August 2017 Archives by thread

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Starting: Tue Aug 1 00:11:02 CEST 2017
Ending: Thu Aug 31 22:38:58 CEST 2017
Messages: 643

• [gmx-users] hole in the simulation box   Dallas Warren
  • [gmx-users] hole in the simulation box   edesantis
• [gmx-users] gmx mdmat calculation of heavy atoms of two side chains   Justin Lemkul
• [gmx-users] Creating Custom .rtp files   Justin Lemkul
  • [gmx-users] Creating Custom .rtp files   Momin Ahmad
    • [gmx-users] Creating Custom .rtp files   Justin Lemkul
      • [gmx-users] Creating Custom .rtp files   Momin Ahmad
      • [gmx-users] Creating Custom .rtp files   Justin Lemkul
• [gmx-users] gromacs rerun calculate the energy   Justin Lemkul
  • [gmx-users] gromacs rerun calculate the energy   Varvdekar Bhagyesh Rajendra
    • [gmx-users] gromacs rerun calculate the energy   Mark Abraham
• [gmx-users] How can I implement a radial potential field in GROMACS?   Justin Lemkul
• [gmx-users] ligand topology   Justin Lemkul
  • [gmx-users] ligand topology   Mohammad Zahidul Hossain Khan
    • [gmx-users] ligand topology   Suhaib Shekfeh
      • [gmx-users] ligand topology   Alan
      • [gmx-users] ligand topology   Lucio Ricardo Montero Valenzuela
      • [gmx-users] ligand topology   Justin Lemkul
      • [gmx-users] ligand topology   Mohammad Zahidul Hossain Khan
      • [gmx-users] ligand topology   Alan
      • [gmx-users] ligand topology   Mark Abraham
      • [gmx-users] ligand topology   Mohammad Zahidul Hossain Khan
      • [gmx-users] ligand topology   Mohammad Zahidul Hossain Khan
• [gmx-users] Question on Umbrella Sampling with varied ionic strength.   Justin Lemkul
• [gmx-users] Question on Umbrella Sampling with varied ionic strength.   Yuanchao Liu (MSU)
• [gmx-users] Reg. Umbrella sampling problem with direction   "가디 장데부 고라크스나트"
• [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 1   Мижээ Батсайхан
• [gmx-users] Some problem about the process of calculating MM-PBSA binding free energy   yujie Liu
  • [gmx-users] Some problem about the process of calculating MM-PBSA binding free energy   David van der Spoel
• [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 2   王珍
• [gmx-users] (no subject)   yujie Liu
• [gmx-users] Some problem about the process of calculating MM-PBSA binding free energy   刘玉杰
• [gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)   Andrew Bostick
• [gmx-users] PCA in dihdral space   Gleb Novikov
• [gmx-users] Estimation of the rotations during CG simulations   Gleb Novikov
• [gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI   Hermann, Johannes
• [gmx-users] pme algorithm   王珍
• [gmx-users] pulling of a molecule through protein-membrane system   Alex Mathew
  • [gmx-users] pulling of a molecule through protein-membrane system   Justin Lemkul
• [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Ali Ahmed
  • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Mark Abraham
    • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Ali Ahmed
      • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Dallas Warren
      • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Ali Ahmed
      • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Justin Lemkul
      • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Ali Ahmed
      • [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site   Justin Lemkul
• [gmx-users] Doubt about hessian matrix in Normal mode analysis   Varvdekar Bhagyesh Rajendra
  • [gmx-users] Doubt about hessian matrix in Normal mode analysis   Varvdekar Bhagyesh Rajendra
    • [gmx-users] Doubt about hessian matrix in Normal mode analysis   Varvdekar Bhagyesh Rajendra
• [gmx-users] Umbrella Sampling with Direction-Periodic   Daniel Kozuch
• [gmx-users] Reg. Umbrella sampling problem with direction   "가디 장데부 고라크스나트"
• [gmx-users] pulling of a molecule through protein-membrane system   Alex Mathew
  • [gmx-users] pulling of a molecule through protein-membrane system   Justin Lemkul
• [gmx-users] GPU job failed   Albert
  • [gmx-users] GPU job failed   Mark Abraham
    • [gmx-users] GPU job failed   Albert
• [gmx-users] membrane-protein simulation   Amir Zeb
  • [gmx-users] membrane-protein simulation   Justin Lemkul
    • [gmx-users] membrane-protein simulation   Amir Zeb
• [gmx-users] Clayff forcefield   G R
  • [gmx-users] Clayff forcefield   Justin Lemkul
• [gmx-users] -multidir option in REMD (GROMACS v2016.1)   ABEL Stephane
  • [gmx-users] -multidir option in REMD (GROMACS v2016.1)   Hermann, Johannes
  • [gmx-users] -multidir option in REMD (GROMACS v2016.1)   Mark Abraham
• [gmx-users] Error in the replica order in REMD (GMX v2016.1)   ABEL Stephane
  • [gmx-users] Error in the replica order in REMD (GMX v2016.1)   Mark Abraham
    • [gmx-users] Error in the replica order in REMD (GMX v2016.1)   Hermann, Johannes
• [gmx-users] QM/MM in Gromacs-5.1.4?   Albert
• [gmx-users] Dynamics only for cavity in molecule.   nikolaev at spbau.ru
• [gmx-users] Fwd: meaning of -sigfac option in gmx sigeps   Tamisra Pal
• [gmx-users] Error in itp file   Souvik Dey
  • [gmx-users] Error in itp file   Mohammad Zahidul Hossain Khan
  • [gmx-users] Error in itp file   Justin Lemkul
    • [gmx-users] Error in itp file   Souvik Dey
      • [gmx-users] Error in itp file   Souvik Dey
      • [gmx-users] Error in itp file   Mohammad Zahidul Hossain Khan
      • [gmx-users] Error in itp file   Justin Lemkul
      • [gmx-users] Error in itp file   Souvik Dey
      • [gmx-users] Error in itp file   Mohammad Zahidul Hossain Khan
• [gmx-users] -multidir option in REMD (GROMACS v2016.1) -resolved   ABEL Stephane
• [gmx-users] QM/MM in Gromacs-5.1.4?   Clinton King
• [gmx-users] G_MMPBSA   Suhaib Shekfeh
• [gmx-users] CHARMM36 for GMX   Alex
  • [gmx-users] CHARMM36 for GMX   Justin Lemkul
    • [gmx-users] CHARMM36 for GMX   Alex
      • [gmx-users] CHARMM36 for GMX   Justin Lemkul
      • [gmx-users] CHARMM36 for GMX   Alex
      • [gmx-users] CHARMM36 for GMX   Justin Lemkul
      • [gmx-users] CHARMM36 for GMX   Alex
• [gmx-users] segmentation fault for unknown reason   gangotri dey
  • [gmx-users] segmentation fault for unknown reason   Justin Lemkul
• [gmx-users] AVX related compiler error during build with P100 RHEL7   Guyen Gn
  • [gmx-users] AVX related compiler error during build with P100 RHEL7   Mark Abraham
• [gmx-users] x2top and default dihedral type   Alex
• [gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)   Andrew Bostick
  • [gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)   Mark Abraham
• [gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI   Hermann, Johannes
• [gmx-users] Protein coming out of simulation box.   zaved at tezu.ernet.in
  • [gmx-users] Protein coming out of simulation box.   Mark Abraham
• [gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)   Andrew Bostick
  • [gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)   Mark Abraham
• [gmx-users] Clustering   Pandya, Akash
• [gmx-users] evaluation of simulated frames by procheck   Seera Suryanarayana
• [gmx-users] meaning of -sigfac option in gmx sigeps   Tamisra Pal
  • [gmx-users] meaning of -sigfac option in gmx sigeps   Mark Abraham
• [gmx-users] mutagenesis- Study the role of an aminoacids in proteins.   Nikhil Maroli
• [gmx-users] Pulling   Luca Retattino
• [gmx-users] Gromacs 2016 pulling code   Luca Retattino
• [gmx-users] Problems with continuing simulation after time limit   Searle Duay
  • [gmx-users] Problems with continuing simulation after time limit   Mark Abraham
• [gmx-users] Does gmx distance correct for broken molecules from pbc?   Ramon Crehuet
  • [gmx-users] Does gmx distance correct for broken molecules from pbc?   Mark Abraham
• [gmx-users] The small organic molecule occurred deformation during simulation   yujie liu
  • [gmx-users] The small organic molecule occurred deformation during simulation   Justin Lemkul
• [gmx-users] Could not find clayff forcefield   G R
  • [gmx-users] Could not find clayff forcefield   Justin Lemkul
• [gmx-users] Problem with dihedral restraints   gangotri dey
  • [gmx-users] Problem with dihedral restraints   Mark Abraham
    • [gmx-users] Problem with dihedral restraints   gangotri dey
• [gmx-users] question about gmx do_dssp   YanhuaOuyang
  • [gmx-users] question about gmx do_dssp   Mark Abraham
    • [gmx-users] question about gmx do_dssp   YanhuaOuyang
      • [gmx-users] question about gmx do_dssp   Mark Abraham
      • [gmx-users] question about gmx do_dssp   Justin Lemkul
• [gmx-users] Gmx hbond   farial tavakoli
  • [gmx-users] Gmx hbond   Justin Lemkul
    • [gmx-users] Gmx hbond   farial tavakoli
      • [gmx-users] Gmx hbond   Justin Lemkul
• [gmx-users] MnO2 periodic system   gangotri dey
  • [gmx-users] MnO2 periodic system   Dallas Warren
• [gmx-users] Dynamics only for cavity in molecule.   nikolaev at spbau.ru
  • [gmx-users] Dynamics only for cavity in molecule.   Mark Abraham
    • [gmx-users] Dynamics only for cavity in molecule.   nikolaev at spbau.ru
      • [gmx-users] Dynamics only for cavity in molecule.   Mark Abraham
• [gmx-users] error at nvt equilibrium   Mohammad Zahidul Hossain Khan
• [gmx-users] Help with segmentation fault error   Kunal Maniar
• [gmx-users] Generating topology file for a long polymer chain   Mahsa E
  • [gmx-users] Generating topology file for a long polymer chain   Justin Lemkul
    • [gmx-users] Generating topology file for a long polymer chain   Mahsa E
      • [gmx-users] Generating topology file for a long polymer chain   Justin Lemkul
      • [gmx-users] Generating topology file for a long polymer chain   Mahsa E
• [gmx-users] Generating topology file for a long polymer chain   Mahsa E
• [gmx-users] QSUB commands   Neha Gupta
  • [gmx-users] QSUB commands   Mark Abraham
• [gmx-users] Umbrella Sampling -PME   mohamed mehana
• [gmx-users] The small organic molecule occurred deformation during simulation   yujie liu
• [gmx-users] The small organic molecule occurred deformation during simulation   yujie liu
  • [gmx-users] The small organic molecule occurred deformation during simulation   Justin Lemkul
• [gmx-users] Continuing a run   ‪Mohammad Roostaie‬ ‪
• [gmx-users] TOPOLOGY USING OPLS FORCEFIELD   Vidya R
• [gmx-users] TOPOLOGY USING OPLS FORCEFIELD   Nikhil Maroli
• [gmx-users] How to Identify clusters   Sameer Edirisinghe
  • [gmx-users] How to Identify clusters   Anna Lappala
  • [gmx-users] How to Identify clusters   Mark Abraham
• [gmx-users] Non bonded interaction mapping   Sameer Edirisinghe
  • [gmx-users] Non bonded interaction mapping   Dan Gil
• [gmx-users] How to obtain a proper structure for glycine?   ZHANG Cheng
  • [gmx-users] How to obtain a proper structure for glycine?   Mark Abraham
    • [gmx-users] How to obtain a proper structure for glycine?   ZHANG Cheng
      • [gmx-users] How to obtain a proper structure for glycine?   Dawid das
      • [gmx-users] How to obtain a proper structure for glycine?   ZHANG Cheng
      • [gmx-users] How to obtain a proper structure for glycine?   Dawid das
• [gmx-users] Constraining starting configuration in Coarse-Grain Simulation   Maghesree Chakraborty
  • [gmx-users] Constraining starting configuration in Coarse-Grain Simulation   Mark Abraham
    • [gmx-users] Constraining starting configuration in Coarse-Grain Simulation   Maghesree Chakraborty
      • [gmx-users] Constraining starting configuration in Coarse-Grain Simulation   Mark Abraham
      • [gmx-users] Constraining starting configuration in Coarse-Grain Simulation   Maghesree Chakraborty
• [gmx-users] trans-membrane protein simulation   Amir Zeb
  • [gmx-users] trans-membrane protein simulation   Justin Lemkul
• [gmx-users] time calculations   faru honey
  • [gmx-users] time calculations   Mark Abraham
• [gmx-users] converting xtc to pdb without need to tpr file using trjconv   Neda Rafiee
  • [gmx-users] converting xtc to pdb without need to tpr file using trjconv   Justin Lemkul
    • [gmx-users] converting xtc to pdb without need to tpr file using trjconv   Neda Rafiee
• [gmx-users] amino acid adsorption on metal surface   Rabia Mukhtar
• [gmx-users] Could not find clayff forcefield   G R
• [gmx-users] 2D maps   Yasser Almeida Hernández
• [gmx-users] Visualization of xtc file   farial tavakoli
  • [gmx-users] Visualization of xtc file   Andrea Spitaleri
    • [gmx-users] Visualization of xtc file   farial tavakoli
• [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?   ZHANG Cheng
  • [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?   ZHANG Cheng
• [gmx-users] -com and -rdf options do not work in gmx rdf analysis   faride badalkhani
• [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?   yujie liu
  • [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?   Souvik Dey
• [gmx-users] Performance values   Szilárd Páll
• [gmx-users] Non Standard residues moving Away   Souvik Dey
  • [gmx-users] Non Standard residues moving Away   Mark Abraham
    • [gmx-users] Non Standard residues moving Away   Souvik Dey
      • [gmx-users] Non Standard residues moving Away   Justin Lemkul
• [gmx-users] (no subject)   gangotri dey
  • [gmx-users] (no subject)   Mark Abraham
    • [gmx-users] (no subject)   gangotri dey
      • [gmx-users] (no subject)   Mark Abraham
      • [gmx-users] (no subject)   Alex
      • [gmx-users] (no subject)   gangotri dey
      • [gmx-users] (no subject)   Alex
• [gmx-users] Performance values   Maureen Chew
  • [gmx-users] Performance values   Szilárd Páll
• [gmx-users] solvate only in the z-direction   gangotri dey
  • [gmx-users] solvate only in the z-direction   Mark Abraham
• [gmx-users] clayff forcefield   G R
  • [gmx-users] clayff forcefield   Mark Abraham
• [gmx-users] Memory issues using -ac option of gmx hbond   Jared Sagendorf
  • [gmx-users] Memory issues using -ac option of gmx hbond   Smith, Micholas D.
    • [gmx-users] Memory issues using -ac option of gmx hbond   Mark Abraham
• [gmx-users] [gmx-developers] importing amber parameters to gromacs format?   Justin Lemkul
• [gmx-users] clayff forcefield   G R
  • [gmx-users] clayff forcefield   Justin Lemkul
• [gmx-users] (no subject)   Sorour Hasani
  • [gmx-users] (no subject)   Justin Lemkul
• [gmx-users] convert .tpr to include energy groups   Tushar Ranjan Moharana
  • [gmx-users] convert .tpr to include energy groups   Justin Lemkul
  • [gmx-users] convert .tpr to include energy groups   Tushar Ranjan Moharana
• [gmx-users] Problem with Ryzen, threads and core dumps?   Steffen Graether
  • [gmx-users] Problem with Ryzen, threads and core dumps?   Mark Abraham
  • [gmx-users] Problem with Ryzen, threads and core dumps?   Steffen Graether
• [gmx-users] vdw and Electrostatic energy   Mohammad Zahidul Hossain Khan
  • [gmx-users] vdw and Electrostatic energy   Justin Lemkul
• [gmx-users] MM/PBSA   Kingsley Theras Primus Dass .
• [gmx-users] MM/PBSA   Amir Zeb
  • [gmx-users] MM/PBSA   Kingsley Theras Primus Dass .
    • [gmx-users] MM/PBSA   Amir Zeb
    • [gmx-users] Ris: MM/PBSA   Andrea Spitaleri
• [gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN   Vidya R
• [gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN   Nikhil Maroli
• [gmx-users] clayff forcefield   G R
  • [gmx-users] clayff forcefield   Mark Abraham
• [gmx-users] Position restrains during alchemical transformation   Hermann, Johannes
  • [gmx-users] Position restrains during alchemical transformation   Mark Abraham
    • [gmx-users] Position restrains during alchemical transformation   Hermann, Johannes
• [gmx-users] Atom OXT in residue was not found   Qinghua Liao
  • [gmx-users] Atom OXT in residue was not found   Justin Lemkul
    • [gmx-users] Atom OXT in residue was not found   Qinghua Liao
• [gmx-users] g_hbonds calculation on GPU   Rituraj Purohit
  • [gmx-users] g_hbonds calculation on GPU   Erik Marklund
• [gmx-users] remove the jumps over the boundaries   ‪farial tavakoli‬ ‪
  • [gmx-users] remove the jumps over the boundaries   Milan Melichercik
    • [gmx-users] remove the jumps over the boundaries   farial tavakoli
• [gmx-users] electronic fields   Li, Tong
• [gmx-users] g_cluster and g_hbond calculation on GPU   Kishwar Hayat Khan
  • [gmx-users] g_cluster and g_hbond calculation on GPU   Mark Abraham
• [gmx-users] transmembrane protein simulation   abhisek Mondal
  • [gmx-users] transmembrane protein simulation   Justin Lemkul
• [gmx-users] gmx sasa   Mohammad Zahidul Hossain Khan
  • [gmx-users] gmx sasa   Justin Lemkul
• [gmx-users] (no subject)   saranya
• [gmx-users] (no subject)   saranya
  • [gmx-users] (no subject)   Tasneem Kausar
    • [gmx-users] (no subject)   saranya
  • [gmx-users] Fwd:   saranya
    • [gmx-users] Fwd:   Justin Lemkul
      • [gmx-users] Fwd:   saranya
      • [gmx-users] Fwd:   Justin Lemkul
• [gmx-users] problem with n2t file   Niko Ukkonen
  • [gmx-users] problem with n2t file   Justin Lemkul
• [gmx-users] grompp warning   Qinghua Liao
• [gmx-users] (no subject)   Iman Ahmadabadi
  • [gmx-users] (no subject)   Dan Gil
• [gmx-users] Potential Shift Verlet   Natalie Paige Schieber
  • [gmx-users] Potential Shift Verlet   Mark Abraham
• [gmx-users] Donors and Acceptors - gmx hbond   Marcelo Depólo
  • [gmx-users] Donors and Acceptors - gmx hbond   Mark Abraham
• [gmx-users] non zero free energy values in mass transformation   deepak bapat
  • [gmx-users] non zero free energy values in mass transformation   André Farias de Moura
    • [gmx-users] non zero free energy values in mass transformation   Dan Gil
      • [gmx-users] non zero free energy values in mass transformation   deepak bapat
      • [gmx-users] non zero free energy values in mass transformation   deepak bapat
      • [gmx-users] non zero free energy values in mass transformation   Dan Gil
      • [gmx-users] non zero free energy values in mass transformation   deepak bapat
• [gmx-users] Simulations showing that mass contributes to the solvation free energy in a thermodynamic cycle   Dan Gil
• [gmx-users] Pull Code: direction-periodic with 3 dimensions   Daniel Kozuch
  • [gmx-users] Pull Code: direction-periodic with 3 dimensions   Justin Lemkul
• [gmx-users] Pull Code: direction-periodic with 3 dimensions   Daniel Kozuch
• [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Steffen Graether
  • [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Mark Abraham
• [gmx-users] ligand   ‪farial tavakoli‬ ‪
  • [gmx-users] ligand   Justin Lemkul
    • [gmx-users] ligand   farial tavakoli
      • [gmx-users] ligand   Justin Lemkul
      • [gmx-users] ligand   ‪farial tavakoli‬ ‪
      • [gmx-users] ligand   Justin Lemkul
      • [gmx-users] ligand   ‪farial tavakoli‬ ‪
• [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   ZHANG Cheng
  • [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   ZHANG Cheng
    • [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   Justin Lemkul
    • [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   ZHANG Cheng
      • [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   Justin Lemkul
      • [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   ZHANG Cheng
      • [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)   Justin Lemkul
• [gmx-users] NVT error   Justin Lemkul
• [gmx-users] Difference in omega angles!!   Seera Suryanarayana
  • [gmx-users] Difference in omega angles!!   Justin Lemkul
    • [gmx-users] Difference in omega angles!!   Alex
      • [gmx-users] Difference in omega angles!!   Justin Lemkul
• [gmx-users] PBC ISSUES IN GROMACS   Neha Gupta
  • [gmx-users] PBC ISSUES IN GROMACS   David van der Spoel
  • [gmx-users] PBC ISSUES IN GROMACS   Mark Abraham
• [gmx-users] Drift with groups+tabulated potential.   sperez14 at us.es
• [gmx-users] Position Restraint for production MD   Pandya, Akash
  • [gmx-users] Position Restraint for production MD   Justin Lemkul
    • [gmx-users] Position Restraint for production MD   Mark Abraham
• [gmx-users] Can I specify the residue numbers for RMSD?   ZHANG Cheng
  • [gmx-users] Can I specify the residue numbers for RMSD?   Justin Lemkul
• [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Steffen Graether
  • [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Mark Abraham
    • [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Steffen Graether
    • [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Steffen Graether
      • [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests   Mark Abraham
• [gmx-users] ligand   farial tavakoli
• [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 63   Faez Iqbal Khan
  • [gmx-users] NVT error   Justin Lemkul
• [gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67   Marcelo Depólo
• [gmx-users] How to use the index.ndx when running rms?   ZHANG Cheng
  • [gmx-users] How to use the index.ndx when running rms?   Justin Lemkul
  • [gmx-users] How to use the index.ndx when running rms?   ZHANG Cheng
    • [gmx-users] How to use the index.ndx when running rms?   ZHANG Cheng
• [gmx-users] Question on gmx_wham with two reaction coordinates.   Yuanchao Liu (MSU)
  • [gmx-users] Fwd: Question on gmx_wham with two reaction coordinates.   Yuanchao Liu (MSU)
• [gmx-users] Kudos to trjconv -pbc cluster coder   Dallas Warren
• [gmx-users] umbrella sampling   Kingsley Theras Primus Dass .
• [gmx-users] Scaling in gromacs   praveen kumar
  • [gmx-users] Scaling in gromacs   Mark Abraham
• [gmx-users] (Don't know if mail worked last time)Drift with groups+tabulated potential.   sperez14 at us.es
• [gmx-users] how to make molecular model with both ion channel and lipid bilayer?   Li, Tong
  • [gmx-users] how to make molecular model with both ion channel and lipid bilayer?   h.alizadeh at znu.ac.ir
• [gmx-users] Doing restart   ‪farial tavakoli‬ ‪
• [gmx-users] npt simulation error   Mohammad Zahidul Hossain Khan
  • [gmx-users] npt simulation error   Justin Lemkul
    • [gmx-users] npt simulation error   Mohammad Zahidul Hossain Khan
      • [gmx-users] npt simulation error   Justin Lemkul
      • [gmx-users] npt simulation error   Mohammad Zahidul Hossain Khan
• [gmx-users] positioning molecule at desired location   Alex Mathew
  • [gmx-users] positioning molecule at desired location   Justin Lemkul
• [gmx-users] (no subject)   zaved at tezu.ernet.in
  • [gmx-users] (no subject)   RAHUL SURESH
• [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 74   Naba
• [gmx-users] COM pulling   Naba
  • [gmx-users] COM pulling   Justin Lemkul
• [gmx-users] Compiling DSSP-2.2.1 from source   João Henriques
  • [gmx-users] Compiling DSSP-2.2.1 from source   João Henriques
• [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 75   zaved at tezu.ernet.in
• [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Dilip H N
  • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Justin Lemkul
    • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Dilip H N
      • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Justin Lemkul
      • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Dilip H N
      • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Justin Lemkul
      • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Dilip H N
      • [gmx-users] Regarding naming dipeptide in charmm36 Forcefield   Justin Lemkul
• [gmx-users] Gromacs enquiry   Odame Agyapong
  • [gmx-users] Gromacs enquiry   Mark Abraham
    • [gmx-users] Gromacs enquiry   Odame Agyapong
      • [gmx-users] Gromacs enquiry   Mark Abraham
  • [gmx-users] Gromacs enquiry   Subhomoi Borkotoky
• [gmx-users] Pbc   farial tavakoli
  • [gmx-users] Pbc   Justin Lemkul
• [gmx-users] dielectric constant 4   Mohammad Zahidul Hossain Khan
  • [gmx-users] dielectric constant 4   Alex
    • [gmx-users] dielectric constant 4   Mohammad Zahidul Hossain Khan
  • [gmx-users] dielectric constant 4   Mark Abraham
    • [gmx-users] dielectric constant 4   Mohammad Zahidul Hossain Khan
      • [gmx-users] dielectric constant 4   Justin Lemkul
• [gmx-users] InflateGRO script   "가디 장데부 고라크스나트"
  • [gmx-users] InflateGRO script   Odame Agyapong
  • [gmx-users] InflateGRO script   Justin Lemkul
• [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   edesantis
  • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Peter Kroon
    • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Piggot T.
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Peter Kroon
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Thomas Piggot
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   edesantis
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Thomas Piggot
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Thomas Piggot
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   edesantis
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Thomas Piggot
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   Thomas Piggot
      • [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings   edesantis
• [gmx-users] Software inconsistency error: Lost particles while sorting   Alex Mathew
  • [gmx-users] Software inconsistency error: Lost particles while sorting   Mark Abraham
• [gmx-users] Use of providing -ix pullx.xvg in WHAM   jay patil
  • [gmx-users] Use of providing -ix pullx.xvg in WHAM   Justin Lemkul
    • [gmx-users] Use of providing -ix pullx.xvg in WHAM   jay patil
• [gmx-users] extending umbrella sampling simulations   Irem Altan
• [gmx-users] CHARMM36 & Gromacs   Mateusz Marianski
  • [gmx-users] CHARMM36 & Gromacs   Justin Lemkul
• [gmx-users] periodic boundary conditions   JAVAD MAHMOUDZADEH
• [gmx-users] Dear gmx-users,   Sithara Perera
• [gmx-users] Applying a potential gradient   Sithara Perera
• [gmx-users] ForceField of ethanol and the default parameters in Gromacs   ZUO Taisen
  • [gmx-users] ForceField of ethanol and the default parameters in Gromacs   Mark Abraham
• [gmx-users] RDF   RAHUL SURESH
  • [gmx-users] RDF   Dan Gil
    • [gmx-users] RDF   RAHUL SURESH
      • [gmx-users] RDF   Dan Gil
      • [gmx-users] RDF   Dallas Warren
      • [gmx-users] RDF   RAHUL SURESH
      • [gmx-users] RDF   Dallas Warren
      • [gmx-users] RDF   RAHUL SURESH
      • [gmx-users] RDF   Dallas Warren
      • [gmx-users] RDF   RAHUL SURESH
• [gmx-users] problem in extending a simulation run   manindersingh rajawat
  • [gmx-users] problem in extending a simulation run   Tasneem Kausar
    • [gmx-users] problem in extending a simulation run   manindersingh rajawat
  • [gmx-users] problem in extending a simulation run   Mark Abraham
    • [gmx-users] problem in extending a simulation run   manindersingh rajawat
• [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA   Ming Tang
  • [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA   Justin Lemkul
• [gmx-users] Error with MPICH   Souparno Adhikary
  • [gmx-users] Error with MPICH   Mark Abraham
    • [gmx-users] Error with MPICH   Souparno Adhikary
      • [gmx-users] Error with MPICH   Szilárd Páll
• [gmx-users] umbrella sample Question   yujie liu
  • [gmx-users] umbrella sample Question   Justin Lemkul
• [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA   Ming Tang
  • [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA   Justin Lemkul
• [gmx-users] umbrella sample Question   yujie liu
  • [gmx-users] umbrella sample Question   Justin Lemkul
• [gmx-users] setting up simulated annealing   Seera Suryanarayana
• [gmx-users] Simulated annealing   Seera Suryanarayana
• [gmx-users] umbrella sample Question   Nikhil Maroli
• [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation   Alex Mathew
  • [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation   Justin Lemkul
• [gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi   Xingcheng Lin
  • [gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi   Justin Lemkul
• [gmx-users] HSE in Charmm-gui membrane builder   Мижээ Батсайхан
  • [gmx-users] HSE in Charmm-gui membrane builder   Justin Lemkul
• [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation   Alex Mathew
  • [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation   Alex
• [gmx-users] umbrella sample Question   yujie liu
• [gmx-users] HSE in Charmm-gui membrane builder   Nikhil Maroli
• [gmx-users] Average and bfactors.pdb   farial tavakoli
  • [gmx-users] Average and bfactors.pdb   Justin Lemkul
    • [gmx-users] Average and bfactors.pdb   farial tavakoli
      • [gmx-users] Average and bfactors.pdb   Justin Lemkul
      • [gmx-users] Average and bfactors.pdb   farial tavakoli
      • [gmx-users] Average and bfactors.pdb   Justin Lemkul
      • [gmx-users] Average and bfactors.pdb   farial tavakoli
• [gmx-users] Calculating the dielectric constant of a ligand   Sajad Ahrari
• [gmx-users] Doubt about hessian matrix in Normal mode analysis   Varvdekar Bhagyesh Rajendra
• [gmx-users] Setting up SA   Seera Suryanarayana
• [gmx-users] Setting up SA   Nikhil Maroli
• [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA   Ming Tang
• [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation   Alex Mathew
• [gmx-users] Error in simulated annealing   Seera Suryanarayana
  • [gmx-users] Error in simulated annealing   Justin Lemkul
• [gmx-users] Residue 1 mapping problem?   morpheus
  • [gmx-users] Residue 1 mapping problem?   Justin Lemkul
  • [gmx-users] Fwd: Residue 1 mapping problem?   morpheus
    • [gmx-users] Fwd: Residue 1 mapping problem?   Justin Lemkul
• [gmx-users] MPICH2 error   Souparno Adhikary
  • [gmx-users] MPICH2 error   Mark Abraham
    • [gmx-users] MPICH2 error   Souparno Adhikary
      • [gmx-users] MPICH2 error   Mark Abraham
      • [gmx-users] MPICH2 error   Souparno Adhikary
• [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
  • [gmx-users] FEP calculations on multiple nodes   Michael Shirts
    • [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
• [gmx-users] Regarding Unknown cmap torsion between atoms   Dilip H N
  • [gmx-users] Regarding Unknown cmap torsion between atoms   Mark Abraham
    • [gmx-users] Regarding Unknown cmap torsion between atoms   Dilip H N
      • [gmx-users] Regarding Unknown cmap torsion between atoms   Mark Abraham
      • [gmx-users] Regarding Unknown cmap torsion between atoms   Dilip H N
      • [gmx-users] Regarding Unknown cmap torsion between atoms   Mark Abraham
      • [gmx-users] Regarding Unknown cmap torsion between atoms   Dilip H N
      • [gmx-users] Regarding Unknown cmap torsion between atoms   Mark Abraham
• [gmx-users] FEP calculations on multiple nodes   Nikhil Maroli
  • [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
• [gmx-users] Trouble with gmx distance   Sotirios Dionysios I. Papadatos
  • [gmx-users] Trouble with gmx distance   Vytautas Rakeviius
    • [gmx-users] Trouble with gmx distance   Sotirios Dionysios I. Papadatos
• [gmx-users] FEP calculations on multiple nodes   Nikhil Maroli
  • [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
    • [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
      • [gmx-users] FEP calculations on multiple nodes   Mark Abraham
      • [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
      • [gmx-users] FEP calculations on multiple nodes   Mark Abraham
      • [gmx-users] FEP calculations on multiple nodes   Leandro Bortot
      • [gmx-users] FEP calculations on multiple nodes   Mark Abraham
      • [gmx-users] FEP calculations on multiple nodes   Vikas Dubey
      • [gmx-users] FEP calculations on multiple nodes   Mark Abraham
• [gmx-users] Fwd: Unusual bonding between residues in vmd   ISHRAT JAHAN
  • [gmx-users] Fwd: Unusual bonding between residues in vmd   Mark Abraham
    • [gmx-users] Fwd: Unusual bonding between residues in vmd   ISHRAT JAHAN
      • [gmx-users] Fwd: Unusual bonding between residues in vmd   ISHRAT JAHAN
• [gmx-users] Fwd: Unusual bonding between residues in vmd   Nikhil Maroli
  • [gmx-users] Fwd: Unusual bonding between residues in vmd   ISHRAT JAHAN
• [gmx-users] COM pulling with gromacs 5.0.x   Romain Gautier IPMC
• [gmx-users] Gromacs_GPU_Compiling_Problem   郭逸峰
• [gmx-users] Gromacs_GPU_Compiling_Problem   Nikhil Maroli
  • [gmx-users] Gromacs_GPU_Compiling_Problem   Peter Kroon
• [gmx-users] Related to fluctuation in Pressure   ISHRAT JAHAN
• [gmx-users] dielectric constant measurment   Sajad Ahrari
• [gmx-users] Related to fluctuation in Pressure   Syed Azeem
• [gmx-users] Can I used slipids.ff + charmm36.ff to create a system?   Carlos Navarro
• [gmx-users] Can I used slipids.ff + charmm36.ff to create a system?   Carlos Navarro
• [gmx-users] Extract only last frame from a trr   CLARK NICOLAS Joan
  • [gmx-users] Extract only last frame from a trr   Mark Abraham
• [gmx-users] Regarding indexing the atom labelled same in peptide   Dilip H N
  • [gmx-users] Regarding indexing the atom labelled same in peptide   Mark Abraham
• [gmx-users] installation_server machine_error   Kashif
  • [gmx-users] installation_server machine_error   Vytautas Rakeviius
  • [gmx-users] installation_server machine_error   Mark Abraham
• [gmx-users] Missing values in enery EDR   Sergio Manzetti
  • [gmx-users] Missing values in enery EDR   Mark Abraham
• [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?   Carlos Navarro
  • [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?   Mark Abraham
    • [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?   Carlos Navarro
• [gmx-users] 2nd CfP: From Virtual Reality to Immersive Analytics in Bioinformatics (SD&A 2018)   Björn Sommer
• [gmx-users] g_cluster   Smolin, Nikolai
  • [gmx-users] g_cluster   Erik Marklund
• [gmx-users] FEP: mdp setting for mutation   Alex Mathew
• [gmx-users] Torsion analysis   RAHUL SURESH
  • [gmx-users] Torsion analysis   João Henriques
• [gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms   Dilip H N
  • [gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms   Mark Abraham
• [gmx-users] Gromacs simulation of two or more peptide chain   Kalyanashis Jana
  • [gmx-users] Gromacs simulation of two or more peptide chain   Vytautas Rakeviius
• [gmx-users] pullx (gromacs 4.6 vs 2016)   gromacs query
  • [gmx-users] pullx (gromacs 4.6 vs 2016)   gromacs query
• [gmx-users] gmx distance   Sergio Manzetti
  • [gmx-users] gmx distance   Vytautas Rakeviius
  • [gmx-users] gmx distance   Tasneem Kausar
• [gmx-users] GROMACS with Torque: Job stuck   Souparno Adhikary
  • [gmx-users] GROMACS with Torque: Job stuck   Vytautas Rakeviius
  • [gmx-users] GROMACS with Torque: Job stuck   Mark Abraham
    • [gmx-users] GROMACS with Torque: Job stuck   Souparno Adhikary
      • [gmx-users] GROMACS with Torque: Job stuck   Mark Abraham
• [gmx-users] Restraining molecule near interface   Deepak Ojha
• [gmx-users] gromacs error   Neha Gupta
  • [gmx-users] gromacs error   Vytautas Rakeviius
    • [gmx-users] gromacs error   Neha Gupta
      • [gmx-users] gromacs error   Justin Lemkul
• [gmx-users] QM/MM simulation   Mostafa Javaheri
• [gmx-users] finding Dihedrals with x2top   Ali Shomali
• [gmx-users] About the possibility of calculating dipole moment vectors of individual waters around polar solutes   Sajeewa Pemasinghe
• [gmx-users] Andersen thermostat with NPT - nstcomm < nstcalenergy   Simon Kit Sang Chu
• [gmx-users] Unable to install 5.1.14   Rajat Desikan
  • [gmx-users] Unable to install 5.1.14   Vytautas Rakeviius
    • [gmx-users] Unable to install 5.1.14   Rajat Desikan
• [gmx-users] ERROR IN EXECUTION ---GMX   Neha Gupta
• [gmx-users] ERROR IN EXECUTION ---GMX   Nikhil Maroli
  • [gmx-users] ERROR IN EXECUTION ---GMX   Neha Gupta
  • [gmx-users] ERROR IN EXECUTION ---GMX   Nikhil Maroli
    • [gmx-users] ERROR IN EXECUTION ---GMX   Neha Gupta
      • [gmx-users] ERROR IN EXECUTION ---GMX   Tasneem Kausar
• [gmx-users] QM/MM simulation (Mostafa Javaheri)   Groenhof, Gerrit
• [gmx-users] problem installing plumed-2.3.2   spss4 at iacs.res.in
  • [gmx-users] problem installing plumed-2.3.2   Giovanni Bussi
• [gmx-users] Corrupted checkpoint file from MD simulation   Alexander Yang
  • [gmx-users] Corrupted checkpoint file from MD simulation   melichercik at leaf.nh.cas.cz
• [gmx-users] Surface Tension Calculation   Lei
  • [gmx-users] Surface Tension Calculation   Dan Gil
• [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc   Apramita Chand
  • [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc   Erik Marklund
• [gmx-users] nstcomm < nstcalenergy   Simon Kit Sang Chu
  • [gmx-users] nstcomm < nstcalenergy   Justin Lemkul
• [gmx-users] Coordination vs cumulative number in gmx_rdf   Dilip H N
• [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   neha chaudhary
• [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   Nikhil Maroli
• [gmx-users] nstcomm < nstcalenergy   yujie liu
• [gmx-users] gmx analyze Luzar analysis   Valerio Ferrario
  • [gmx-users] gmx analyze Luzar analysis   Erik Marklund
    • [gmx-users] gmx analyze Luzar analysis   Valerio Ferrario
• [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc   Apramita Chand
  • [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc   Erik Marklund
• [gmx-users] Difference in hydrogen bond lifetimes with and without pbc   Apramita Chand
  • [gmx-users] Difference in hydrogen bond lifetimes with and without pbc   Erik Marklund
• [gmx-users] Surface tension for water   Iman Ahmadabadi
  • [gmx-users] Surface tension for water   Dan Gil
  • [gmx-users] Surface tension for water   Iman Ahmadabadi
    • [gmx-users] Surface tension for water   Dan Gil
    • [gmx-users] Surface tension for water   Dan Gil
    • [gmx-users] Surface tension for water   Iman Ahmadabadi
      • [gmx-users] Surface tension for water   Dan Gil
      • [gmx-users] Surface tension for water   Iman Ahmadabadi
      • [gmx-users] Surface tension for water   André Farias de Moura
• [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   neha chaudhary
• [gmx-users] Surface Tension Calculation   Lei
• [gmx-users] Pure repulsive LJ potential for OPLSAA   Lei
• [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   Nikhil Maroli
  • [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   neha chaudhary
• [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   Nikhil Maroli
  • [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   neha chaudhary
    • [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa   neha chaudhary
• [gmx-users] Fwd: Difference in Hydrogen Bond Lifetimes on using pbc   Apramita Chand
  • [gmx-users] Difference in Hydrogen Bond Lifetimes on using pbc   Apramita Chand
• [gmx-users] Showing different RMSD values   Seera Suryanarayana
• [gmx-users] Showing different RMSD values   Nikhil Maroli
• [gmx-users] difference in potential energy   Emran Heshmati
  • [gmx-users] difference in potential energy   Justin Lemkul
• [gmx-users] gmxdump gmxcheck commands not found   Apramita Chand
  • [gmx-users] gmxdump gmxcheck commands not found   Justin Lemkul
• [gmx-users] Setting different intial velocities   Apramita Chand
  • [gmx-users] Setting different intial velocities   Justin Lemkul
• [gmx-users] possible bug in posre   Sergio Manzetti
  • [gmx-users] possible bug in posre   Justin Lemkul
    • [gmx-users] possible bug in posre   Sergio Manzetti
      • [gmx-users] possible bug in posre   Justin Lemkul
      • [gmx-users] possible bug in posre   Sergio Manzetti
      • [gmx-users] possible bug in posre   Justin Lemkul
      • [gmx-users] possible bug in posre   Sergio Manzetti
      • [gmx-users] possible bug in posre   Justin Lemkul
• [gmx-users] triclinic box   Niko Ukkonen
  • [gmx-users] triclinic box   Hermann, Johannes
• [gmx-users] Bug?! Lost particles while sorting   Mohsen Ramezanpour
  • [gmx-users] Bug?! Lost particles while sorting   Mark Abraham
    • [gmx-users] Bug?! Lost particles while sorting   Mohsen Ramezanpour
• [gmx-users] Error regarding missing hydrogen atoms   Vishal Pandya
• [gmx-users] gmx mindist   ‪Mohammad Roostaie‬ ‪
• [gmx-users] RMSD   Apramita Chand
• [gmx-users] Fwd: Potential gradient in NVE simulation   Saumyak Mukherjee
• [gmx-users] Symmetry corrections in FEP   Dries Van Rompaey

Last message date: Thu Aug 31 22:38:58 CEST 2017
Archived on: Thu Aug 31 22:38:59 CEST 2017

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