January 2016 Archives by thread

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Starting: Fri Jan 1 20:17:08 CET 2016
Ending: Sun Jan 31 20:36:11 CET 2016
Messages: 610

• [gmx-users] Force-switch algorithm   Pallavi Banerjee
  • [gmx-users] Force-switch algorithm   Justin Lemkul
• [gmx-users] how to add martini force field in gromacs   vinshal shalini
• [gmx-users] US perl scripts fails index error   Nikhil Maroli
  • [gmx-users] US perl scripts fails index error   Justin Lemkul
    • [gmx-users] US perl scripts fails index error   Nikhil
      • [gmx-users] US perl scripts fails index error   Justin Lemkul
• [gmx-users] Force-switch algorithm   Pallavi Banerjee
  • [gmx-users] Force-switch algorithm   Mark Abraham
• [gmx-users] inserting TM protein dimer into lipid bilayer using Gromacs   Nash, Anthony
• [gmx-users] Cannot write trajectory frame   masoud keramati
  • [gmx-users] Cannot write trajectory frame   Mark Abraham
    • [gmx-users] Cannot write trajectory frame   masoud keramati
      • [gmx-users] Cannot write trajectory frame   Mark Abraham
      • [gmx-users] Cannot write trajectory frame   Teemu Murtola
      • [gmx-users] Cannot write trajectory frame   masoud keramati
      • [gmx-users] Cannot write trajectory frame   masoud keramati
• [gmx-users] Problem in Free Energy Calculations   shagun krishna
  • [gmx-users] Problem in Free Energy Calculations   Justin Lemkul
    • [gmx-users] Problem in Free Energy Calculations   shagun krishna
      • [gmx-users] Problem in Free Energy Calculations   Justin Lemkul
      • [gmx-users] Problem in Free Energy Calculations   shagun krishna
      • [gmx-users] Problem in Free Energy Calculations   shagun krishna
      • [gmx-users] Problem in Free Energy Calculations   Mark Abraham
      • [gmx-users] Problem in Free Energy Calculations   Justin Lemkul
• [gmx-users] Force-switch algorithm   Pallavi Banerjee
  • [gmx-users] Force-switch algorithm   Mark Abraham
• [gmx-users] Problem using gromacs   soumi
  • [gmx-users] Problem using gromacs   shagun krishna
  • [gmx-users] Problem using gromacs   Justin Lemkul
    • [gmx-users] Problem using gromacs   masoud keramati
      • [gmx-users] Problem using gromacs   Justin Lemkul
• [gmx-users] FFTW with AVX   Oliver Schillinger
  • [gmx-users] FFTW with AVX   Mark Abraham
    • [gmx-users] FFTW with AVX   Oliver Schillinger
• [gmx-users] Plumed-2.2.0 installation issue   tarak karmakar
  • [gmx-users] Plumed-2.2.0 installation issue   Justin Lemkul
• [gmx-users] Implementing Gupta potential - different formulism   Gould, Anna
• [gmx-users] Problem with editconf   abhishek khetan
• [gmx-users] Simulation of nonaqueous solvents   abhishek khetan
  • [gmx-users] Simulation of nonaqueous solvents   Justin Lemkul
  • [gmx-users] Simulation of nonaqueous solvents   Mark Abraham
  • [gmx-users] Simulation of nonaqueous solvents   David van der Spoel
    • [gmx-users] Simulation of nonaqueous solvents   Diana Lousa
      • [gmx-users] Simulation of nonaqueous solvents   abhishek khetan
      • [gmx-users] Simulation of nonaqueous solvents   abhishek khetan
      • [gmx-users] Simulation of nonaqueous solvents   Diana Lousa
      • [gmx-users] Simulation of nonaqueous solvents   Justin Lemkul
      • [gmx-users] Simulation of nonaqueous solvents   abhishek khetan
• [gmx-users] fix simulation box corners NVE   Sereda, Yuriy Vladimirovich
  • [gmx-users] fix simulation box corners NVE   Tsjerk Wassenaar
    • [gmx-users] fix simulation box corners NVE   Sereda, Yuriy Vladimirovich
      • [gmx-users] fix simulation box corners NVE   Tsjerk Wassenaar
      • [gmx-users] fix simulation box corners NVE   Mark Abraham
      • [gmx-users] fix simulation box corners NVE   Erik Marklund
  • [gmx-users] fix simulation box corners NVE   Erik Marklund
• [gmx-users] Scripts to the gromacs   Elsaid Younes
  • [gmx-users] Scripts to the gromacs   Justin Lemkul
• [gmx-users] Restarting Simulations   Soumya Lipsa Rath
  • [gmx-users] Restarting Simulations   Justin Lemkul
  • [gmx-users] Restarting Simulations   Soumya Lipsa Rath
• [gmx-users] Force-switch algorithm   Pallavi Banerjee
  • [gmx-users] Force-switch algorithm   Justin Lemkul
    • [gmx-users] Force-switch algorithm   Mark Abraham
      • [gmx-users] Force-switch algorithm   Mark Abraham
  • [gmx-users] Force-switch algorithm   Mark Abraham
• [gmx-users] draw histogram   Sana Saeed
  • [gmx-users] draw histogram   Justin Lemkul
• [gmx-users] Protein-Protein distance   Life Sciences Inc
  • [gmx-users] Protein-Protein distance   Justin Lemkul
    • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Justin Lemkul
      • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Mark Abraham
      • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Mark Abraham
      • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Mark Abraham
      • [gmx-users] Protein-Protein distance   Life Sciences Inc
      • [gmx-users] Protein-Protein distance   Mark Abraham
• [gmx-users] Force-switch algorithm   Pallavi Banerjee
  • [gmx-users] Force-switch algorithm   Mark Abraham
• [gmx-users] umbrella sampling error   Nikhil Maroli
  • [gmx-users] umbrella sampling error   Justin Lemkul
• [gmx-users] Constraints in BAR   Dries Van Rompaey
• [gmx-users] pbc   Parvez Mh
  • [gmx-users] pbc   Justin Lemkul
• [gmx-users] How to adjust the box size to correct density?   Chang Woon Jang
  • [gmx-users] How to adjust the box size to correct density?   abhishek khetan
    • [gmx-users] How to adjust the box size to correct density?   Chang Woon Jang
      • [gmx-users] How to adjust the box size to correct density?   Justin Lemkul
      • [gmx-users] How to adjust the box size to correct density?   Chang Woon Jang
      • [gmx-users] How to adjust the box size to correct density?   Justin Lemkul
• [gmx-users] how to adjust the box size to correct density?   Chang Woon Jang
  • [gmx-users] how to adjust the box size to correct density?   Mark Abraham
    • [gmx-users] how to adjust the box size to correct density?   Chang Woon Jang
      • [gmx-users] how to adjust the box size to correct density?   Mark Abraham
      • [gmx-users] how to adjust the box size to correct density?   Chang Woon Jang
• [gmx-users] How to adjust the box size to correct density?   Chang Woon Jang
  • [gmx-users] How to adjust the box size to correct density?   Justin Lemkul
    • [gmx-users] How to adjust the box size to correct density?   Chang Woon Jang
• [gmx-users] There is no domain decomposition   Ahmet Yıldırım
  • [gmx-users] There is no domain decomposition   Justin Lemkul
• [gmx-users] Unusual use for GMX   Alex
• [gmx-users] Force-switch algorithm   Pallavi Banerjee
• [gmx-users] pmf-gwham   Rasha Alqus
• [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   shagun krishna
  • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   Justin Lemkul
    • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   shagun krishna
      • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   Justin Lemkul
      • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   shagun krishna
      • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   shagun krishna
      • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   Justin Lemkul
      • [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach   Justin Lemkul
• [gmx-users] about the output of g_density   ibrahim khalil
• [gmx-users] Nvt T-coupling error   Poncho Arvayo Zatarain
  • [gmx-users] Nvt T-coupling error   Justin Lemkul
• [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   hubert santuz
  • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Mark Abraham
    • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Hubert Santuz
      • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Mark Abraham
      • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Hubert Santuz
      • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Mark Abraham
      • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Hubert Santuz
      • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Mark Abraham
      • [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT   Hubert Santuz
• [gmx-users] membed in mdrun VERSION 5.0.4   Nash, Anthony
  • [gmx-users] membed in mdrun VERSION 5.0.4   Justin Lemkul
    • [gmx-users] membed in mdrun VERSION 5.0.4   Nash, Anthony
      • [gmx-users] membed in mdrun VERSION 5.0.4   Justin Lemkul
      • [gmx-users] membed in mdrun VERSION 5.0.4   Mark Abraham
      • [gmx-users] membed in mdrun VERSION 5.0.4   Nash, Anthony
      • [gmx-users] membed in mdrun VERSION 5.0.4   Nash, Anthony
      • [gmx-users] membed in mdrun VERSION 5.0.4   Nash, Anthony
      • [gmx-users] membed in mdrun VERSION 5.0.4   Mark Abraham
• [gmx-users] error using pdb2gmx   Irem Altan
  • [gmx-users] error using pdb2gmx   Mark Abraham
    • [gmx-users] error using pdb2gmx   Irem Altan
• [gmx-users] error using pdb2gmx   Irem Altan
• [gmx-users] error using pdb2gmx   Irem Altan
  • [gmx-users] error using pdb2gmx   Mark Abraham
    • [gmx-users] error using pdb2gmx   Irem Altan
• [gmx-users] distance dependent energy   Cuong Nguyen
• [gmx-users] Launch hybrid MPI/openMP run on multiple nodes   Chunlei ZHANG
• [gmx-users] Connections   Chiara Bello
  • [gmx-users] Connections   Justin Lemkul
• [gmx-users] preapration of non-standard residue   Marta Wisniewska
  • [gmx-users] preapration of non-standard residue   Mark Abraham
• [gmx-users] Generating topology of 3b68.ent   Simone Bolognini
  • [gmx-users] Generating topology of 3b68.ent   Mark Abraham
    • [gmx-users] Generating topology of 3b68.ent   Simone Bolognini
      • [gmx-users] Generating topology of 3b68.ent   Peter Stern
      • [gmx-users] Generating topology of 3b68.ent   Simone Bolognini
• [gmx-users] Visualization of conf.gro and confout.gro   Chang Woon Jang
  • [gmx-users] Visualization of conf.gro and confout.gro   Justin Lemkul
• [gmx-users] Correct method to do Cartesian PCA   Bin Liu
  • [gmx-users] Correct method to do Cartesian PCA   Tsjerk Wassenaar
• [gmx-users] How to get a compressed pull force output from SMD simulation ?   Agnivo Gosai
  • [gmx-users] How to get a compressed pull force output from SMD simulation ?   Justin Lemkul
• [gmx-users] Error while running mdrun with rerun option for LIE calculation   shagun krishna
  • [gmx-users] Error while running mdrun with rerun option for LIE calculation   Justin Lemkul
    • [gmx-users] Error while running mdrun with rerun option for LIE calculation   shagun krishna
      • [gmx-users] Error while running mdrun with rerun option for LIE calculation   Justin Lemkul
• [gmx-users] Serine phosphorylation   Simone Bolognini
  • [gmx-users] Serine phosphorylation   Changrong Ge
    • [gmx-users] Serine phosphorylation   Simone Bolognini
      • [gmx-users] Serine phosphorylation   Catarina A. Carvalheda dos Santos
      • [gmx-users] Serine phosphorylation   Peter Stern
      • [gmx-users] Serine phosphorylation   Catarina A. Carvalheda dos Santos
      • [gmx-users] Serine phosphorylation   Simone Bolognini
      • [gmx-users] Serine phosphorylation   Justin Lemkul
      • [gmx-users] Serine phosphorylation   Simone Bolognini
      • [gmx-users] Serine phosphorylation   Changrong Ge
• [gmx-users] Problem in using pdb2gmx to generate top file   张敏华
  • [gmx-users] Problem in using pdb2gmx to generate top file   Justin Lemkul
• [gmx-users] Correct method to do Cartesian PCA   Bin Liu
  • [gmx-users] Correct method to do Cartesian PCA   Tsjerk Wassenaar
• [gmx-users] Correct method to do Cartesian PCA   Bin Liu
  • [gmx-users] Correct method to do Cartesian PCA   Antonio Baptista
• [gmx-users] ionic liquids - viscosity using green kubo relation   shanmuga sundaram
• [gmx-users] MSD calculation   凌未风
• [gmx-users] Error while running gmx_mpi mdrun - Gromacs-5.1.1   Ashalatha Sreshty
• [gmx-users] Constant Potential on Walls of Electrodes   Alireza Moradzadeh
  • [gmx-users] Constant Potential on Walls of Electrodes   Alex
    • [gmx-users] Constant Potential on Walls of Electrodes   Moradzadeh, Alireza
      • [gmx-users] Constant Potential on Walls of Electrodes   Alex
• [gmx-users] hydrophobic interactions   Chiara Bello
  • [gmx-users] hydrophobic interactions   Justin Lemkul
    • [gmx-users] hydrophobic interactions   David van der Spoel
• [gmx-users] non-bonded parameter   m g
  • [gmx-users] non-bonded parameter   Justin Lemkul
• [gmx-users] Tau-t should be at least 20 times larger than nsttcouple*dt   Poncho Arvayo Zatarain
  • [gmx-users] Tau-t should be at least 20 times larger than nsttcouple*dt   Justin Lemkul
• [gmx-users] doubled atoms   Marta Wisniewska
  • [gmx-users] doubled atoms   Alex
• [gmx-users] non-bond   m g
  • [gmx-users] non-bond   Justin Lemkul
    • [gmx-users] non-bond   Thomas Piggot
• [gmx-users] Spatial Orientational Correlation Function g(r)   ayşe K
• [gmx-users] Pull constrain makes simulation unstable   Michail Palaiokostas Avramidis
  • [gmx-users] Pull constrain makes simulation unstable   Justin Lemkul
    • [gmx-users] Pull constrain makes simulation unstable   Michail Palaiokostas Avramidis
• [gmx-users] viscosity using green kubo relation for ionic liquids   shanmuga sundaram
  • [gmx-users] viscosity using green kubo relation for ionic liquids   David van der Spoel
    • [gmx-users] viscosity using green kubo relation for ionic liquids   shanmuga sundaram
      • [gmx-users] viscosity using green kubo relation for ionic liquids   VITALY V. CHABAN
      • [gmx-users] viscosity using green kubo relation for ionic liquids   Shanmuga
      • [gmx-users] viscosity using green kubo relation for ionic liquids   David van der Spoel
      • [gmx-users] viscosity using green kubo relation for ionic liquids   Shanmuga
• [gmx-users] g_dipoles_mpi   ayşe K
  • [gmx-users] g_dipoles_mpi   VITALY V. CHABAN
• [gmx-users] genion with Na or Ca   Turgay Cakmak
  • [gmx-users] genion with Na or Ca   Justin Lemkul
    • [gmx-users] genion with Na or Ca   Smith, Micholas D.
  • [gmx-users] genion with Na or Ca   VITALY V. CHABAN
    • [gmx-users] genion with Na or Ca   Turgay Cakmak
• [gmx-users] planarity restrain for ligand   ansuman at physics.iisc.ernet.in
  • [gmx-users] planarity restrain for ligand   Justin Lemkul
• [gmx-users] Non-Integral Charges   sun
  • [gmx-users] Non-Integral Charges   Justin Lemkul
  • [gmx-users] Non-Integral Charges   VITALY V. CHABAN
    • [gmx-users] Non-Integral Charges   sun
      • [gmx-users] Non-Integral Charges   Justin Lemkul
• [gmx-users] How to delete Zinc atom from .xtc and .gro files   Hassan Aaryapour
  • [gmx-users] How to delete Zinc atom from .xtc and .gro files   Justin Lemkul
• [gmx-users] g-membed +KALP in dppc   ‪neda razavi‬ ‪
  • [gmx-users] g-membed +KALP in dppc   Justin Lemkul
• [gmx-users] How to fix miising atoms in a pdb file?   Seera Suryanarayana
  • [gmx-users] How to fix miising atoms in a pdb file?   Simone Bolognini
    • [gmx-users] How to fix miising atoms in a pdb file?   Tsjerk Wassenaar
• [gmx-users] Installation of two versions of Gromacs on one system   Indu Kumari
  • [gmx-users] Installation of two versions of Gromacs on one system   Szilárd Páll
  • [gmx-users] Installation of two versions of Gromacs on one system   Peter Stern
    • [gmx-users] Installation of two versions of Gromacs on one system   Indu Kumari
• [gmx-users] query on umbrella sampling of association of two plates   Jagannath Mondal
• [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble   Christian Bope Domilongo
  • [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble   luigi
    • [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble   Christian Bope Domilongo
      • [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble   luigi
      • [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble   Christian Bope Domilongo
      • [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble   Tsjerk Wassenaar
• [gmx-users] Encountered with error after executing the command "gmx solvate"   Seera Suryanarayana
  • [gmx-users] Encountered with error after executing the command "gmx solvate"   Mark Abraham
• [gmx-users] AMBER99SB and gaff X OS P X dihedral parameters   tarak karmakar
• [gmx-users] problem with do_dssp   Chiara Bello
  • [gmx-users] problem with do_dssp   Mark Abraham
• [gmx-users] Regarding Umbrella Sampling Analysis Step   Misa Banno
• [gmx-users] pdb2gmx, chain and segment names in the output pdb   Maxim Igaev
  • [gmx-users] pdb2gmx, chain and segment names in the output pdb   Mark Abraham
  • [gmx-users] pdb2gmx, chain and segment names in the output pdb   Alexey Shvetsov
• [gmx-users] Why GROMACS is generating so many output trajectory files?   Swapnil Wagle
  • [gmx-users] Why GROMACS is generating so many output trajectory files?   Elton Carvalho
• [gmx-users] Help for gmx enemat   valerio di giulio
  • [gmx-users] Help for gmx enemat   Peter Stern
    • [gmx-users] Help for gmx enemat   valerio di giulio
      • [gmx-users] Help for gmx enemat   Peter Stern
      • [gmx-users] Help for gmx enemat   Justin Lemkul
      • [gmx-users] Help for gmx enemat   valerio di giulio
      • [gmx-users] Help for gmx enemat   Justin Lemkul
      • [gmx-users] Help for gmx enemat   valerio di giulio
• [gmx-users] how to maintain planarity of graphene sheet   jagannath mondal
  • [gmx-users] how to maintain planarity of graphene sheet   Justin Lemkul
  • [gmx-users] how to maintain planarity of graphene sheet   VITALY V. CHABAN
    • [gmx-users] how to maintain planarity of graphene sheet   jagannath mondal
      • [gmx-users] how to maintain planarity of graphene sheet   VITALY V. CHABAN
      • [gmx-users] how to maintain planarity of graphene sheet   jagannath mondal
• [gmx-users] necessary input files during simulation   mah maz
  • [gmx-users] necessary input files during simulation   Tsjerk Wassenaar
  • [gmx-users] necessary input files during simulation   mah maz
• [gmx-users] Electric field unit   mah maz
  • [gmx-users] Electric field unit   David van der Spoel
  • [gmx-users] Electric field unit   mah maz
    • [gmx-users] Electric field unit   David van der Spoel
    • [gmx-users] Electric field unit   mah maz
      • [gmx-users] Electric field unit   David van der Spoel
      • [gmx-users] Electric field unit   mah maz
• [gmx-users] Issue in Steep descent minimization (Free energy calculation)   Live King
  • [gmx-users] Issue in Steep descent minimization (Free energy calculation)   Justin Lemkul
• [gmx-users] Implementation of 12-6-4 non-bonded Potential in GROMACS   Biswajit Sadhu
• [gmx-users] Installation of two versions of Gromacs on one system   Tushar Ranjan Moharana
  • [gmx-users] Installation of two versions of Gromacs on one system   Peter Stern
• [gmx-users] Normal mode analysis after equilibration   Mario Fernández Pendás
  • [gmx-users] Normal mode analysis after equilibration   David van der Spoel
    • [gmx-users] Normal mode analysis after equilibration   Mario Fernández Pendás
• [gmx-users] tabulated dihedral potential   Parvez Mh
• [gmx-users] Constraining positions according to B-factors   Irem Altan
  • [gmx-users] Constraining positions according to B-factors   Tsjerk Wassenaar
    • [gmx-users] Constraining positions according to B-factors   Irem Altan
      • [gmx-users] Constraining positions according to B-factors   Tsjerk Wassenaar
      • [gmx-users] Constraining positions according to B-factors   Irem Altan
      • [gmx-users] Constraining positions according to B-factors   Tsjerk Wassenaar
• [gmx-users] Launch hybrid MPI/openMP run on multiple nodes   Chunlei ZHANG
  • [gmx-users] Launch hybrid MPI/openMP run on multiple nodes   Szilárd Páll
    • [gmx-users] Launch hybrid MPI/openMP run on multiple nodes   Mark Abraham
    • [gmx-users] Launch hybrid MPI/openMP run on multiple nodes   Chunlei ZHANG
      • [gmx-users] Launch hybrid MPI/openMP run on multiple nodes   Mark Abraham
• [gmx-users] how to maintain planarity of graphene sheet   VITALY V. CHABAN
• [gmx-users] Out of memory error for g_density and trjconv   Wheeler S.R.
  • [gmx-users] Out of memory error for g_density and trjconv   Justin Lemkul
• [gmx-users] Membrane simulation npt problem   Marco Franzoi
  • [gmx-users] Membrane simulation npt problem   VITALY V. CHABAN
    • [gmx-users] Membrane simulation npt problem   Marco Franzoi
      • [gmx-users] Membrane simulation npt problem   VITALY V. CHABAN
  • [gmx-users] Membrane simulation npt problem   Justin Lemkul
    • [gmx-users] Membrane simulation npt problem   Marco Franzoi
      • [gmx-users] Membrane simulation npt problem   Justin Lemkul
• [gmx-users] Vesicle simulation crashed with dry martini force field   Shule Liu
  • [gmx-users] Vesicle simulation crashed with dry martini force field   Szilárd Páll
• [gmx-users] temperatures of residues   Ali Mohyeddin
  • [gmx-users] temperatures of residues   Justin Lemkul
    • [gmx-users] temperatures of residues   Ali Mohyeddin
      • [gmx-users] temperatures of residues   Justin Lemkul
• [gmx-users] Problem with DHT residue not found.   Domenico Schitti
  • [gmx-users] Problem with DHT residue not found.   Tsjerk Wassenaar
    • [gmx-users] Problem with DHT residue not found.   Domenico Schitti
      • [gmx-users] Problem with DHT residue not found.   Justin Lemkul
• [gmx-users] split MD trajectory into trajectories of smaller time duration   Swapnil Wagle
  • [gmx-users] split MD trajectory into trajectories of smaller time duration   Sudip Das
• [gmx-users] cut the trajectory in small sub-trajectories   Cuong Nguyen
  • [gmx-users] cut the trajectory in small sub-trajectories   Tsjerk Wassenaar
    • [gmx-users] cut the trajectory in small sub-trajectories   Cuong Nguyen
      • [gmx-users] cut the trajectory in small sub-trajectories   Elton Carvalho
      • [gmx-users] cut the trajectory in small sub-trajectories   Cuong Nguyen
• [gmx-users] Query about g_mindist   soumadwip ghosh
  • [gmx-users] Query about g_mindist   Tsjerk Wassenaar
• [gmx-users] Query about g_mindist   soumadwip ghosh
• [gmx-users] Alkane parameters for charm forcefield on gromacs   carlos.navarro87 at gmail.com
  • [gmx-users] Alkane parameters for charm forcefield on gromacs   Justin Lemkul
    • [gmx-users] Alkane parameters for charm forcefield on gromacs   carlos.navarro87 at gmail.com
      • [gmx-users] Alkane parameters for charm forcefield on gromacs   Justin Lemkul
• [gmx-users] Vesicle simulation crashed with dry martini force field   Szilárd Páll
• [gmx-users] cgenff script failed   Albert
  • [gmx-users] cgenff script failed   Justin Lemkul
    • [gmx-users] cgenff script failed   Albert
• [gmx-users] Extending job error   Abid Channa
  • [gmx-users] Extending job error   Justin Lemkul
• [gmx-users] Position restraints missing from topol.top   David Swainsbury
  • [gmx-users] Position restraints missing from topol.top   Tsjerk Wassenaar
• [gmx-users] Simulation terminated after 260 ns of simulation   anu chandra
  • [gmx-users] Simulation terminated after 260 ns of simulation   Mark Abraham
  • [gmx-users] Simulation terminated after 260 ns of simulation   Szilárd Páll
• [gmx-users] Gromacs Tutorial   Tsjerk Wassenaar
  • [gmx-users] Gromacs Tutorial   XAvier Periole
    • [gmx-users] Gromacs Tutorial   Simone Bolognini
  • [gmx-users] Gromacs Tutorial   Peter Stern
    • [gmx-users] Gromacs Tutorial   João Henriques
      • [gmx-users] Gromacs Tutorial   Tsjerk Wassenaar
• [gmx-users] pdb2gmx with GROMOS   Dries Van Rompaey
  • [gmx-users] pdb2gmx with GROMOS   Justin Lemkul
  • [gmx-users] pdb2gmx with GROMOS   Marco Franzoi
• [gmx-users] tabulated dihedral potential   Parvez Mh
  • [gmx-users] tabulated dihedral potential   Mark Abraham
• [gmx-users] multiple nodes, GPUs on a Cray system   Michael Weiner
  • [gmx-users] multiple nodes, GPUs on a Cray system   Smith, Micholas D.
    • [gmx-users] multiple nodes, GPUs on a Cray system   Szilárd Páll
  • [gmx-users] multiple nodes, GPUs on a Cray system   Michael Weiner
    • [gmx-users] multiple nodes, GPUs on a Cray system   Szilárd Páll
      • [gmx-users] multiple nodes, GPUs on a Cray system   Smith, Micholas D.
• [gmx-users] GROMACS performance with an NVidia Tesla k40c   Michail Palaiokostas Avramidis
  • [gmx-users] GROMACS performance with an NVidia Tesla k40c   Szilárd Páll
    • [gmx-users] GROMACS performance with an NVidia Tesla k40c   Michail Palaiokostas Avramidis
      • [gmx-users] GROMACS performance with an NVidia Tesla k40c   Szilárd Páll
• [gmx-users] pdb2gmx with GROMOS   Dries Van Rompaey
  • [gmx-users] pdb2gmx with GROMOS   Justin Lemkul
• [gmx-users] find hbond between different groups during simulation   Mahboobe Sadr
  • [gmx-users] find hbond between different groups during simulation   Justin Lemkul
    • [gmx-users] find hbond between different groups during simulation   Mahboobe Sadr
      • [gmx-users] find hbond between different groups during simulation   Mark Abraham
      • [gmx-users] find hbond between different groups during simulation   Justin Lemkul
• [gmx-users] question on editconf   Sotirios Dionysios I. Papadatos
• [gmx-users] Gromacs Tutorial   João Rodrigues
• [gmx-users] gmx energy block averaging   Andreas Mecklenfeld
• [gmx-users] HREMD output   Shyno Mathew
  • [gmx-users] HREMD output   Mark Abraham
• [gmx-users] custom force constants   Irem Altan
  • [gmx-users] custom force constants   Mark Abraham
    • [gmx-users] custom force constants   Irem Altan
• [gmx-users] Relative alchemical free energy calculations: some confusion about options   Ryan Muraglia
• [gmx-users] disabling pbc while using trjconv   Irem Altan
  • [gmx-users] disabling pbc while using trjconv   Peter Stern
    • [gmx-users] disabling pbc while using trjconv   Irem Altan
• [gmx-users] Error estimate for order parameter   m g
  • [gmx-users] Error estimate for order parameter   Justin Lemkul
• [gmx-users] Constraints errors   Alireza Moradzadeh
  • [gmx-users] Constraints errors   Justin Lemkul
• [gmx-users] Not enough memory. Failed to calloc :   Nikhil Maroli
  • [gmx-users] Not enough memory. Failed to calloc :   Mark Abraham
  • [gmx-users] Not enough memory. Failed to calloc :   Justin Lemkul
    • [gmx-users] Not enough memory. Failed to calloc :   Nikhil Maroli
      • [gmx-users] Not enough memory. Failed to calloc :   Mark Abraham
      • [gmx-users] Not enough memory. Failed to calloc :   Nikhil Maroli
• [gmx-users] Error bar of order parameter   m g
  • [gmx-users] Error bar of order parameter   Justin Lemkul
• [gmx-users] Error bar of order parameter   Justin Lemkul
• [gmx-users] Error bar   Justin Lemkul
• [gmx-users] trivial question about water molecules   Marta Wisniewska
  • [gmx-users] trivial question about water molecules   Smith, Micholas D.
  • [gmx-users] trivial question about water molecules   Justin Lemkul
• [gmx-users] Contact_Angles_Calculation   HZJ
  • [gmx-users] Contact_Angles_Calculation   Michael Shirts
    • [gmx-users] Contact_Angles_Calculation   HZJ
      • [gmx-users] Contact_Angles_Calculation   Michael Shirts
• [gmx-users] Umbrella Sampling, Analysis Step   Misa Banno
• [gmx-users] trivial question about water molecules   Justin Lemkul
• [gmx-users] does gromac "mdrun" produce predicted 3d structure?   Arron Lacey
  • [gmx-users] does gromac "mdrun" produce predicted 3d structure?   Justin Lemkul
    • [gmx-users] does gromac "mdrun" produce predicted 3d structure?   Arron Lacey
      • [gmx-users] does gromac "mdrun" produce predicted 3d structure?   Justin Lemkul
• [gmx-users] Topology for Sphingomyelin   Ganesh Shahane
  • [gmx-users] Topology for Sphingomyelin   Justin Lemkul
    • [gmx-users] Topology for Sphingomyelin   Ganesh Shahane
      • [gmx-users] Topology for Sphingomyelin   Ganesh Shahane
      • [gmx-users] Topology for Sphingomyelin   Justin Lemkul
• [gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations   anu chandra
  • [gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations   Justin Lemkul
• [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93   lloyd riggs
  • [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93   Justin Lemkul
• [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93   lloyd riggs
• [gmx-users] gmx chi: chi.log output all rotamers always 0   Ebert Maximilian
• [gmx-users] Energy profile of a single water molecule on Ni surface   Alexander Alexander
  • [gmx-users] Energy profile of a single water molecule on Ni surface   Justin Lemkul
    • [gmx-users] Energy profile of a single water molecule on Ni surface   Alexander Alexander
      • [gmx-users] Energy profile of a single water molecule on Ni surface   Justin Lemkul
      • [gmx-users] Energy profile of a single water molecule on Ni surface   Alexander Alexander
      • [gmx-users] Energy profile of a single water molecule on Ni surface   Justin Lemkul
  • [gmx-users] Energy profile of a single water molecule on Ni surface   VITALY V. CHABAN
• [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist   Nikhil Maroli
  • [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist   Justin Lemkul
    • [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist   Nikhil Maroli
      • [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist   Mark Abraham
      • [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist   Justin Lemkul
      • [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist   Nikhil Maroli
• [gmx-users] Query on Protein-ligand interaction energy calculation   abhinav kv
  • [gmx-users] Query on Protein-ligand interaction energy calculation   David van der Spoel
    • [gmx-users] Query on Protein-ligand interaction energy calculation   Justin Lemkul
• [gmx-users] GPU efficiency   Albert
  • [gmx-users] GPU efficiency   Mark Abraham
    • [gmx-users] GPU efficiency   Albert
      • [gmx-users] GPU efficiency   Szilárd Páll
  • [gmx-users] GPU efficiency   Stéphane Téletchéa
    • [gmx-users] GPU efficiency   Mark Abraham
• [gmx-users] Logfile incorrectly (?) has dVbonded/dl terms   Dries Van Rompaey
  • [gmx-users] Logfile incorrectly (?) has dVbonded/dl terms   David van der Spoel
• [gmx-users] (no subject)   Sepideh Momeninezhad
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Koji Tanaka
  • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Mark Abraham
    • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Nicolas Cheron
      • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Mark Abraham
      • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Koji Tanaka
      • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Nicolas Cheron
      • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Mark Abraham
      • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Koji Tanaka
      • [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3   Nicolas Cheron
• [gmx-users] Surface tension: output units   VITALY V. CHABAN
  • [gmx-users] Surface tension: output units   Mark Abraham
• [gmx-users] MDRUN warning during minimization   Agnivo Gosai
  • [gmx-users] MDRUN warning during minimization   Justin Lemkul
• [gmx-users] How to get an index file containing non polar atoms in gromacs?   Shima ebrahimi
  • [gmx-users] How to get an index file containing non polar atoms in gromacs?   Catarina A. Carvalheda dos Santos
• [gmx-users] Gromos96 53a6 and Berger Lipids   Kindlein, Moritz
  • [gmx-users] Gromos96 53a6 and Berger Lipids   Piggot T.
• [gmx-users] Error in comparison of Coulomb-14 potential?   Andreas Mecklenfeld
  • [gmx-users] Error in comparison of Coulomb-14 potential?   Mark Abraham
• [gmx-users] Error - syntax   Chang Woon Jang
  • [gmx-users] Error - syntax   Mark Abraham
    • [gmx-users] Error - syntax   Chang Woon Jang
      • [gmx-users] Error - syntax   Justin Lemkul
• [gmx-users] Temperature Annealing   abdus sabuj
  • [gmx-users] Temperature Annealing   Mark Abraham
    • [gmx-users] Temperature Annealing   abdus sabuj
      • [gmx-users] Temperature Annealing   Justin Lemkul
      • [gmx-users] Temperature Annealing   abdus sabuj
      • [gmx-users] Temperature Annealing   Justin Lemkul
      • [gmx-users] Temperature Annealing   abdus sabuj
      • [gmx-users] Temperature Annealing   Justin Lemkul
• [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 106   lloyd riggs
• [gmx-users] Changing a quantity at each time step using a formula   AshutoshAkshay Shah
  • [gmx-users] Changing a quantity at each time step using a formula   Mark Abraham
• [gmx-users] Brefeldin A and GDP parameters   Jeremy T First
• [gmx-users] g_correlation   Felix W.-H. Weng
  • [gmx-users] g_correlation   Samuel Bowerman
    • [gmx-users] g_correlation   Felix W.-H. Weng
• [gmx-users] Temperature or Pressure Coupling   sun
  • [gmx-users] Temperature or Pressure Coupling   VITALY V. CHABAN
    • [gmx-users] Temperature or Pressure Coupling   sun
• [gmx-users] Gromos96 53a6 and Berger Lipids   Kindlein, Moritz
  • [gmx-users] Gromos96 53a6 and Berger Lipids   Piggot T.
• [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   Yong Wang
  • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   VITALY V. CHABAN
    • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   Mark Abraham
      • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   Yong Wang
      • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   Mark Abraham
      • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   Yong Wang
      • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   VITALY V. CHABAN
      • [gmx-users] how to modify the code to generate more controllable checkpoints to restart?   Tsjerk Wassenaar
• [gmx-users] Deuterium order parameter for DPPC   Him Shweta
• [gmx-users] Deuterium order parameter for DPPC   Him Shweta
  • [gmx-users] Deuterium order parameter for DPPC   Justin Lemkul
• [gmx-users] refining a TI calculation - additional lambda points   Oliwia Maria Szklarczyk
  • [gmx-users] refining a TI calculation - additional lambda points   Hannes Loeffler
• [gmx-users] cannot find AVX compiler flag   SAKO MIRZAIE
  • [gmx-users] cannot find AVX compiler flag   Szilárd Páll
• [gmx-users] Question   Eric Smoll
  • [gmx-users] Question   Justin Lemkul
• [gmx-users] Placing water molecules in a defined space in the model   Agnivo Gosai
  • [gmx-users] Placing water molecules in a defined space in the model   Justin Lemkul
• [gmx-users] Using Lincs   Alireza Moradzadeh
  • [gmx-users] Using Lincs   Justin Lemkul
  • [gmx-users] Using Lincs   Alireza Moradzadeh
    • [gmx-users] Using Lincs   Mark Abraham
• [gmx-users] Blender Molecular Visualization Workshop at VizBi 2016   Björn Sommer
• [gmx-users] MDRUN warning during minimization   Agnivo Gosai
  • [gmx-users] MDRUN warning during minimization   Justin Lemkul
• [gmx-users] the end-to-end rotation of a triple helix   Ming Tang
  • [gmx-users] the end-to-end rotation of a triple helix   Tsjerk Wassenaar
• [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 115   Him Shweta
  • [gmx-users] Deuterium order parameter for DPPC   Justin Lemkul
• [gmx-users] Problems in Decoupling LJ Potential   Live King
• [gmx-users] Simulation runs indefinitely   anu chandra
  • [gmx-users] Simulation runs indefinitely   Justin Lemkul
    • [gmx-users] Simulation runs indefinitely   Mark Abraham
      • [gmx-users] Simulation runs indefinitely   anu chandra
      • [gmx-users] Simulation runs indefinitely   Mark Abraham
• [gmx-users] High temperature simulation with GROMOS96 54a7   sunita at tifrh.res.in
  • [gmx-users] High temperature simulation with GROMOS96 54a7   Justin Lemkul
• [gmx-users] Define custom moltype for free energy calculations   Tom Newport
  • [gmx-users] Define custom moltype for free energy calculations   Justin Lemkul
• [gmx-users] About Anisotropic NPT equilibration to equilibrate the systm.   Sunil Pokharel
• [gmx-users] A possible bug in gmx density?   Ganesh Shahane
• [gmx-users] question   Mass
  • [gmx-users] question:Justin toturial   Mass
• [gmx-users] Definition of mol_cog   Xingcheng Lin
  • [gmx-users] Definition of mol_cog   Justin Lemkul
• [gmx-users] pdb2gmx illegal instruction (core dumped)   Md. Imrul Reza Shishir
  • [gmx-users] pdb2gmx illegal instruction (core dumped)   David van der Spoel
    • [gmx-users] pdb2gmx illegal instruction (core dumped)   Md. Imrul Reza Shishir
• [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 120   Him Shweta
• [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 121   sunita at tifrh.res.in
• [gmx-users] Water tutorial   Arpita Srivastava
  • [gmx-users] Water tutorial   Justin Lemkul
  • [gmx-users] Water tutorial   Maxim Igaev
  • [gmx-users] Water tutorial   Maxim Igaev
  • [gmx-users] Water tutorial   Carmen Di Giovanni
• [gmx-users] protein-protein interaction   Mahboobeh Eslami
  • [gmx-users] protein-protein interaction   Smith, Micholas D.
  • [gmx-users] protein-protein interaction   Justin Lemkul
    • [gmx-users] protein-protein interaction   Mahboobeh Eslami
• [gmx-users] add new atom   Malihe Hasanzadeh
  • [gmx-users] add new atom   Justin Lemkul
• [gmx-users] new atom   Malihe Hasanzadeh
• [gmx-users] metal-surfactant ligand topology   Parthiban Marimuthu
  • [gmx-users] metal-surfactant ligand topology   Justin Lemkul
• [gmx-users] free energy calculations   Marta Wisniewska
  • [gmx-users] free energy calculations   Justin Lemkul
  • [gmx-users] free energy calculations   Stefania Evoli
• [gmx-users] (no subject)   Sepideh Momeninezhad
  • [gmx-users] (no subject)   Justin Lemkul
• [gmx-users] (no subject)   Sepideh Momeninezhad
  • [gmx-users] (no subject)   Justin Lemkul
• [gmx-users] error about x of the xxx bonded interactions could not be calculated ....   Chang Woon Jang
  • [gmx-users] error about x of the xxx bonded interactions could not be calculated ....   Mark Abraham
    • [gmx-users] error about x of the xxx bonded interactions could not be calculated ....   Chang Woon Jang
      • [gmx-users] error about x of the xxx bonded interactions could not be calculated ....   Mark Abraham
• [gmx-users] add new residue and new atom   Malihe Hasanzadeh
  • [gmx-users] add new residue and new atom   Justin Lemkul
    • [gmx-users] add new residue and new atom   Malihe Hasanzadeh
      • [gmx-users] add new residue and new atom   Justin Lemkul
      • [gmx-users] add new residue and new atom   Malihe Hasanzadeh
      • [gmx-users] add new residue and new atom   Justin Lemkul
      • [gmx-users] add new residue and new atom   Malihe Hasanzadeh
      • [gmx-users] add new residue and new atom   Justin Lemkul
      • [gmx-users] add new residue and new atom   Malihe Hasanzadeh
      • [gmx-users] add new residue and new atom   Justin Lemkul
• [gmx-users] add new residue and new atom   Malihe Hasanzadeh
• [gmx-users] Heat capacity (C_{v}) for a solid   Alexander Alexander
  • [gmx-users] Heat capacity (C_{v}) for a solid   David van der Spoel
    • [gmx-users] Heat capacity (C_{v}) for a solid   Alexander Alexander
      • [gmx-users] Heat capacity (C_{v}) for a solid   David van der Spoel
• [gmx-users] adding water with genbox   Irem Altan
  • [gmx-users] adding water with genbox   Justin Lemkul
    • [gmx-users] adding water with genbox   Mark Abraham
• [gmx-users] Fattal error in gmx dos   Alexander Alexander
  • [gmx-users] Fattal error in gmx dos   Justin Lemkul
    • [gmx-users] Fattal error in gmx dos   Alexander Alexander
      • [gmx-users] Fattal error in gmx dos   Justin Lemkul
• [gmx-users] freeze group in NPT ensemble in gromacs 5.x   jagannath mondal
  • [gmx-users] freeze group in NPT ensemble in gromacs 5.x   Justin Lemkul
• [gmx-users] relative binding free energy calculation Gromacs 5.0.5   Stefania Evoli
  • [gmx-users] relative binding free energy calculation Gromacs 5.0.5   hannes.loeffler at stfc.ac.uk
• [gmx-users] gmx sasa   Eric Smoll
  • [gmx-users] gmx sasa   Justin Lemkul

Last message date: Sun Jan 31 20:36:11 CET 2016
Archived on: Sun Jan 31 20:36:12 CET 2016

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