November 2015 Archives by author

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Starting: Sun Nov 1 21:01:49 CET 2015
Ending: Mon Nov 30 23:01:33 CET 2015
Messages: 461

[gmx-users] How can I split .xtc file to two part? Hassan Aaryapour
[gmx-users] plus and minus signs in rtp files Mark Abraham
[gmx-users] workstation Mark Abraham
[gmx-users] workstation Mark Abraham
[gmx-users] problem of compiling Mark Abraham
[gmx-users] Flat-bottomed potential from user-defined reference Mark Abraham
[gmx-users] How to determine box shape and parameters from a run Mark Abraham
[gmx-users] using charmm36 force field with gromacs Mark Abraham
[gmx-users] Energy conservation in NVE simulations Mark Abraham
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem Mark Abraham
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem Mark Abraham
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem Mark Abraham
[gmx-users] How to build a correct structure file beyond 99999 atoms using pdb or gro extend format ? Mark Abraham
[gmx-users] GROMACS 5.1.1 official release Mark Abraham
[gmx-users] grompp error Mark Abraham
[gmx-users] mpirun Mark Abraham
[gmx-users] How to restrain the center of gravity Mark Abraham
[gmx-users] Query regarding water not settled Mark Abraham
[gmx-users] Query regarding water not settled Mark Abraham
[gmx-users] Velocities with constraints Mark Abraham
[gmx-users] Velocities with constraints Mark Abraham
[gmx-users] Tabulated potential error Mark Abraham
[gmx-users] Re : Tabulated potential error Mark Abraham
[gmx-users] Multiple time step MD Mark Abraham
[gmx-users] Problems with trjconv Mark Abraham
[gmx-users] Problems with trjconv Mark Abraham
[gmx-users] Problems with trjconv Mark Abraham
[gmx-users] restart issues with Gromacs Mark Abraham
[gmx-users] Choosing LINCS setting / rcon for parallel mdrun Mark Abraham
[gmx-users] Choosing LINCS setting / rcon for parallel mdrun Mark Abraham
[gmx-users] Profiling mdrun with GProf Mark Abraham
[gmx-users] Profiling mdrun with GProf Mark Abraham
[gmx-users] Profiling mdrun with GProf Mark Abraham
[gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD Mark Abraham
[gmx-users] SASA Problem Mark Abraham
[gmx-users] Profiling mdrun with GProf Mark Abraham
[gmx-users] gmx mdrun std::bad_alloc whilst using PLUMED Mark Abraham
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Mark Abraham
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Mark Abraham
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Mark Abraham
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Mark Abraham
[gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD Mark Abraham
[gmx-users] segmentation fault with GPU Mark Abraham
[gmx-users] support mmcif format? Mark Abraham
[gmx-users] support mmcif format? Mark Abraham
[gmx-users] support mmcif format? Mark Abraham
[gmx-users] pme_loadbal problem Mark Abraham
[gmx-users] H-REMD in umbrella sampling Adam.Orlowski
[gmx-users] updates about ACPYPE Alan
[gmx-users] problem of compiling Albert
[gmx-users] problem of compiling Albert
[gmx-users] g_select problem Albert
[gmx-users] support mmcif format? Albert
[gmx-users] support mmcif format? Albert
[gmx-users] support mmcif format? Albert
[gmx-users] service broken? Albert
[gmx-users] (no subject) Mehriar Amininasab
[gmx-users] g_tcaf use issue Jones de Andrade
[gmx-users] g_tcaf use issue Jones de Andrade
[gmx-users] g_tcaf use issue Jones de Andrade
[gmx-users] using charmm36 force field with gromacs Yoav Atsmon-Raz
[gmx-users] using charmm36 force field with gromacs Yoav Atsmon-Raz
[gmx-users] using charmm36 force field with gromacs Yoav Atsmon-Raz
[gmx-users] g_cluster Daniele Avancini
[gmx-users] Tabulated potential error Pallavi Banerjee
[gmx-users] Re : Tabulated potential error Pallavi Banerjee
[gmx-users] workstation Cyril Bauvais
[gmx-users] Coarse grained: non bonded interactions via iterative Boltzmann inversion Liz Bell
[gmx-users] Problems with mktop 2.2.1 Chiara Bello
[gmx-users] Computing of reaction coordinate by g_wham Damiano Buratto
[gmx-users] Computing of reaction coordinate by g_wham Damiano Buratto
[gmx-users] gmx sasa output confusion Francesco Carbone
[gmx-users] gmx sasa output confusion Francesco Carbone
[gmx-users] Velocities with constraints Miguel Caro
[gmx-users] Velocities with constraints Miguel Caro
[gmx-users] Velocities with constraints Miguel Caro
[gmx-users] Velocities with constraints Miguel Caro
[gmx-users] Problem with running crystal simulation Elton Carvalho
[gmx-users] Problem with running crystal simulation Elton Carvalho
[gmx-users] NPT compress Box using negative Pressure Elton Carvalho
[gmx-users] mdrun error Elton Carvalho
[gmx-users] Fwd: removing some atoms Elton Carvalho
[gmx-users] periodic molecule Pierre-André Cazade
[gmx-users] periodic molecule Pierre-André Cazade
[gmx-users] Flat-bottomed potential from user-defined reference Vitaly V. Chaban
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem Vitaly V. Chaban
[gmx-users] energy autocorrelation function Vitaly V. Chaban
[gmx-users] energy autocorrelation function: bug? Vitaly V. Chaban
[gmx-users] seeking a little help Subho Chakraborty
[gmx-users] combine two pdb files Chandan Choudhury
[gmx-users] Distance matrix between chains Clarke, Benjamin (NIH/NIDDK) [F]
[gmx-users] dimer split Clarke, Benjamin (NIH/NIDDK) [F]
[gmx-users] Flat-bottomed potential from user-defined reference Cosseddu, S.M.
[gmx-users] Flat-bottomed potential from user-defined reference Cosseddu, S.M.
[gmx-users] [Spam] Re: Flat-bottomed potential from user-defined reference Cosseddu, S.M.
[gmx-users] Building gromacs 5.1.1: doesn't build all programs like grompp Stephen Cousins
[gmx-users] How to determine box shape and parameters from a run Ramon Crehuet
[gmx-users] How to determine box shape and parameters from a run Ramon Crehuet
[gmx-users] S**2 order parameter from a trajectory Ramon Crehuet
[gmx-users] rotacf in Gromacs 5.1 gives unexpected results Ramon Crehuet
[gmx-users] Potential energy positive Suman Das
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Siva Dasetty
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Siva Dasetty
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Siva Dasetty
[gmx-users] NPT compress Box using negative Pressure Christian Bope Domilongo
[gmx-users] problem with equilibration of DLiPC membrane Shiva Emami
[gmx-users] problem with equilibration of DLiPC membrane Shiva Emami
[gmx-users] problem with equilibration of DLiPC membrane Shiva Emami
[gmx-users] No convergence with g_nmeig KARAKAS Esra
[gmx-users] No convergence with g_nmeig KARAKAS Esra
[gmx-users] No convergence with g_nmeig KARAKAS Esra
[gmx-users] No convergence with g_nmeig KARAKAS Esra
[gmx-users] Error DSSP Gromacs 5.0.4 Stefania Evoli
[gmx-users] Error DSSP Gromacs 5.0.4 Stefania Evoli
[gmx-users] Error DSSP Gromacs 5.0.4 Stefania Evoli
[gmx-users] Error DSSP Gromacs 5.0.4 Stefania Evoli
[gmx-users] Error DSSP Gromacs 5.0.4 Stefania Evoli
[gmx-users] Errors pdb2gmx Stefania Evoli
[gmx-users] topology of ligand contains boron Low Chen Fei
[gmx-users] mpirun Samuel Flores
[gmx-users] mpirun Samuel Flores
[gmx-users] H-REMD in umbrella sampling Yuri Garmay
[gmx-users] H-REMD in umbrella sampling Yuri Garmay
[gmx-users] Restarting a crashed with gromacs-5.0 Zhaleh Ghaemi
[gmx-users] symtab get_symtab_handle error Zhaleh Ghaemi
[gmx-users] symtab get_symtab_handle error Zhaleh Ghaemi
[gmx-users] Choosing LINCS setting / rcon for parallel mdrun Agnivo Gosai
[gmx-users] Choosing LINCS setting / rcon for parallel mdrun Agnivo Gosai
[gmx-users] gmx energy doesn't calculate LJ-SR and Coul-SR Hovakim Grabski
[gmx-users] 2. QM/MM (Timofey Tyugashev) Groenhof, Gerrit
[gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 45 Groenhof, Gerrit
[gmx-users] Dear Gromaces users, I have a problem JINGJING HUANG
[gmx-users] (MD with constraints giving LINCS error using N cores not on 1 core) JINGJING HUANG
[gmx-users] Running ultiple job in core? Hardy, Adam
[gmx-users] Collaboration request Malihe Hasanzadeh
[gmx-users] Fwd: OPLA Mehrnoosh Hazrati
[gmx-users] Error DSSP Gromacs 5.0.4 João Henriques
[gmx-users] Error DSSP Gromacs 5.0.4 João Henriques
[gmx-users] Error DSSP Gromacs 5.0.4 João Henriques
[gmx-users] TIP3P for GROMOS96 force field João Henriques
[gmx-users] Explicit and implicit solvent João Henriques
[gmx-users] How to restrain the center of gravity Hirayama, Kazunori
[gmx-users] about .trr input file format Ayesha Kanwal
[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file Sajjad Kavyani
[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file Sajjad Kavyani
[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file Sajjad Kavyani
[gmx-users] tutorial umbrella sampling Matthias Kiesel
[gmx-users] tutorial umbrella sampling Matthias Kiesel
[gmx-users] electric field Maryam Kowsar
[gmx-users] electric field Maryam Kowsar
[gmx-users] AIREBO and multibody non-bonded potentials in GROMACS Peter Kroon
[gmx-users] g_tcaf use issue Peter Kroon
[gmx-users] Definition in martini CG force field Peter Kroon
[gmx-users] AIREBO and multibody non-bonded potentials in GROMACS Peter Kroon
[gmx-users] using charmm36 force field with gromacs Krzysztof Kuczera
[gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD Krzysztof Kuczera
[gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD Krzysztof Kuczera
[gmx-users] covariance matrix obtained from g_covar Amit Kumawat
[gmx-users] problem of compiling Kutzner, Carsten
[gmx-users] Bug in option parsing? Kutzner, Carsten
[gmx-users] Bug in option parsing? Kutzner, Carsten
[gmx-users] Umbrella sampling with spherical coordinate Yuno Lee
[gmx-users] How to monitor restrained force (F_i) used for distance restraints Yuno Lee
[gmx-users] gmx energy doesn't calculate LJ-SR and Coul-SR Justin Lemkul
[gmx-users] protein complex Justin Lemkul
[gmx-users] Fwd: hydrogen bonds Justin Lemkul
[gmx-users] plus and minus signs in rtp files Justin Lemkul
[gmx-users] input file Justin Lemkul
[gmx-users] nvt error Justin Lemkul
[gmx-users] Flat-bottomed potential from user-defined reference Justin Lemkul
[gmx-users] implicit solvent with periodic molecules Justin Lemkul
[gmx-users] How to determine box shape and parameters from a run Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] Issues Using CHARMM22* Force Field with GROMACS 5.1 Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] Problems with mktop 2.2.1 Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] Automating pdb2gmx Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] Error DSSP Gromacs 5.0.4 Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] long-stick molecule solvation Justin Lemkul
[gmx-users] Disribution Function Justin Lemkul
[gmx-users] Distribution function Justin Lemkul
[gmx-users] Error DSSP Gromacs 5.0.4 Justin Lemkul
[gmx-users] using charmm36 force field with gromacs Justin Lemkul
[gmx-users] Error DSSP Gromacs 5.0.4 Justin Lemkul
[gmx-users] Error DSSP Gromacs 5.0.4 Justin Lemkul
[gmx-users] dimer split Justin Lemkul
[gmx-users] Charmm27 forcefield parameters for carbon nanotubes Justin Lemkul
[gmx-users] Protein-ligand error pdb2gmx Justin Lemkul
[gmx-users] Free solvation, problems with g_bar Justin Lemkul
[gmx-users] Tools for energy of solvation in polimers Justin Lemkul
[gmx-users] mpirun Justin Lemkul
[gmx-users] Tools for energy of solvation in polimers Justin Lemkul
[gmx-users] mpirun Justin Lemkul
[gmx-users] Problem with Charges Justin Lemkul
[gmx-users] mpirun Justin Lemkul
[gmx-users] DPPC hlothane Residue DPP not found in residue topology database Justin Lemkul
[gmx-users] mpirun Justin Lemkul
[gmx-users] Getting a crystal topology file from pdb2gmx Justin Lemkul
[gmx-users] Getting a crystal topology file from pdb2gmx Justin Lemkul
[gmx-users] Getting a crystal topology file from pdb2gmx Justin Lemkul
[gmx-users] segmentation fault in equilibrium Justin Lemkul
[gmx-users] [gmx-developers] difference between Protein and protein-H Justin Lemkul
[gmx-users] segmentation fault in equilibrium Justin Lemkul
[gmx-users] Center of mass removal for a trajectory which is already created Justin Lemkul
[gmx-users] Choosing LINCS setting / rcon for parallel mdrun Justin Lemkul
[gmx-users] difference between entropic energy and free energy Justin Lemkul
[gmx-users] SASA: Gromacs5 vs Gromacs4 Justin Lemkul
[gmx-users] output forces with trjconv Justin Lemkul
[gmx-users] Polarizable Li+ Drude Simulations Justin Lemkul
[gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD Justin Lemkul
[gmx-users] surfactant.itp file Justin Lemkul
[gmx-users] cannot open traj.xtc Justin Lemkul
[gmx-users] Computing of reaction coordinate by g_wham Justin Lemkul
[gmx-users] Umbrella sampling tutorial - V-rescale or Berendsen thermostat Justin Lemkul
[gmx-users] surfactant.itp file Justin Lemkul
[gmx-users] Building gromacs 5.1.1: doesn't build all programs like grompp Justin Lemkul
[gmx-users] POPC simulation with heavy hydrogens and 4 fs timestep Justin Lemkul
[gmx-users] charge calculations and topology Justin Lemkul
[gmx-users] symtab get_symtab_handle error Justin Lemkul
[gmx-users] cannot open traj.xtc Justin Lemkul
[gmx-users] Dumping centers of mass of molecules during MD simulation Justin Lemkul
[gmx-users] How can I split .xtc file to two part? Justin Lemkul
[gmx-users] H-REMD in umbrella sampling Justin Lemkul
[gmx-users] tutorial umbrella sampling Justin Lemkul
[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file Justin Lemkul
[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field Justin Lemkul
[gmx-users] seeking a little help Justin Lemkul
[gmx-users] topology of ligand contains boron Justin Lemkul
[gmx-users] topology of ligand contains boron Justin Lemkul
[gmx-users] Errors pdb2gmx Justin Lemkul
[gmx-users] Problem compiling 4.6.7 with gpu support Saverio Lemme
[gmx-users] support mmcif format? Hannes Loeffler
[gmx-users] Fwd: hydrogen bonds James Lord
[gmx-users] removing some atoms James Lord
[gmx-users] Fwd: removing some atoms James Lord
[gmx-users] Polarizable Li+ Drude Simulations Tuanan Lourenço
[gmx-users] Problems with trjconv Shantanu Maheshwari
[gmx-users] Problems with trjconv Shantanu Maheshwari
[gmx-users] using charmm36 force field with gromacs Erik Marklund
[gmx-users] using charmm36 force field with gromacs Erik Marklund
[gmx-users] using charmm36 force field with gromacs Erik Marklund
[gmx-users] Problem with GROMACS simulation Erik Marklund
[gmx-users] electric field Erik Marklund
[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution? Erik Marklund
[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file Erik Marklund
[gmx-users] Fwd: removing some atoms João Martins
[gmx-users] Gromacs mdrun for k20 and cpu Alex Mathew
[gmx-users] Profiling mdrun with GProf Dave Michael
[gmx-users] Profiling mdrun with GProf Dave Michael
[gmx-users] Profiling mdrun with GProf Dave Michael
[gmx-users] Profiling mdrun with GProf Dave Michael
[gmx-users] Profiling mdrun with GProf Dave Michael
[gmx-users] Velocities with constraints Caro Miguel
[gmx-users] Explicit and implicit solvent Tushar Ranjan Moharana
[gmx-users] TIP3P for GROMOS96 force field Ali Mohyeddin
[gmx-users] Dumping centers of mass of molecules during MD simulation S.M. Golam Mortuza
[gmx-users] per atom stress tensor from g_energy Moultos, Othon
[gmx-users] per atom stress tensor Sab Moultos, Othon
[gmx-users] vir term in g_energy Moultos, Othon
[gmx-users] output forces with trjconv Moultos, Othon
[gmx-users] topology of ligand contains boron André Farias de Moura
[gmx-users] gmx sasa output confusion Teemu Murtola
[gmx-users] gmx sasa output confusion Teemu Murtola
[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file Teemu Murtola
[gmx-users] restart issues with Gromacs Nash, Anthony
[gmx-users] restart issues with Gromacs Nash, Anthony
[gmx-users] gmx mdrun std::bad_alloc whilst using PLUMED Nash, Anthony
[gmx-users] gmx mdrun std::bad_alloc whilst using PLUMED Nash, Anthony
[gmx-users] plus and minus signs in rtp files Joan Clark Nicolas
[gmx-users] Multiple time step MD Joan Clark Nicolas
[gmx-users] Multiple time step MD Joan Clark Nicolas
[gmx-users] Ligand Virtual Sites Joan Clark Nicolas
[gmx-users] Warning:Some of these results violate the Second Law of Thermodynamics Mishelle Oña
[gmx-users] Problems with g_bar Mishelle Oña
[gmx-users] Free solvation, problems with g_bar Mishelle Oña
[gmx-users] Free solvation, problems with g_bar Mishelle Oña
[gmx-users] Tools for energy of solvation in polimers Mishelle Oña
[gmx-users] Tools for energy of solvation in polimers Mishelle Oña
[gmx-users] gmx-users at gromacs.org Mishelle Oña
[gmx-users] Problems with trjconv Mishelle Oña
[gmx-users] Problems with trjconv Mishelle Oña
[gmx-users] Problems with trjconv Mishelle Oña
[gmx-users] Problems with trjconv Mishelle Oña
[gmx-users] Problems with trjconv Mishelle Oña
[gmx-users] periodic molecule CHEN Pan
[gmx-users] Umbrella sampling tutorial - V-rescale or Berendsen thermostat Martin Nors Pedersen
[gmx-users] energy autocorrelation function Mario Fernández Pendás
[gmx-users] Realistic water simulation Mario Fernández Pendás
[gmx-users] Realistic water simulation Mario Fernández Pendás
[gmx-users] Center of mass removal for a trajectory which is already created Faezeh Pousaneh
[gmx-users] Center of mass removal for a trajectory which is already created Faezeh Pousaneh
[gmx-users] Center of mass removal for a trajectory which is already created Faezeh Pousaneh
[gmx-users] ligand topology & charge calculations Chetan Puri
[gmx-users] charge calculations and topology Chetan Puri
[gmx-users] Gromacs mdrun for k20 and cpu Szilárd Páll
[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2 Szilárd Páll
[gmx-users] Running ultiple job in core? Szilárd Páll
[gmx-users] Problem compiling 4.6.7 with gpu support Szilárd Páll
[gmx-users] nhbdist option in gmx hbond? Gmx QA
[gmx-users] nhbdist option in gmx hbond? Gmx QA
[gmx-users] Running ultiple job in core? RJ
[gmx-users] Charmm27 forcefield parameters for carbon nanotubes Sanchaita Rajkhowa
[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field Rakesh Ramachandran
[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field Rakesh Ramachandran
[gmx-users] No convergence with g_nmeig Joaquim Rui de Castro Rodrigues
[gmx-users] Issues Using CHARMM22* Force Field with GROMACS 5.1 David Rosenman
[gmx-users] Issues Using CHARMM22* Force Field with GROMACS 5.1 David Rosenman
[gmx-users] mdrun error Golnaz Roudsari
[gmx-users] Select waters in a specific pore with gmx select Mahboobe Sadr
[gmx-users] Fwd: Select waters in a specific pore with gmx select Mahboobe Sadr
[gmx-users] Regarding Umbrella sampling PMF Bikash Ranjan Sahoo
[gmx-users] mpirun Said
[gmx-users] Bug in option parsing? Åke Sandgren
[gmx-users] Bug in option parsing? Åke Sandgren
[gmx-users] Profiling mdrun with GProf Åke Sandgren
[gmx-users] using charmm36 force field with gromacs Catarina A. Carvalheda dos Santos
[gmx-users] using charmm36 force field with gromacs Catarina A. Carvalheda dos Santos
[gmx-users] using charmm36 force field with gromacs Catarina A. Carvalheda dos Santos
[gmx-users] problem with equilibration of DLiPC membrane Catarina A. Carvalheda dos Santos
[gmx-users] problem with equilibration of DLiPC membrane Catarina A. Carvalheda dos Santos
[gmx-users] problem with equilibration of DLiPC membrane Catarina A. Carvalheda dos Santos
[gmx-users] Gromacs GPU got hang M Teguh Satria
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem Ganesh Shahane
[gmx-users] POPC simulation with heavy hydrogens and 4 fs timestep Ganesh Shahane
[gmx-users] Backmapping of POPE Ganesh Shahane
[gmx-users] Hamiltonian REMD Michael Shirts
[gmx-users] Example of H REMD Michael Shirts
[gmx-users] Fwd: Problem with GROMACS simulation Shantanu Singh
[gmx-users] Fwd: Problem with GROMACS simulation Shantanu Singh
[gmx-users] Problem with GROMACS simulation Shantanu Singh
[gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)" Shantanu Singh
[gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)" Shantanu Singh
[gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)" Shantanu Singh
[gmx-users] Getting a crystal topology file from pdb2gmx Smith, Micholas D.
[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution? Smith, Micholas D.
[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution? Smith, Micholas D.
[gmx-users] Realistic water simulation David van der Spoel
[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution? David van der Spoel
[gmx-users] Normal Mode Dan Sponseller
[gmx-users] Fwd: OPLA Peter Stern
[gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34 Peter Stern
[gmx-users] Problem with GROMACS simulation Peter Stern
[gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)" Peter Stern
[gmx-users] service broken? Peter Stern
[gmx-users] combine two pdb files Peter Stern
[gmx-users] combine two pdb files Peter Stern
[gmx-users] tutorial for "dual" alchemical transformation in gromacs? Sebastian Stolzenberg
[gmx-users] tutorial for "dual" alchemical transformation in gromacs? Sebastian Stolzenberg
[gmx-users] How can I split .xtc file to two part? Téletchéa Stéphane
[gmx-users] Getting a crystal topology file from pdb2gmx Ben Tam
[gmx-users] Getting a crystal topology file from pdb2gmx Ben Tam
[gmx-users] Getting a crystal topology file from pdb2gmx Ben Tam
[gmx-users] Getting a crystal topology file from pdb2gmx Ben Tam
[gmx-users] Problem with running crystal simulation Ben Tam
[gmx-users] Problem with running crystal simulation Ben Tam
[gmx-users] difference between entropic energy and free energy Ming Tang
[gmx-users] SASA question Tom
[gmx-users] SASA Problem Tom
[gmx-users] SASA Problem (Mark Abraham) Tom
[gmx-users] QM/MM Timofey Tyugashev
[gmx-users] 2. QM/MM (Timofey Tyugashev) Timofey Tyugashev
[gmx-users] Checking solvent water positions Timofey Tyugashev
[gmx-users] input file Urszula Uciechowska
[gmx-users] nvt error Urszula Uciechowska
[gmx-users] electric field Man Hoang Viet
[gmx-users] How to determine box shape and parameters from a run Tsjerk Wassenaar
[gmx-users] Backmapping of POPE Tsjerk Wassenaar
[gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation Tomek Wlodarski
[gmx-users] calculate apolar contact area Linlin Yang
[gmx-users] mpirun Elsaid Younes
[gmx-users] mpirun Elsaid Younes
[gmx-users] mpirun Elsaid Younes
[gmx-users] mpirun Elsaid Younes
[gmx-users] Protein-ligand error pdb2gmx Poncho Arvayo Zatarain
[gmx-users] DPPC hlothane Residue DPP not found in residue topology database Poncho Arvayo Zatarain
[gmx-users] binding free energy calculation and enegy decomposition in gmx Marc Zhang
[gmx-users] Automating pdb2gmx Jernej Zidar
[gmx-users] Automating pdb2gmx Jernej Zidar
[gmx-users] Hamiltonian REMD Sanja Zivanovic
[gmx-users] Example of H REMD Sanja Zivanovic
[gmx-users] H-REMD in umbrella sampling adam
[gmx-users] H-REMD in umbrella sampling adam
[gmx-users] Definition in martini CG force field mohammad agha
[gmx-users] Definition in martini CG force field mohammad agha
[gmx-users] segmentation fault in equilibrium mohammad agha
[gmx-users] Problem with Charges faride badalkhani
[gmx-users] NVT to NVE ensemble, energy drifting problem gozde ergin
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem gozde ergin
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem gozde ergin
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem gozde ergin
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem gozde ergin
[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem gozde ergin
[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force gozde ergin
[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force gozde ergin
[gmx-users] Umbrella sampling force autocorrelation gozde ergin
[gmx-users] cannot open traj.xtc soumadwip ghosh
[gmx-users] Compile error in Gromacs-5.1 and icc2011+openmpi+cuda5.5 jzhang
[gmx-users] Compile error in Gromacs-5.1 and icc2011+openmpi+cuda5.5 jzhang
[gmx-users] combine two pdb files masoud keramati
[gmx-users] combine two pdb files masoud keramati
[gmx-users] combine two pdb files masoud keramati
[gmx-users] pme_loadbal problem himanshu khandelia
[gmx-users] Disribution Function thomas knitter
[gmx-users] Distribution function thomas knitter
[gmx-users] Gromacs 5 and Shake luigi
[gmx-users] cannot open traj.xtc surbhi mahajan
[gmx-users] cannot open traj.xtc surbhi mahajan
[gmx-users] SASA: Gromacs5 vs Gromacs4 morpheus
[gmx-users] Query regarding water not settled shalini muralikumar
[gmx-users] inertia tensor sarman at ownit.nu
[gmx-users] produce the surfactant.itp file mahdiyeh poorsargol
[gmx-users] surfactant.itp file mahdiyeh poorsargol
[gmx-users] surfactant.itp file mahdiyeh poorsargol
[gmx-users] surfactant.itp file mahdiyeh poorsargol
[gmx-users] surfactant.itp file mahdiyeh poorsargol
[gmx-users] (no subject) mahdiyeh poorsargol
[gmx-users] surfactant.itp file mahdiyeh poorsargol
[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution? xieshaoqu at qq.com
[gmx-users] g_wham error asasa qsqs
[gmx-users] g_wham error asasa qsqs
[gmx-users] pdo files asasa qsqs
[gmx-users] convert amber files to gromacs mohammad r
[gmx-users] segmentation fault in equilibrium sara soleimanzadegan
[gmx-users] segmentation fault in equilibrium sara soleimanzadegan
[gmx-users] tutorial for "dual" alchemical transformation in gromacs? hannes.loeffler at stfc.ac.uk
[gmx-users] tutorial for "dual" alchemical transformation in gromacs? hannes.loeffler at stfc.ac.uk
[gmx-users] topology of ligand contains boron subho_1997 at yahoo.com
[gmx-users] charge assign elham tazikeh
[gmx-users] Charmm27 forcefield parameters for carbon nanotubes ashan wettasinghe
[gmx-users] segmentation fault with GPU xiao
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] long-stick molecule solvation xy21hb
[gmx-users] dimer split xy21hb
[gmx-users] dimer split xy21hb
[gmx-users] implicit solvent with periodic molecules Анна Павловна Толстова
[gmx-users] grompp error محمد گره گشا
[gmx-users] LINC warning 凌未风
[gmx-users] LINC warning after long time simulations 凌未风
[gmx-users] Energy conservation in NVE simulations 张正财
[gmx-users] Energy conservation in NVE simulations 张正财
[gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34 张正财
[gmx-users] How to build a correct structure file beyond 99999 atoms using pdb or gro extend format ? 田会全
[gmx-users] How to build a correct structure file beyond 99999 atoms using pdb or gro extend format ? 田会全

Last message date: Mon Nov 30 23:01:33 CET 2015
Archived on: Mon Nov 30 23:01:33 CET 2015

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