb Carlos Navarro
    - [gmx-users] POPC Berger lipids parameters for AMBER99sb Justin Lemkul
[gmx-users] Tetrahedral order Omkar Singh
- [gmx-users] Tetrahedral order Justin Lemkul
  - [gmx-users] Tetrahedral order Omkar Singh
[gmx-users] what's the maximum number of atoms that GROMACS can simulate? 张驭洲
- [gmx-users] what's the maximum number of atoms that GROMACS can simulate? Kutzner, Carsten
  - [gmx-users] what's the maximum number of atoms that GROMACS can simulate? 张驭洲
[gmx-users] How to let mdrun not generate trr file sunyeping
- [gmx-users] How to let mdrun not generate trr file Mark Abraham
- [gmx-users] How to let mdrun not generate trr file atb files
[gmx-users] questions about Ryckaert-Bellemans type dihedrals Yunhui Ge
- [gmx-users] questions about Ryckaert-Bellemans type dihedrals Mark Abraham
[gmx-users] rtx 2080 gpu Stefano Guglielmo
- [gmx-users] rtx 2080 gpu Benson Muite
  - [gmx-users] rtx 2080 gpu Stefano Guglielmo
    - [gmx-users] rtx 2080 gpu Szilárd Páll
- [gmx-users] rtx 2080 gpu Szilárd Páll
[gmx-users] make test failed during installing gromacs sunyeping
- [gmx-users] make test failed during installing gromacs Benson Muite
[gmx-users] acpype error Mahboobeh Eslami
- [gmx-users] acpype error Alan
[gmx-users] missing prepare-qmmm.py Benson Muite
[gmx-users] convergence of bilayer simulation Prasanth G, Research Scholar
- [gmx-users] convergence of bilayer simulation Prasanth G, Research Scholar
  - [gmx-users] convergence of bilayer simulation Justin Lemkul
  - [gmx-users] convergence of bilayer simulation Prasanth G, Research Scholar
    - [gmx-users] convergence of bilayer simulation Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 183, Issue 27 convergence of bilayer simulation Roshan Shrestha
[gmx-users] part of ligand molecule leaves protein Andrew Bostick
- [gmx-users] part of ligand molecule leaves protein Gaurav Goel
[gmx-users] GROMOS force field for small molecules Edjan Silva
- [gmx-users] GROMOS force field for small molecules Justin Lemkul
[gmx-users] virtual sites for ligands? Carlos Navarro
- [gmx-users] virtual sites for ligands? Mark Abraham
[gmx-users] SIMD for gmx and sudden break in MDRUN kalpana
- [gmx-users] SIMD for gmx and sudden break in MDRUN Justin Lemkul
[gmx-users] Specific heat calculations using gmx energy Pragati Sharma
- [gmx-users] Specific heat calculations using gmx energy David van der Spoel
  - [gmx-users] Specific heat calculations using gmx energy Pragati Sharma
[gmx-users] Warning Bratin Kumar Das
- [gmx-users] Warning Mark Abraham
  - [gmx-users] Warning Quyen Vu
    - [gmx-users] Warning Bratin Kumar Das
[gmx-users] cluster size in gmx clustsize Iuliia Voroshylova
[gmx-users] About g_sdf in version 4.6.5. Henry Vider
- [gmx-users] About g_sdf in version 4.6.5. Dallas Warren
  - [gmx-users] About g_sdf in version 4.6.5. Henry Vider
    - [gmx-users] About g_sdf in version 4.6.5. Dallas Warren
[gmx-users] force constant (K_fb) Alex
- [gmx-users] force constant (K_fb) Mark Abraham
[gmx-users] Xeon Gold + RTX 5000 Alex
- [gmx-users] Xeon Gold + RTX 5000 Szilárd Páll
  - [gmx-users] Xeon Gold + RTX 5000 Alex
    - [gmx-users] Xeon Gold + RTX 5000 Szilárd Páll
    - [gmx-users] Xeon Gold + RTX 5000 Moir, Michael (MMoir)
    - [gmx-users] Xeon Gold + RTX 5000 Alex
    - [gmx-users] Xeon Gold + RTX 5000 Moir, Michael (MMoir)
    - [gmx-users] Xeon Gold + RTX 5000 Moir, Michael (MMoir)
    - [gmx-users] Xeon Gold + RTX 5000 Alex
    - [gmx-users] Xeon Gold + RTX 5000 Szilárd Páll
    - [gmx-users] Xeon Gold + RTX 5000 Szilárd Páll
    - [gmx-users] Xeon Gold + RTX 5000 Michael Williams
    - [gmx-users] older server CPUs with recent GPUs for GROMACS Szilárd Páll
[gmx-users] Calculation of LJ-SR and Coulomb-SR between atoms within protein Ashraya Ravikumar
[gmx-users] Flat-bottomed Restrain ehsan shahini
- [gmx-users] Flat-bottomed Restrain Mark Abraham
  - [gmx-users] Flat-bottomed Restrain ehsan shahini
  - [gmx-users] Flat-bottomed Restrain Salman Zarrini
    - [gmx-users] Flat-bottomed Restrain ehsan shahini
    - [gmx-users] Flat-bottomed Restrain Mark Abraham
    - [gmx-users] Flat-bottomed Restrain Salman Zarrini
[gmx-users] Generating Ramachandran Plot monitoring movie. Muneeswaran S
[gmx-users] heat capacity collection Amin Rouy
- [gmx-users] heat capacity collection David van der Spoel
  - [gmx-users] heat capacity collection Amin Rouy
[gmx-users] Hydrogen bond analysis mary ko
[gmx-users] Keep having to path gromacs when opening a new terminal Israel Estrada
- [gmx-users] Keep having to path gromacs when opening a new terminal Alex
- [gmx-users] Keep having to path gromacs when opening a new terminal KRISHNA PRASAD GHANTA
[gmx-users] Drude force field Myunggi Yi
[gmx-users] decreased performance with free energy David de Sancho
- [gmx-users] decreased performance with free energy Szilárd Páll
[gmx-users] make manual fails Michael Brunsteiner
- [gmx-users] make manual fails Szilárd Páll
[gmx-users] Drude force field Myunggi Yi
- [gmx-users] Drude force field Justin Lemkul
  - [gmx-users] Drude force field Myunggi Yi
  - [gmx-users] Drude force field Myunggi Yi
    - [gmx-users] Drude force field Justin Lemkul
    - [gmx-users] Drude force field Myunggi Yi
    - [gmx-users] Drude force field Justin Lemkul
  - [gmx-users] Drude force field Myunggi Yi
[gmx-users] remd error Bratin Kumar Das
- [gmx-users] remd error Szilárd Páll
  - [gmx-users] remd error Bratin Kumar Das
    - [gmx-users] remd error Justin Lemkul
    - [gmx-users] remd error Bratin Kumar Das
[gmx-users] Drude force field Gordan Horvat
- [gmx-users] Drude force field Justin Lemkul
[gmx-users] decreased performance with free energy David de Sancho
- [gmx-users] decreased performance with free energy Szilárd Páll
[gmx-users] core dump error in grompp command (학생) 박세영 (에너지및화학공학부)
- [gmx-users] core dump error in grompp command Mark Abraham
[gmx-users] tcaf Amin Rouy
[gmx-users] Need to install latest Gromacs on ios andrew goring
- [gmx-users] Need to install latest Gromacs on ios Szilárd Páll
[gmx-users] Trajectory Alex
- [gmx-users] Trajectory Dallas Warren
[gmx-users] make manual fails Michael Brunsteiner
[gmx-users] inexplicable rmsf error - Too many iterations in routine JACOBI Mala L Radhakrishnan
- [gmx-users] inexplicable rmsf error - Too many iterations in routine JACOBI Mala L Radhakrishnan
[gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Carlos Navarro
- [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Carlos Navarro
  - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Szilárd Páll
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Carlos Navarro
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Mark Abraham
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Carlos Navarro
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Justin Lemkul
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Mark Abraham
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Carlos Navarro
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Szilárd Páll
    - [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm Szilárd Páll
[gmx-users] Amide hydrogen naming in charmm 36 forcefield Dilip.H.N
- [gmx-users] Amide hydrogen naming in charmm 36 forcefield Justin Lemkul
  - [gmx-users] Amide hydrogen naming in charmm 36 forcefield Dilip.H.N
    - [gmx-users] Amide hydrogen naming in charmm 36 forcefield Justin Lemkul
[gmx-users] New ACPYPE server Alan
[gmx-users] Improper dihedral parameters for peptide bond Dawid das
[gmx-users] Improper dihedral parameters for peptide bond Dawid das
[gmx-users] Doubts about molecular dynamics of a protein with one ZN binding site Sebas Ayala
[gmx-users] Free energy of hydration for metal ion complexed with ligand Meena Singh
- [gmx-users] Free energy of hydration for metal ion complexed with ligand Bratin Kumar Das
[gmx-users] Normal mode segmentation fault - memory problem ? Marlon Sidore
- [gmx-users] Normal mode segmentation fault - memory problem ? David van der Spoel
[gmx-users] Viscosity calculations Nicholas Michelarakis
[gmx-users] Variation in free energy between GROMACS versions? Kenneth Huang
- [gmx-users] Variation in free energy between GROMACS versions? Mark Abraham
  - [gmx-users] Variation in free energy between GROMACS versions? Kenneth Huang
    - [gmx-users] Variation in free energy between GROMACS versions? Mark Abraham
[gmx-users] Sun Solaris amitabh jayaswal
- [gmx-users] Sun Solaris Szilárd Páll
[gmx-users] Angular distribution Omkar Singh
- [gmx-users] Angular distribution Justin Lemkul
[gmx-users] simulation on 2 gpus Stefano Guglielmo
- [gmx-users] simulation on 2 gpus Kevin Boyd
  - [gmx-users] simulation on 2 gpus Gregory Man Kai Poon
    - [gmx-users] simulation on 2 gpus Mark Abraham
    - [gmx-users] simulation on 2 gpus Kevin Boyd
    - [gmx-users] simulation on 2 gpus Stefano Guglielmo
[gmx-users] gmx insert-molecules question Mala L Radhakrishnan
- [gmx-users] gmx insert-molecules question Justin Lemkul
  - [gmx-users] gmx insert-molecules question Mala L Radhakrishnan
[gmx-users] topol. top file Dhrubajyoti Maji
- [gmx-users] topol. top file KRISHNA PRASAD GHANTA
  - [gmx-users] topol. top file Dhrubajyoti Maji
[gmx-users] Gromos force field with Tip5p water model nevjernik at gmail.com
- [gmx-users] Gromos force field with Tip5p water model KRISHNA PRASAD GHANTA
  - [gmx-users] Gromos force field with Tip5p water model Justin Lemkul
[gmx-users] Simulated tampering using GROMACS software package (protein+membrane) Pratiti Bhadra
- [gmx-users] Simulated tampering using GROMACS software package (protein+membrane) KRISHNA PRASAD GHANTA
- [gmx-users] Simulated tempering using GROMACS software package (protein+membrane) Gregory Man Kai Poon
[gmx-users] charge correction in prodrg Andrew Bostick
- [gmx-users] charge correction in prodrg Justin Lemkul
[gmx-users] charge correction in prodrg Andrew Bostick
- [gmx-users] charge correction in prodrg Justin Lemkul
[gmx-users] space dependent electric field Maryam
- [gmx-users] space dependent electric field David van der Spoel
[gmx-users] maximum force does not converge m g
- [gmx-users] maximum force does not converge Justin Lemkul
[gmx-users] Regarding OH, HH vector distribution Omkar Singh
- [gmx-users] Regarding OH, HH vector distribution David van der Spoel
  - [gmx-users] Regarding OH, HH vector distribution Omkar Singh
    - [gmx-users] Regarding OH, HH vector distribution David van der Spoel
    - [gmx-users] Regarding OH, HH vector distribution Omkar Singh
    - [gmx-users] Regarding OH, HH vector distribution David van der Spoel
    - [gmx-users] Regarding OH, HH vector distribution Omkar Singh
    - [gmx-users] Regarding OH, HH vector distribution David van der Spoel
    - [gmx-users] Regarding OH, HH vector distribution Omkar Singh
    - [gmx-users] Regarding OH, HH vector distribution David van der Spoel
[gmx-users] cvff question Yi Lu
[gmx-users] clashes after energy minimization - Ser2 multiple copies David de Sancho
[gmx-users] REMD Bratin Kumar Das
[gmx-users] gromacs pullcode zhaox
[gmx-users] GROMOS 54a7 mapping warning Gselman, Larissa
- [gmx-users] GROMOS 54a7 mapping warning David van der Spoel
[gmx-users] Normal mode segmentation fault - memory problem ? Marlon Sidore

Last message date: Wed Jul 31 21:22:14 CEST 2019
Archived on: Wed Jul 31 21:22:15 CEST 2019

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