March 2015 Archives by author

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Starting: Sun Mar 1 00:01:20 CET 2015
Ending: Tue Mar 31 20:25:36 CEST 2015
Messages: 620

[gmx-users] Thermostats and MSD sujithkakkat .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] First frame already out of box, getting very large RMSD yunshi11 .
[gmx-users] command line with gangle ABEL Stephane 175950
[gmx-users] command line with gangle ABEL Stephane 175950
[gmx-users] Forcefield parameters for Zinc Emma A
[gmx-users] Forcefield parameters for Zinc Emma A
[gmx-users] umbrella sampling - gromcas 5.0.4 CARDELLINI ANNALISA
[gmx-users] umbrella sampling - gromcas 5.0.4 CARDELLINI ANNALISA
[gmx-users] gmx_mtop_atomlookup_settle_init called without settles Mark Abraham
[gmx-users] solvate with an exact number of solvent molecules Mark Abraham
[gmx-users] GMX5.0 g_select Mark Abraham
[gmx-users] using g_energy Mark Abraham
[gmx-users] using g_energy Mark Abraham
[gmx-users] topology include file "gmx43a1.ff/ffG43a1.itp " not found Mark Abraham
[gmx-users] GMX5.0 g_select Mark Abraham
[gmx-users] Separate .xtc file according to the result from g_cluster Mark Abraham
[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 41 Mark Abraham
[gmx-users] definition of "eigenvector" in gromacs Mark Abraham
[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck Mark Abraham
[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 41 Mark Abraham
[gmx-users] REMD exchange probabilities Mark Abraham
[gmx-users] Writing out the neighbor list Mark Abraham
[gmx-users] Writing out the neighbor list Mark Abraham
[gmx-users] template parallelization Mark Abraham
[gmx-users] enemat output Mark Abraham
[gmx-users] Compiler Mark Abraham
[gmx-users] Segmentation fault Mark Abraham
[gmx-users] genbox + python bug? Mark Abraham
[gmx-users] Format of bond type directives Mark Abraham
[gmx-users] Query- Ligand topology Mark Abraham
[gmx-users] Inconsistency of multicore simulations in Gromacs 4.5.3 Mark Abraham
[gmx-users] pdb2gmx error Mark Abraham
[gmx-users] Langevin temperature coupling in Gromacs Mark Abraham
[gmx-users] questions about remove PBC condition from trajectory Mark Abraham
[gmx-users] Did this MD simulation run correctly? If so, how do I visualize it nicely? Mark Abraham
[gmx-users] g_sans_mpi problem: bus error (core dumped) Mark Abraham
[gmx-users] g_sans_mpi problem: bus error (core dumped) Mark Abraham
[gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie Mark Abraham
[gmx-users] Feature wishlist Mark Abraham
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Alex
[gmx-users] OPLS/AA support for DNA Alex
[gmx-users] OPLS/AA support for DNA Alex
[gmx-users] OPLS/AA support for DNA Alex
[gmx-users] Setting custom atoms in FF Alex
[gmx-users] Setting custom atoms in FF Alex
[gmx-users] Setting custom atoms in FF Alex
[gmx-users] Setting custom atoms in FF Alex
[gmx-users] Setting custom atoms in FF Alex
[gmx-users] Density of pure tetrolic acid does not agree with experimental data Alex
[gmx-users] Density of pure tetrolic acid does not agree with experimental data Alex
[gmx-users] Setting custom atoms in FF Alex
[gmx-users] topology file from glycam/gaff to gromacs Rasha Alqus
[gmx-users] Removing molecules around protein Todor Antonijevic
[gmx-users] walls + domain decomposition Aranha, Michelle
[gmx-users] Walls - segmentation fault Aranha, Michelle
[gmx-users] walls - segmentation fault Aranha, Michelle
[gmx-users] Simulation of polarizable Carbon nanotubes Jashimuddin Ashraf
[gmx-users] ethanol solvation (equilibrated ethanol .gro file) Jashimuddin Ashraf
[gmx-users] Simulation of polarizable Carbon nanotubes Jashimuddin Ashraf
[gmx-users] question about g_bundle BIRD
[gmx-users] crossing angle value BIRD
[gmx-users] definition of "eigenvector" in gromacs Antonio Baptista
[gmx-users] van hove correlation function Ipsita Basu
[gmx-users] How to set a system consists of membranes and cholestrols Batdorj Batsaikhan
[gmx-users] Inconsistency in gmx sasa/g_sas buried SASA? Leandro Bortot
[gmx-users] Removing molecules around protein Leandro Bortot
[gmx-users] pdb2gmx and specbond with arbitrary ligand Leandro Bortot
[gmx-users] Force field choosing and parameterization Leandro Bortot
[gmx-users] pdb2gmx and specbond with arbitrary ligand Leandro Bortot
[gmx-users] Forcefield parameters for Zinc Leandro Bortot
[gmx-users] changing partial charge/atom type upon covalent bonding Leandro Bortot
[gmx-users] parametrization of protein-ligand covalent bond Leandro Bortot
[gmx-users] parametrization of protein-ligand covalent bond Leandro Bortot
[gmx-users] Normal mode analysis Leandro Bortot
[gmx-users] MD on protein-RNA complex Brett
[gmx-users] MD on protein-RNA complex Brett
[gmx-users] MD on protein-RNA complex Brett
[gmx-users] definition of "eigenvector" in gromacs Brett
[gmx-users] distribution of water molecules in system Turgay Cakmak
[gmx-users] distribution of water molecules Turgay Cakmak
[gmx-users] Segmentation fault Wim Rm Cardoen
[gmx-users] Langevin temperature coupling in Gromacs Kevin C Chan
[gmx-users] translate problem Chandan Choudhury
[gmx-users] template parallelization Chandan Choudhury
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Bogdan Costescu
[gmx-users] Inconsistency in gmx sasa/g_sas buried SASA? João M. Damas
[gmx-users] Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das
[gmx-users] Error in make index.ndx Priya Das
[gmx-users] Error in make index.ndx Priya Das
[gmx-users] Query- Advice needed Priya Das
[gmx-users] Query: Protein-ligand simulation Priya Das
[gmx-users] Query- position restraining Priya Das
[gmx-users] Query- Ligand topology Priya Das
[gmx-users] Query- Ligand topology Priya Das
[gmx-users] Query- Ligand parametrization Priya Das
[gmx-users] Query- Ligand parameterization Priya Das
[gmx-users] Query- Ligand parametrization Priya Das
[gmx-users] Query- Ligand parametrization Priya Das
[gmx-users] Query- Ligand parametrization Priya Das
[gmx-users] Query- Ligand parametrization Priya Das
[gmx-users] Advice needed Priya Das
[gmx-users] Advice needed Priya Das
[gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4 Satyabrata Das
[gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4 Satyabrata Das
[gmx-users] genbox + python bug? Marcelo Depólo
[gmx-users] genbox + python bug? Marcelo Depólo
[gmx-users] DNA-protein complex Marcelo Depólo
[gmx-users] DNA-protein complex Marcelo Depólo
[gmx-users] Carbohydrate force fields in GROMACS Marcelo Depólo
[gmx-users] Carbohydrate force fields in GROMACS Marcelo Depólo
[gmx-users] Carbohydrate force fields in GROMACS Marcelo Depólo
[gmx-users] comm removal in xy-direction only Diddo Diddens
[gmx-users] helix rotation Natalia Alveal F.
[gmx-users] trjorder Natalia Alveal F.
[gmx-users] solvate with an exact number of solvent molecules Rebeca García Fandiño
[gmx-users] solvate with an exact number of solvent molecules Rebeca García Fandiño
[gmx-users] different mdrun errors in different machines Rebeca García Fandiño
[gmx-users] different mdrun errors in different machines Rebeca García Fandiño
[gmx-users] coarse-grained topology for vitamin E Rebeca García Fandiño
[gmx-users] fine-grained and coarse-grained Rebeca García Fandiño
[gmx-users] fixed number of clusters from a MD simulation Rebeca García Fandiño
[gmx-users] Umbrella Sampling result Warren Gallin
[gmx-users] Umbrella Sampling result Warren Gallin
[gmx-users] Umbrella Sampling result Warren Gallin
[gmx-users] REMD exchange probabilities Neha Gandhi
[gmx-users] CUDA fails to allocate memory to mdrun Akshay Kumar Ganguly
[gmx-users] mdrun blowing up with PME node error in 1 window of umbrella sampling Agnivo Gosai
[gmx-users] mdrun blowing up with PME node error in 1 window of umbrella sampling Agnivo Gosai
[gmx-users] LIE beta(Van der Waals) term for DNA-ligand interaction Hovakim Grabski
[gmx-users] factor of 1.25 in lipid and GROMOS87 parameter Rakesh Gupta
[gmx-users] KALP-15 in DPPC tutorial BAOLIN HUANG
[gmx-users] Core Dump BAOLIN HUANG
[gmx-users] Core Dump BAOLIN HUANG
[gmx-users] Density of pure tetrolic acid does not agree with experimental data Nathan K Houtz
[gmx-users] Ensemble average in dipole correlation function Kim Q Hwan
[gmx-users] Potential modification Christoph Junghans
[gmx-users] KALP-15 in DPPC tutorial RINU KHATTRI
[gmx-users] KALP-15 in DPPC tutorial RINU KHATTRI
[gmx-users] g_dist RINU KHATTRI
[gmx-users] g_dist RINU KHATTRI
[gmx-users] Hamiltonian replica exchange with umbrella sampling Maria Kalimeri
[gmx-users] Feature wishlist Sridhar Kumar Kannam
[gmx-users] charge vibrating periodically abhijit Kayal
[gmx-users] vibrating charge abhijit Kayal
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) abhijit Kayal
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x abhijit Kayal
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x abhijit Kayal
[gmx-users] Running gromacs on Rocks cluster Lang Kong
[gmx-users] Binding free energy of an ion from alchemical transformation Wojciech Kopeć
[gmx-users] Validation suite for force fields for Proteins, RNA, DNA and Lipids? James Kress
[gmx-users] Simulation of polarizable Carbon nanotubes Peter Kroon
[gmx-users] Placing system at the centre of the box. Rajan Kumar
[gmx-users] Placing system at the centre of the box. Rajan Kumar
[gmx-users] Format of bond type directives Rajan Kumar
[gmx-users] LINCS waring during MD. Rajan Kumar
[gmx-users] CNT going out of the simulation box after NVT. HANNIBAL LECTER
[gmx-users] Umbrella Sampling result Alexander Law
[gmx-users] Umbrella Sampling result Alexander Law
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] high temperature Justin Lemkul
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] translate problem Justin Lemkul
[gmx-users] make_ndx specific residues backbone in Chain A and B Justin Lemkul
[gmx-users] First frame already out of box, getting very large RMSD Justin Lemkul
[gmx-users] high temperature Justin Lemkul
[gmx-users] Bond connectivity not found during visualization in VMD Justin Lemkul
[gmx-users] high temperature Justin Lemkul
[gmx-users] How to define the center of mass for a droplet consisting of different ions and molecules? Justin Lemkul
[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems Justin Lemkul
[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems Justin Lemkul
[gmx-users] high temperature Justin Lemkul
[gmx-users] regarding glycolipids parameters for GROMACS Justin Lemkul
[gmx-users] high temperature Justin Lemkul
[gmx-users] high temperature Justin Lemkul
[gmx-users] MD on protein-RNA complex Justin Lemkul
[gmx-users] MD on protein-RNA complex Justin Lemkul
[gmx-users] Build oligosaccharide topology with pdb2gmx Justin Lemkul
[gmx-users] Build oligosaccharide topology with pdb2gmx Justin Lemkul
[gmx-users] Simulation of polarizable Carbon nanotubes Justin Lemkul
[gmx-users] questions about umbrella sampling Justin Lemkul
[gmx-users] Simulation of polarizable Carbon nanotubes Justin Lemkul
[gmx-users] CNT going out of the simulation box after NVT. Justin Lemkul
[gmx-users] g_select same residue as Justin Lemkul
[gmx-users] different mdrun errors in different machines Justin Lemkul
[gmx-users] different mdrun errors in different machines Justin Lemkul
[gmx-users] CNT going outside during NVT Justin Lemkul
[gmx-users] Unable to maintain proper density of polyunsaturated fatty acid Justin Lemkul
[gmx-users] Docked ligand, umbrella sampling and "aiming" Justin Lemkul
[gmx-users] Docked ligand, umbrella sampling and "aiming" Justin Lemkul
[gmx-users] System blowing up - equilibration step - CG simulation Justin Lemkul
[gmx-users] Energy Decomposition Justin Lemkul
[gmx-users] MD on protein-RNA complex Justin Lemkul
[gmx-users] Best strategy to set up a system for an Umbrella sampling simulations Justin Lemkul
[gmx-users] Embedding protein into lipid bilayer Justin Lemkul
[gmx-users] GMX5.0 g_select Justin Lemkul
[gmx-users] topology include file "gmx43a1.ff/ffG43a1.itp " not found Justin Lemkul
[gmx-users] initial position? Justin Lemkul
[gmx-users] Error in make index.ndx Justin Lemkul
[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck Justin Lemkul
[gmx-users] initial position? Justin Lemkul
[gmx-users] Morse potential conversion. Justin Lemkul
[gmx-users] Comparing two Ptn-Ptn docking models Justin Lemkul
[gmx-users] add. residue in topology database Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] Comparing two Ptn-Ptn docking models Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] pdb2gmx and specbond with arbitrary ligand Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] trajectory film Justin Lemkul
[gmx-users] boron atom Justin Lemkul
[gmx-users] problems with pressure control when using implicit solvent Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] Correlation of dynamics between pairs of residues Justin Lemkul
[gmx-users] problems with pressure control when using implicit solvent Justin Lemkul
[gmx-users] problem in defining protonation state of amino acids Justin Lemkul
[gmx-users] Query: Protein-ligand simulation Justin Lemkul
[gmx-users] Query- position restraining Justin Lemkul
[gmx-users] Query- Ligand topology Justin Lemkul
[gmx-users] ethanol solvation (equilibrated ethanol .gro file) Justin Lemkul
[gmx-users] Query- Ligand topology Justin Lemkul
[gmx-users] gmx rmsdist: rmsmax vs. rmscmax Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] KALP-15 in DPPC tutorial Justin Lemkul
[gmx-users] Problem in making index.ndx and disres.itp Justin Lemkul
[gmx-users] A jump in potential just after extension Justin Lemkul
[gmx-users] error in grompp : No such molecule type Protein Justin Lemkul
[gmx-users] g_dist Justin Lemkul
[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro Justin Lemkul
[gmx-users] Problem in making index.ndx and disres.itp Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] Normal mode analysis error Justin Lemkul
[gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial) Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] DNA-protein complex Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
[gmx-users] jump problem Justin Lemkul
[gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial) Justin Lemkul
[gmx-users] error while equilibration Justin Lemkul
[gmx-users] Core Dump Justin Lemkul
[gmx-users] Core Dump Justin Lemkul
[gmx-users] potential energy is from energy mimization Justin Lemkul
[gmx-users] g_dist Justin Lemkul
[gmx-users] Tutorial For Installing Gromacs on window Justin Lemkul
[gmx-users] Mixed Solvent (H2O/CH3CN) Justin Lemkul
[gmx-users] dihedral restraints Justin Lemkul
[gmx-users] parallel calculation problem in implicit solvent modeling Justin Lemkul
[gmx-users] command line with gangle Justin Lemkul
[gmx-users] Carbohydrate force fields in GROMACS Justin Lemkul
[gmx-users] Carbohydrate force fields in GROMACS Justin Lemkul
[gmx-users] Carbohydrate force fields in GROMACS Justin Lemkul
[gmx-users] Carbohydrate force fields in GROMACS Justin Lemkul
[gmx-users] Performance drops when simulating protein with small ligands Justin Lemkul
[gmx-users] Performance drops when simulating protein with small ligands Justin Lemkul
[gmx-users] Did this MD simulation run correctly? If so, how do I visualize it nicely? Justin Lemkul
[gmx-users] Mixed Solvent (H2O/CH3CN) Justin Lemkul
[gmx-users] vibrating charge Justin Lemkul
[gmx-users] Query- Ligand parametrization Justin Lemkul
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Justin Lemkul
[gmx-users] forcefield error for atoms Justin Lemkul
[gmx-users] parametrization of protein-ligand covalent bond Justin Lemkul
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Justin Lemkul
[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value Justin Lemkul
[gmx-users] Simulation of polarizable Carbon nanotubes Justin Lemkul
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Justin Lemkul
[gmx-users] oleic acid incorporation in the protein box.. Justin Lemkul
[gmx-users] Correlation of dynamics between pairs of residues Justin Lemkul
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Justin Lemkul
[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time) Justin Lemkul
[gmx-users] Correlation of dynamics between pairs of residues Justin Lemkul
[gmx-users] unusual error in Gromacs Justin Lemkul
[gmx-users] forcefield error for atoms Justin Lemkul
[gmx-users] parameters obtained after NPT Justin Lemkul
[gmx-users] Topology for Cross linked polymer chains Justin Lemkul
[gmx-users] factor of 1.25 in lipid and GROMOS87 parameter Justin Lemkul
[gmx-users] Query- Ligand parameterization Justin Lemkul
[gmx-users] Lumping different molecule types together as "rest" Justin Lemkul
[gmx-users] OPLS/AA support for DNA Justin Lemkul
[gmx-users] parameters obtained after NPT Justin Lemkul
[gmx-users] forcefield error for atoms Justin Lemkul
[gmx-users] OPLS/AA support for DNA Justin Lemkul
[gmx-users] Sending an email, question Justin Lemkul
[gmx-users] Coul-SR energy component - CG simulation Justin Lemkul
[gmx-users] OPLS/AA support for DNA Justin Lemkul
[gmx-users] Query- Ligand parametrization Justin Lemkul
[gmx-users] Distance of residue’s centre of mass to a surface (COM) Justin Lemkul
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x Justin Lemkul
[gmx-users] Topology for Cross linked polymer chains Justin Lemkul
[gmx-users] Distance of residue’s centre of mass to a surface (COM) Justin Lemkul
[gmx-users] fatal error in DNA-ligand simulation Justin Lemkul
[gmx-users] Query- Ligand parametrization Justin Lemkul
[gmx-users] Query- Ligand parametrization Justin Lemkul
[gmx-users] Oleic acid.....topology problem... Justin Lemkul
[gmx-users] About g_enemat tool Justin Lemkul
[gmx-users] Setting custom atoms in FF Justin Lemkul
[gmx-users] Setting custom atoms in FF Justin Lemkul
[gmx-users] Reg g_energy tool Justin Lemkul
[gmx-users] Setting custom atoms in FF Justin Lemkul
[gmx-users] Oleic acid.....topology problem... Justin Lemkul
[gmx-users] Setting custom atoms in FF Justin Lemkul
[gmx-users] Advice needed Justin Lemkul
[gmx-users] [gmx-developers] Problem with creating a topolgy from PDB file Justin Lemkul
[gmx-users] dihedral restraints Jessica Leuchter
[gmx-users] dihedral restraints Jessica Leuchter
[gmx-users] dihedral restraints Jessica Leuchter
[gmx-users] The umbrella sampling with the coordinate of energy gap Tanping Li
[gmx-users] gmx5.0.2 with GPU acceleration problem Wayne Liang
[gmx-users] gmx5.0.2 with GPU acceleration problem Wayne Liang
[gmx-users] Build oligosaccharide topology with pdb2gmx Elena Lilkova
[gmx-users] Build oligosaccharide topology with pdb2gmx Elena Lilkova
[gmx-users] Build oligosaccharide topology with pdb2gmx Elena Lilkova
[gmx-users] Build oligosaccharide topology with pdb2gmx Elena Lilkova
[gmx-users] Separate .xtc file according to the result from g_cluster Xingcheng Lin
[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 41 Xingcheng Lin
[gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial) Thomas Lipscomb
[gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial) Thomas Lipscomb
[gmx-users] KALP15 in DPPC tutorial: system_shrink1.gro error? Thomas Lipscomb
[gmx-users] Performance drops when simulating protein with small ligands Yunlong Liu
[gmx-users] Performance drops when simulating protein with small ligands Yunlong Liu
[gmx-users] Distance of residue’s centre of mass to a surface (COM) James Lord
[gmx-users] Distance of residue’s centre of mass to a surface (COM) James Lord
[gmx-users] g_select same residue as Josip Lovrić
[gmx-users] MD on protein-RNA complex Johnny Lu
[gmx-users] Writing out the neighbor list Alan Manning
[gmx-users] Writing out the neighbor list Alan Manning
[gmx-users] gmx rmsdist: rmsmax vs. rmscmax Alan Manning
[gmx-users] gmx rmsdist: rmsmax vs. rmscmax Alan Manning
[gmx-users] DNA-protein complex distorted in vacuum simulation Erik Marklund
[gmx-users] Correlation of dynamics between pairs of residues Ebert Maximilian
[gmx-users] Correlation of dynamics between pairs of residues Ebert Maximilian
[gmx-users] Correlation of dynamics between pairs of residues Ebert Maximilian
[gmx-users] Umbrella Sampling result Felipe Merino
[gmx-users] (no subject) Tushar Ranjan Moharana
[gmx-users] Unable to maintain proper density of polyunsaturated fatty acid Tushar Ranjan Moharana
[gmx-users] Unable to maintain proper density of polyunsaturated fatty acid Tushar Ranjan Moharana
[gmx-users] problem in defining protonation state of amino acids Tushar Ranjan Moharana
[gmx-users] problem in defining protonation state of amino acids Tushar Ranjan Moharana
[gmx-users] Problem in making index.ndx and disres.itp Tushar Ranjan Moharana
[gmx-users] Problem in making index.ndx and disres.itp Tushar Ranjan Moharana
[gmx-users] (no subject) Tushar Ranjan Moharana
[gmx-users] Error while using pbc = xy Segmentation fault (core dumped) Tushar Ranjan Moharana
[gmx-users] Force field choosing and parameterization Gustavo Avelar Molina
[gmx-users] Force field choosing and parameterization Gustavo Avelar Molina
[gmx-users] Force field choosing and parameterization Gustavo Avelar Molina
[gmx-users] Force field choosing and parameterization Gustavo Avelar Molina
[gmx-users] command line with gangle Teemu Murtola
[gmx-users] grompp_d fatal error in Amber FF Nash, Anthony
[gmx-users] grompp_d fatal error in Amber FF Nash, Anthony
[gmx-users] Gromacs with InflateGro Nash, Anthony
[gmx-users] g_density appears broken in version 5 Christopher Neale
[gmx-users] Lumping different molecule types together as "rest" Stella Nickerson
[gmx-users] Fwd: Gromacs: data distribution and work distribution Federico Padua
[gmx-users] g_sans_mpi problem: bus error (core dumped) CHEN Pan
[gmx-users] g_sans_mpi problem: bus error (core dumped) CHEN Pan
[gmx-users] g_sans_mpi problem: bus error (core dumped) CHEN Pan
[gmx-users] regarding glycolipids parameters for GROMACS Xavier Periole
[gmx-users] Build oligosaccharide topology with pdb2gmx Thomas Piggot
[gmx-users] Carbohydrate force fields in GROMACS Thomas Piggot
[gmx-users] Time frames for collecting data Faezeh Pousaneh
[gmx-users] Time frames for collecting data Faezeh Pousaneh
[gmx-users] boron atom Faezeh Pousaneh
[gmx-users] boron atom Faezeh Pousaneh
[gmx-users] boron atom Faezeh Pousaneh
[gmx-users] Jump in potential after extension Faezeh Pousaneh
[gmx-users] A jump in potential just after extension Faezeh Pousaneh
[gmx-users] A jump in potential just after extension Faezeh Pousaneh
[gmx-users] A jump in potential just after extension Faezeh Pousaneh
[gmx-users] comparison of entropy and enthalpy at different temperatures Faezeh Pousaneh
[gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie NISHA Prakash
[gmx-users] Fwd: Gromacs: data distribution and work distribution Szilárd Páll
[gmx-users] Fwd: Gromacs: data distribution and work distribution Szilárd Páll
[gmx-users] gmx5.0.2 with GPU acceleration problem Szilárd Páll
[gmx-users] gmx5.0.2 with GPU acceleration problem Szilárd Páll
[gmx-users] CUDA fails to allocate memory to mdrun Szilárd Páll
[gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4 Szilárd Páll
[gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4 Szilárd Páll
[gmx-users] make_ndx specific residues backbone in Chain A and B RJ
[gmx-users] free energy perturbation methods in gmx RJ
[gmx-users] pdb2gmx error RJ
[gmx-users] trjconv - pbc centering and fitting Nixon Raj
[gmx-users] adding parameters for selenium ion Meenakshi Rajput
[gmx-users] adding metal ion Meenakshi Rajput
[gmx-users] RMSD between two groups Mohsen Ramezanpour
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x Hao Ren
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x Hao Ren
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x Hao Ren
[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x Hao Ren
[gmx-users] regarding glycolipids parameters for GROMACS Carlos Navarro Retamal
[gmx-users] regarding glycolipids parameters for GROMACS Carlos Navarro Retamal
[gmx-users] System blowing up - equilibration step - CG simulation Carlos Navarro Retamal
[gmx-users] System blowing up - equilibration step - CG simulation Carlos Navarro Retamal
[gmx-users] System blowing up - equilibration step - CG simulation Carlos Navarro Retamal
[gmx-users] System blowing up - equilibration step - CG simulation Carlos Navarro Retamal
[gmx-users] System blowing up - equilibration step - CG simulation Carlos Navarro Retamal
[gmx-users] Best strategy to set up a system for an Umbrella sampling simulations Carlos Navarro Retamal
[gmx-users] gmx mindist issue Carlos Navarro Retamal
[gmx-users] gmx mindist issue Carlos Navarro Retamal
[gmx-users] non-matching atom names in CG simulations Carlos Navarro Retamal
[gmx-users] non-matching atom names in CG simulations Carlos Navarro Retamal
[gmx-users] Coul-SR energy component - CG simulation Carlos Navarro Retamal
[gmx-users] Coul-SR energy component - CG simulation Carlos Navarro Retamal
[gmx-users] Coul-SR energy component - CG simulation Carlos Navarro Retamal
[gmx-users] dihedral restraints Andrew Ritchie
[gmx-users] dihedral restraints Andrew Ritchie
[gmx-users] potential energy is from energy mimization Rj
[gmx-users] oleic acid incorporation in the protein box.. Kamalesh Roy
[gmx-users] Oleic acid.....topology problem... Kamalesh Roy
[gmx-users] Oleic acid.....topology problem... Kamalesh Roy
[gmx-users] Did this MD simulation run correctly? If so, how do I visualize it nicely? Jonathan Saboury
[gmx-users] Did this MD simulation run correctly? If so, how do I visualize it nicely? Jonathan Saboury
[gmx-users] initial position? Sadeghi, Ehsan
[gmx-users] Mixed Solvent (H2O/CH3CN) Debashis Sahu
[gmx-users] Mixed Solvent (H2O/CH3CN) Debashis Sahu
[gmx-users] Tutorial For Installing Gromacs on window Rajneet kaur Saini
[gmx-users] regarding installation of gromacs Rajneet kaur Saini
[gmx-users] Potential modification Tuhin Samanta
[gmx-users] Triclinic box output error Sevasteiadis, Michail
[gmx-users] Triclinic box output error Sevasteiadis, Michail
[gmx-users] Triclinic box output error Sevasteiadis, Michail
[gmx-users] Thermostats and MSD Michael Shirts
[gmx-users] Thermostats and MSD Michael Shirts
[gmx-users] time constant and tau p values for pressure coupling Mohammad Sirajuddin
[gmx-users] trjconv -center tool Mohammad Sirajuddin
[gmx-users] adding metal ion Smith, Micholas D.
[gmx-users] g_sans_mpi problem: bus error (core dumped) Smith, Micholas D.
[gmx-users] OPLS/AA support for DNA Smith, Micholas D.
[gmx-users] Protein-ligand interaction analysis after MD simulation Smith, Micholas D.
[gmx-users] OPLS/AA support for DNA Smith, Micholas D.
[gmx-users] umbrella sampling - gromcas 5.0.4 Nima Soltani
[gmx-users] umbrella sampling tutorial Nima Soltani
[gmx-users] solvate with an exact number of solvent molecules David van der Spoel
[gmx-users] g_rotacf and P 1,2,3 meaning David van der Spoel
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch David van der Spoel
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch David van der Spoel
[gmx-users] Morse potential conversion. Dan Sponseller
[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value Sandhyaa Subramanian
[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value Sandhyaa Subramanian
[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value Sandhyaa Subramanian
[gmx-users] Comparing two Ptn-Ptn docking models Diogo Martins de Sá
[gmx-users] Comparing two Ptn-Ptn docking models Diogo Martins de Sá
[gmx-users] Comparing two Ptn-Ptn docking models Diogo Martins de Sá
[gmx-users] enemat output Diogo Martins de Sá
[gmx-users] Comparing two Ptn-Ptn docking models Diogo Martins de Sá
[gmx-users] Comparing two Ptn-Ptn docking models Diogo Martins de Sá
[gmx-users] Triple helix built by THeBuScr can not transform by pdb2gmx in Gromacs Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] problems with pressure control when using implicit solvent Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] problems with pressure control when using implicit solvent Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] how to fix the center of mass of the three N-terminal atoms in a triple helix? Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] umbrella sampling tutorial Ming Tang
[gmx-users] parallel calculation problem in implicit solvent modeling Ming Tang
[gmx-users] Unexpected trjconv -nojump behaviour Trayder Thomas
[gmx-users] CNT going outside during NVT Naga Rajesh Tummala
[gmx-users] Compiler Alexander Tzanov
[gmx-users] Compiler Alexander Tzanov
[gmx-users] DNA-protein complex Urszula Uciechowska
[gmx-users] DNA-protein complex Urszula Uciechowska
[gmx-users] high temperature V.V.Chaban
[gmx-users] add. residue in topology database Daniele Veclani
[gmx-users] add. residue in topology database Daniele Veclani
[gmx-users] solvate with an exact number of solvent molecules Jennifer Vo
[gmx-users] why rotational correlation function decays to negative Jennifer Vo
[gmx-users] why rotational correlation function decays to negative Jennifer Vo
[gmx-users] How to interpret g_principal output calculates Jennifer Vo
[gmx-users] g_rotacf and P 1,2,3 meaning Jennifer Vo
[gmx-users] diisopropylethylene topology Jennifer Vo
[gmx-users] fine-grained and coarse-grained Mirco Wahab
[gmx-users] Triple helix built by THeBuScr can not transform by pdb2gmx in Gromacs Tsjerk Wassenaar
[gmx-users] Triple helix built by THeBuScr can not transform by pdb2gmx in Gromacs Tsjerk Wassenaar
[gmx-users] why rotational correlation function decays to negative Tsjerk Wassenaar
[gmx-users] Triclinic box output error Tsjerk Wassenaar
[gmx-users] Triclinic box output error Tsjerk Wassenaar
[gmx-users] System blowing up - equilibration step - CG simulation Tsjerk Wassenaar
[gmx-users] System blowing up - equilibration step - CG simulation Tsjerk Wassenaar
[gmx-users] System blowing up - equilibration step - CG simulation Tsjerk Wassenaar
[gmx-users] definition of "eigenvector" in gromacs Tsjerk Wassenaar
[gmx-users] Gromacs with InflateGro Tsjerk Wassenaar
[gmx-users] g_anaeig error Tsjerk Wassenaar
[gmx-users] Cardiolipin in insane.py (MARTINI) Tsjerk Wassenaar
[gmx-users] g_anaeig error inconsistent shifts Tsjerk Wassenaar
[gmx-users] query regarding coarse grained simulation of a peripheral membrane protein Tsjerk Wassenaar
[gmx-users] Placing system at the centre of the box. Tsjerk Wassenaar
[gmx-users] Placing system at the centre of the box. Tsjerk Wassenaar
[gmx-users] jump problem Tsjerk Wassenaar
[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value Tsjerk Wassenaar
[gmx-users] Correlation of dynamics between pairs of residues Tsjerk Wassenaar
[gmx-users] non-matching atom names in CG simulations Tsjerk Wassenaar
[gmx-users] fixed number of clusters from a MD simulation Tsjerk Wassenaar
[gmx-users] Density of pure tetrolic acid does not agree with experimental data Tsjerk Wassenaar
[gmx-users] Unexpected trjconv -nojump behaviour Tsjerk Wassenaar
[gmx-users] How to define the center of mass for a droplet consisting of different ions and molecules? Kester Wong
[gmx-users] walls function in gromacs-4.6.7 Makoto Yoneya
[gmx-users] Sending an email, question Poncho Arvayo Zatarain
[gmx-users] FW: Sending an email, question Poncho Arvayo Zatarain
[gmx-users] Inconsistency of multicore simulations in Gromacs 4.5.3 Fei Zhang
[gmx-users] Docked ligand, umbrella sampling and "aiming" Jernej Zidar
[gmx-users] Docked ligand, umbrella sampling and "aiming" Jernej Zidar
[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 31 Jernej Zidar
[gmx-users] error while equilibration ananyachatterjee
[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems faride badalkhani
[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems faride badalkhani
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch atanu das
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch atanu das
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch atanu das
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch atanu das
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch atanu das
[gmx-users] topolobuild error marzieh dehghan
[gmx-users] topology include file "gmx43a1.ff/ffG43a1.itp " not found marzieh dehghan
[gmx-users] Normal mode analysis error rahul dhakne
[gmx-users] DNA-protein complex distorted in vacuum simulation rahul dhakne
[gmx-users] Normal mode analysis rahul dhakne
[gmx-users] Topology for Cross linked polymer chains sridhar dwadasi
[gmx-users] Topology for Cross linked polymer chains sridhar dwadasi
[gmx-users] Post-Processing on the REMD trj 14110220035 at fudan.edu.cn
[gmx-users] Bond connectivity not found during visualization in VMD soumadwip ghosh
[gmx-users] CNT going out of the simulation box after NVT. soumadwip ghosh
[gmx-users] CNT going outside during NVT soumadwip ghosh
[gmx-users] PDB for nafion soumadwip ghosh
[gmx-users] How to build up a nafion PDB soumadwip ghosh
[gmx-users] unusual error in Gromacs soumadwip ghosh
[gmx-users] error Can not invert matrix, determinant = soumadwip ghosh
[gmx-users] parameters obtained after NPT soumadwip ghosh
[gmx-users] parameters obtained after NPT soumadwip ghosh
[gmx-users] using g_energy sang eun jee
[gmx-users] using g_energy sang eun jee
[gmx-users] simulation of infinite chains sang eun jee
[gmx-users] using g_energy sang eun jee
[gmx-users] inconsistent shifts warning sang eun jee
[gmx-users] cutting off the backbone bonds in polymer hjqian at jlu.edu.cn
[gmx-users] Distance restraints tarak karmakar
[gmx-users] g_anaeig error tasneem kausar
[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 49 tasneem kausar
[gmx-users] g_anaeig error inconsistent shifts tasneem kausar
[gmx-users] Compiler melichercik at leaf.nh.cas.cz
[gmx-users] (no subject) pirate man
[gmx-users] (no subject) pirate man
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] high temperature mah maz
[gmx-users] trajectory film mah maz
[gmx-users] trajectory film mah maz
[gmx-users] forcefield error for atoms mah maz
[gmx-users] forcefield error for atoms mah maz
[gmx-users] forcefield error for atoms mah maz
[gmx-users] query regarding coarse grained simulation of a peripheral membrane protein Antara mazumdar
[gmx-users] error in grompp : No such molecule type Protein Antara mazumdar
[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro Antara mazumdar
[gmx-users] Carbohydrate force fields in GROMACS mish
[gmx-users] Carbohydrate force fields in GROMACS mish
[gmx-users] Carbohydrate force fields in GROMACS mish
[gmx-users] Carbohydrate force fields in GROMACS mish
[gmx-users] Carbohydrate force fields in GROMACS mish
[gmx-users] definition of "eigenvector" in gromacs ms
[gmx-users] MARTINI POPG simulation temperature shivangi nangia
[gmx-users] Cardiolipin in insane.py (MARTINI) shivangi nangia
[gmx-users] Cardiolipin in insane.py (MARTINI) shivangi nangia
[gmx-users] peptide orientation with respect to bilayer normal shivangi nangia
[gmx-users] How to convert Xplor distance restraints to gromacs format srinivas penumutchu
[gmx-users] time depended electric field petrishia petrishia
[gmx-users] Application of electric field on membrane petrishia petrishia
[gmx-users] Membrane simulation petrishia petrishia
[gmx-users] Protein-ligand interaction analysis after MD simulation salam pradeep
[gmx-users] Tilt angle asasa qsqs
[gmx-users] translate problem gromacs query
[gmx-users] translate problem gromacs query
[gmx-users] translate problem gromacs query
[gmx-users] gmx_mtop_atomlookup_settle_init called without settles gromacs query
[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck gromacs query
[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck gromacs query
[gmx-users] Problem executing do_dssp in gromacs Aarti rana
[gmx-users] RMSD between two groups leila salimi
[gmx-users] About g_enemat tool vidhya sankar
[gmx-users] About g_enemat tool vidhya sankar
[gmx-users] Reg g_energy tool vidhya sankar
[gmx-users] Reg g_energy tool vidhya sankar
[gmx-users] fatal error in DNA-ligand simulation marziyeh poshteh shirani
[gmx-users] g_select same residue as xy21hb
[gmx-users] g_select same residue as xy21hb
[gmx-users] Energy Decomposition xy21hb
[gmx-users] Energy Decomposition xy21hb
[gmx-users] GMX5.0 g_select xy21hb
[gmx-users] GMX5.0 g_select xy21hb
[gmx-users] GMX5.0 g_select xy21hb
[gmx-users] About gromacs/orca question. xzhao11
[gmx-users] Embedding protein into lipid bilayer yoochan
[gmx-users] Embedding protein into lipid bilayer yoochan
[gmx-users] jump problem Ahmet yıldırım
[gmx-users] questions about umbrella sampling 凌未风
[gmx-users] questions about remove PBC condition from trajectory 凌未风
[gmx-users] problems with g_wham 凌未风

Last message date: Tue Mar 31 20:25:36 CEST 2015
Archived on: Tue Mar 31 20:25:37 CEST 2015

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