January 2016 Archives by author

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

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