December 2014 Archives by author

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Starting: Mon Dec 1 07:19:06 CET 2014
Ending: Wed Dec 31 21:08:30 CET 2014
Messages: 624

[gmx-users] Problems with CO2-water simulation sujithkakkat .
[gmx-users] Problems with CO2-water simulation sujithkakkat .
[gmx-users] Problems with CO2-water simulation sujithkakkat .
[gmx-users] PMF and RDF sujithkakkat .
[gmx-users] PMF and RDF sujithkakkat .
[gmx-users] Problems with CO2-water simulation sujithkakkat .
[gmx-users] Questions about CO2. sujithkakkat .
[gmx-users] how to remove water molecule inside micelle ABEL Stephane 175950
[gmx-users] Performance of GPU Workstation (GPU selection) mail at 2718-mail.de
[gmx-users] Performance of GPU Workstation (GPU selection) mail at 2718-mail.de
[gmx-users] AMD GPUs mail at 2718-mail.de
[gmx-users] Your solvent group size (*) is not a multiple of * Hassan Aaryapour
[gmx-users] Stop protein diffusion in simulation box to make a movie Hassan Aaryapour
[gmx-users] How to choose the best pose of ligand from the trajectory file? Hassan Aaryapour
[gmx-users] Can we calculate rmsd from after energy minimization? Mark Abraham
[gmx-users] error in PME mesh load Mark Abraham
[gmx-users] odd replica excahnge Mark Abraham
[gmx-users] Define Heavy Water Mark Abraham
[gmx-users] Continuing inturepted REMD simulation Mark Abraham
[gmx-users] Why the rmsd value has been varied from different hardware for same protein? Mark Abraham
[gmx-users] no output from rms Mark Abraham
[gmx-users] Continuing inturepted REMD simulation Mark Abraham
[gmx-users] Gromacs 5.0.1 restart simulation Mark Abraham
[gmx-users] Different box volumes from gmxdump and g_energy Mark Abraham
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 10 Mark Abraham
[gmx-users] energy groups rerun from reduced xtc file Mark Abraham
[gmx-users] Regarding parallel run in Gromacs 5.0 Mark Abraham
[gmx-users] multinode issue Mark Abraham
[gmx-users] Regarding parallel run in Gromacs 5.0 Mark Abraham
[gmx-users] multinode issue Mark Abraham
[gmx-users] running g_tune_pme on stampede Mark Abraham
[gmx-users] multinode issue Mark Abraham
[gmx-users] Regarding Gromacs 5.0 parallel installation Mark Abraham
[gmx-users] Precision of xtc-precision Mark Abraham
[gmx-users] energy groups rerun from reduced xtc file Mark Abraham
[gmx-users] trr file time/frame information Mark Abraham
[gmx-users] trr file time/frame information Mark Abraham
[gmx-users] Gromacs 5.0.3 released Mark Abraham
[gmx-users] Installation problem with Gromacs 5.0.2 Mark Abraham
[gmx-users] Morse potential for Specific Group Mark Abraham
[gmx-users] Segmentation fault error Mark Abraham
[gmx-users] xeon-phi and double precision Mark Abraham
[gmx-users] Segmentation fault error Mark Abraham
[gmx-users] Fwd: Question about GPU acceleration in GROMACS 5 Mark Abraham
[gmx-users] trjconv precision lost from double to single conversion Mark Abraham
[gmx-users] Question about GPU acceleration in GROMACS 5 Mark Abraham
[gmx-users] Question about GPU acceleration in GROMACS 5 Mark Abraham
[gmx-users] pmetune and restarting Mark Abraham
[gmx-users] with 5.0: file INSTALL cannot find gmx Mark Abraham
[gmx-users] Segfault on energy minimization Mark Abraham
[gmx-users] Segfault on energy minimization Mark Abraham
[gmx-users] output dispersion correction and coul. recip. for energy groups Mark Abraham
[gmx-users] output dispersion correction and coul. recip. for energy groups Mark Abraham
[gmx-users] content of trr / xtc files + -b/-e flag question + tpr question Mark Abraham
[gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet Mark Abraham
[gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet Mark Abraham
[gmx-users] avx2 with gcc 4.8.3 Mark Abraham
[gmx-users] Gromacs 5.0.4 released Mark Abraham
[gmx-users] avx2 with gcc 4.8.3 Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] AMD GPUs Mark Abraham
[gmx-users] Installing GTX 980 on linux - which distro should i use? Mark Abraham
[gmx-users] Illegal instruction flag raised in GMX 5.0.4 Mark Abraham
[gmx-users] How to use gmx convert-tpr for GMX5.0.4 Mark Abraham
[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995) Mark Abraham
[gmx-users] Obtaining PMF for change in domain position Abhi Acharya
[gmx-users] Obtaining PMF for change in domain position Abhi Acharya
[gmx-users] Obtaining PMF for change in domain position Abhi Acharya
[gmx-users] Converting Amber parameters to gromacs parameters Alan
[gmx-users] g_covar + g_anaeig entropy calculation Albert
[gmx-users] g_covar + g_anaeig entropy calculation Albert
[gmx-users] GXT690 vs GTX Titan black Albert
[gmx-users] GXT690 vs GTX Titan black Albert
[gmx-users] GXT690 vs GTX Titan black Albert
[gmx-users] Xeon Phi benchmark? Albert
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Albert
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Albert
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Albert
[gmx-users] Define a new group for protein-ligand system Shima Arasteh
[gmx-users] Fwd: Define a new group for protein-ligand system Shima Arasteh
[gmx-users] Define a new group for protein-ligand complex system Shima Arasteh
[gmx-users] Need to Sort Out Devender Arora
[gmx-users] a question about Electric ﬁelds BIRD
[gmx-users] Fwd: Question about GPU acceleration in GROMACS 5 Tomy van Batis
[gmx-users] Question about GPU acceleration in GROMACS 5 Tomy van Batis
[gmx-users] Question about GPU acceleration in GROMACS 5 Tomy van Batis
[gmx-users] How can I analyze an interaction between protein and CU ions Batdorj Batsaikhan
[gmx-users] How can I analyze an interaction between protein and CU ions Batdorj Batsaikhan
[gmx-users] Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0? Batdorj Batsaikhan
[gmx-users] Basic GROMACS questions Simone Bolognini
[gmx-users] Basic GROMACS questions Simone Bolognini
[gmx-users] Basic GROMACS questions Simone Bolognini
[gmx-users] Installing GTX 980 on linux - which distro should i use? Mohammad Hossein Borghei
[gmx-users] Installation problem with Gromacs 5.0.2 PAULAMI CHATTERJEE
[gmx-users] Installation problem with Gromacs 5.0.2 PAULAMI CHATTERJEE
[gmx-users] Postdoctoral position at the KAUST Luigi Cavallo
[gmx-users] Simulating Carbon nanotubes as finite systems in GROMACS Dr. Vitaly Chaban
[gmx-users] Preparing a silicon bulk Kevin C Chan
[gmx-users] Preparing a silicon bulk Kevin C Chan
[gmx-users] Preparing a silicon bulk Kevin C Chan
[gmx-users] Preparing a silicon bulk Kevin C Chan
[gmx-users] Preparing a silicon bulk Kevin C Chan
[gmx-users] Preparing a silicon bulk Kevin C Chan
[gmx-users] send this as a post Abid Channa
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74 Abid Channa
[gmx-users] running g_tune_pme on stampede Kevin Chen
[gmx-users] gromacs on GPU Shaohao Chen
[gmx-users] gromacs on GPU Shaohao Chen
[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995) Chandan Choudhury
[gmx-users] output dispersion correction and coul. recip. for energy groups Yongchul Chung
[gmx-users] output dispersion correction and coul. recip. for energy groups Yongchul Chung
[gmx-users] Morse potential for Specific Group Bogdan Costescu
[gmx-users] Query in protein insertion in membrane Priya Das
[gmx-users] Query in protein insertion in membrane Priya Das
[gmx-users] Query in protein insertion in membrane Priya Das
[gmx-users] Error in protein insertion in bilipid layer Priya Das
[gmx-users] Error in protein insertion in bilipid layer Priya Das
[gmx-users] Steered molecular dynamics Priya Das
[gmx-users] Query regarding ligand topology Priya Das
[gmx-users] RDF calculation. Marcelo Depólo
[gmx-users] qm-mm calculation : Gromacs + cpmd Nilesh Dhumal
[gmx-users] how to use gmx convert-tpr for GMX5.0.4 Smart Eagle
[gmx-users] How to use gmx convert-tpr for GMX5.0.4 Smart Eagle
[gmx-users] Morse potential for Specific Group Jackson Chief Elk
[gmx-users] charmm to gromacs Rebeca García Fandiño
[gmx-users] charmm to gromacs Rebeca García Fandiño
[gmx-users] charmm to gromacs Rebeca García Fandiño
[gmx-users] charmm to gromacs Rebeca García Fandiño
[gmx-users] Problem Simulating a protein with small peptides Arash Firouzbakht
[gmx-users] read trr file Patrick Fuchs
[gmx-users] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD
[gmx-users] Segfault on energy minimization Diego Muñoz G.
[gmx-users] Segfault on energy minimization Diego Muñoz G.
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Victor Rosas Garcia
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 1 Victor Rosas Garcia
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Victor Rosas Garcia
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Victor Rosas Garcia
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Victor Rosas Garcia
[gmx-users] multinode issue Éric Germaneau
[gmx-users] multinode issue Éric Germaneau
[gmx-users] multinode issue Éric Germaneau
[gmx-users] multinode issue Éric Germaneau
[gmx-users] default state of "energygrps" in .mdp file Agnivo Gosai
[gmx-users] g_wham 4.67 version output query Agnivo Gosai
[gmx-users] g_wham 4.6.7 version output query Agnivo Gosai
[gmx-users] Make DNA stay in the center of the box during Simulation Hovakim Grabski
[gmx-users] energy groups rerun from reduced xtc file Harry Mark Greenblatt
[gmx-users] energy groups rerun from reduced xtc file Harry Mark Greenblatt
[gmx-users] running solvate twice... Harry Mark Greenblatt
[gmx-users] slight correction... Harry Mark Greenblatt
[gmx-users] running solvate twice... Harry Mark Greenblatt
[gmx-users] running solvate twice... Harry Mark Greenblatt
[gmx-users] avx2 with gcc 4.8.3 Harry Mark Greenblatt
[gmx-users] avx2 with gcc 4.8.3 Harry Mark Greenblatt
[gmx-users] avx2 with gcc 4.8.3 Harry Mark Greenblatt
[gmx-users] avx2 with gcc 4.8.3 Harry Mark Greenblatt
[gmx-users] Illegal instruction flag raised in GMX 5.0.4 Harry Mark Greenblatt
[gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed Mike Hanby
[gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed Mike Hanby
[gmx-users] how to remove water molecule inside micelle? Mina Hashemi
[gmx-users] CG MD Simulation of DNA and PAMAM dendrimers Doa Hawamdeh
[gmx-users] Mplecular Dynamic simulation of DNA and PAMAM dendrimers Doa Hawamdeh
[gmx-users] Non-bonded interactions Doa Hawamdeh
[gmx-users] (no subject) Doa Hawamdeh
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Jason Hill
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Jason Hill
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Jason Hill
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Jason Hill
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 91 Jason Hill
[gmx-users] All-atom vs United-atom force fields and hydrogen bonds Jason Hill
[gmx-users] protein-ligand complex fatal error Yaser Hosseini
[gmx-users] protein-ligand complex fatal error Yaser Hosseini
[gmx-users] fatal erroe in prorein-ligand comlex Yaser Hosseini
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74 Yaser Hosseini
[gmx-users] how can i use acpype Yaser Hosseini
[gmx-users] with 5.0: file INSTALL cannot find gmx Jochen Hub
[gmx-users] with 5.0: file INSTALL cannot find gmx Jochen Hub
[gmx-users] with 5.0: file INSTALL cannot find gmx Jochen Hub
[gmx-users] with 5.0: file INSTALL cannot find gmx Jochen Hub
[gmx-users] merging chains in gromos43a1p Jayant James
[gmx-users] merging chains in gromos43a1p Jayant James
[gmx-users] Illegal instruction flag raised in GMX 5.0.4 Jayant James
[gmx-users] Walls and pressure coupling Jingjie
[gmx-users] Free Energy calculations crash for lambdas higher than 0.8 Julian
[gmx-users] g_angle ayşe K
[gmx-users] error in PME mesh load RINU KHATTRI
[gmx-users] ligand related problem RINU KHATTRI
[gmx-users] Atomtype ZN2+ not found Shankar Prasad Kanaujia
[gmx-users] Atomtype ZN2+ not found Shankar Prasad Kanaujia
[gmx-users] Simulating Carbon nanotubes as finite systems in GROMACS abhijit Kayal
[gmx-users] gromacs installation Amir Khan
[gmx-users] gromacs installation Amir Khan
[gmx-users] -vsite hydrogen Wojciech Kopeć
[gmx-users] Pressure in gromacs Narendra Kumar
[gmx-users] Element naming format in .pdb file Rajan Kumar
[gmx-users] Error in topology using g_x2top Rajan Kumar
[gmx-users] Free energy calculation by MM_PBSA Indu Kumari
[gmx-users] Free energy calculation by MM_PBSA Indu Kumari
[gmx-users] Free energy calculation by MM_PBSA Indu Kumari
[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995) Amit Kumawat
[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995) Amit Kumawat
[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995) Amit Kumawat
[gmx-users] can you please add my email to the mailing list? Vered Kunik
[gmx-users] gromacs workshop in Europe during 2015 Vered Kunik
[gmx-users] Performance of GPU Workstation (GPU selection) Carsten Kutzner
[gmx-users] running g_tune_pme on stampede Carsten Kutzner
[gmx-users] Question about GPU acceleration in GROMACS 5 Carsten Kutzner
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Carsten Kutzner
[gmx-users] GXT690 vs GTX Titan black Carsten Kutzner
[gmx-users] Working on a GPU cluster with GROMACS 5 Carsten Kutzner
[gmx-users] Installing GTX 980 on linux - which distro should i use? Carsten Kutzner
[gmx-users] Illegal instruction flag raised in GMX 5.0.4 Carsten Kutzner
[gmx-users] use of g_hbond Alexander Law
[gmx-users] use of g_hbond Alexander Law
[gmx-users] Umbrella Sampling continuation Alexander Law
[gmx-users] charmm to gromacs Justin Lemkul
[gmx-users] Отв: Position Restraint or remove COM from DNA Justin Lemkul
[gmx-users] ligand related problem Justin Lemkul
[gmx-users] constrained bonds Justin Lemkul
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Justin Lemkul
[gmx-users] Gromacs 5.0.1 restart simulation Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 11 Justin Lemkul
[gmx-users] default state of "energygrps" in .mdp file Justin Lemkul
[gmx-users] Query in protein insertion in membrane Justin Lemkul
[gmx-users] merging chains in gromos43a1p Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 12 Justin Lemkul
[gmx-users] Query in protein insertion in membrane Justin Lemkul
[gmx-users] Query in protein insertion in membrane Justin Lemkul
[gmx-users] Remove rotation from rmsd Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15 Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] g_spatial Justin Lemkul
[gmx-users] Errors about dihidral angle type 9 in free energy perturbation Justin Lemkul
[gmx-users] charmm to gromacs Justin Lemkul
[gmx-users] Errors about dihidral angle type 9 in free energy perturbation Justin Lemkul
[gmx-users] MDP parameters for OPLS-aa + Verlet cutoff scheme Justin Lemkul
[gmx-users] adding a new residue into an existing force field? Justin Lemkul
[gmx-users] using g_hbond between index gps of specific Justin Lemkul
[gmx-users] A small Questions of umbrella samping Justin Lemkul
[gmx-users] A small Questions of umbrella samping Justin Lemkul
[gmx-users] Make DNA stay in the center of the box during Simulation Justin Lemkul
[gmx-users] Отв: Make DNA stay in the center of the box during Simulation Justin Lemkul
[gmx-users] .itp file of choline molecule Justin Lemkul
[gmx-users] Error in protein insertion in bilipid layer Justin Lemkul
[gmx-users] running solvate twice... Justin Lemkul
[gmx-users] Basic GROMACS questions Justin Lemkul
[gmx-users] running solvate twice... Justin Lemkul
[gmx-users] .itp file of choline molecule Justin Lemkul
[gmx-users] Basic GROMACS questions Justin Lemkul
[gmx-users] Question on installation Justin Lemkul
[gmx-users] ProDrg Justin Lemkul
[gmx-users] protein-ligand complex fatal error Justin Lemkul
[gmx-users] Basic GROMACS questions Justin Lemkul
[gmx-users] g_wham 4.6.7 version output query Justin Lemkul
[gmx-users] merging chains in gromos43a1p Justin Lemkul
[gmx-users] PMF and RDF Justin Lemkul
[gmx-users] problem during energy minimization Justin Lemkul
[gmx-users] Your solvent group size (*) is not a multiple of * Justin Lemkul
[gmx-users] PMF and RDF Justin Lemkul
[gmx-users] Regarding the generation of intermolecule disulphide bond between two monomer subunits Justin Lemkul
[gmx-users] protein-ligand complex fatal error Justin Lemkul
[gmx-users] pdb2gmx atom not found Justin Lemkul
[gmx-users] Stop protein diffusion in simulation box to make a movie Justin Lemkul
[gmx-users] adding hydrogen atoms into a POPC membrane Justin Lemkul
[gmx-users] Need to Sort Out Justin Lemkul
[gmx-users] Maximun time-step recommended in the grompp part for each system Justin Lemkul
[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ? Justin Lemkul
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Justin Lemkul
[gmx-users] Maximun time-step recommended in the grompp part for each system Justin Lemkul
[gmx-users] 0 +- 0.5 bar ok? Justin Lemkul
[gmx-users] parametrization of GABA for charmm27 Justin Lemkul
[gmx-users] Ions drifting Justin Lemkul
[gmx-users] Add new residue to forcefield Justin Lemkul
[gmx-users] Renumber atom ids and charge group in topology (.itp) Justin Lemkul
[gmx-users] Renumber atom ids and charge group in topology (.itp) Justin Lemkul
[gmx-users] fatal erroe in prorein-ligand comlex Justin Lemkul
[gmx-users] fatal erroe in prorein-ligand comlex Justin Lemkul
[gmx-users] fatal erroe in prorein-ligand comlex Justin Lemkul
[gmx-users] Force Field for protein in water Justin Lemkul
[gmx-users] fatal erroe in prorein-ligand comlex Justin Lemkul
[gmx-users] fatal erroe in prorein-ligand comlex Justin Lemkul
[gmx-users] Fw: Add new residue to oplsaa force field Justin Lemkul
[gmx-users] Ions drifting Justin Lemkul
[gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified Justin Lemkul
[gmx-users] Ions drifting Justin Lemkul
[gmx-users] PTM force field Justin Lemkul
[gmx-users] PTM force field Justin Lemkul
[gmx-users] Problem Simulating a protein with small peptides Justin Lemkul
[gmx-users] Add new residue to oplsaa force field Justin Lemkul
[gmx-users] how can i use acpype Justin Lemkul
[gmx-users] Preparing a silicon bulk Justin Lemkul
[gmx-users] Preparing a silicon bulk Justin Lemkul
[gmx-users] Atomtype ZN2+ not found Justin Lemkul
[gmx-users] Query regarding ligand topology Justin Lemkul
[gmx-users] Preparing a silicon bulk Justin Lemkul
[gmx-users] Preparing a silicon bulk Justin Lemkul
[gmx-users] Element naming format in .pdb file Justin Lemkul
[gmx-users] Non-bonded interactions Justin Lemkul
[gmx-users] Preparing a silicon bulk Justin Lemkul
[gmx-users] initial velocities Justin Lemkul
[gmx-users] Error in topology using g_x2top Justin Lemkul
[gmx-users] length of beta sheet Justin Lemkul
[gmx-users] Pulling Justin Lemkul
[gmx-users] How to choose the best pose of ligand from the trajectory file? Justin Lemkul
[gmx-users] Umbrella sampling along a dihedral angle Justin Lemkul
[gmx-users] How to plot a droplet radius profile as a function of z-direction? Justin Lemkul
[gmx-users] RDF calculation. Justin Lemkul
[gmx-users] core dumped Justin Lemkul
[gmx-users] Umbrella sampling along a dihedral angle Justin Lemkul
[gmx-users] charge distribution Justin Lemkul
[gmx-users] core dumped Justin Lemkul
[gmx-users] charge distribution Justin Lemkul
[gmx-users] farticle demanding about Small-Molecule Topologies Justin Lemkul
[gmx-users] -vsite hydrogen Justin Lemkul
[gmx-users] Obtaining PMF for change in domain position Justin Lemkul
[gmx-users] pdb information Justin Lemkul
[gmx-users] Obtaining PMF for change in domain position Justin Lemkul
[gmx-users] charge distribution Justin Lemkul
[gmx-users] pdb information Justin Lemkul
[gmx-users] box siz Justin Lemkul
[gmx-users] All-atom vs United-atom force fields and hydrogen bonds Justin Lemkul
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Justin Lemkul
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Justin Lemkul
[gmx-users] charge distriburion Justin Lemkul
[gmx-users] box siz Justin Lemkul
[gmx-users] How to plot a droplet radius profile as a function of z-directio Justin Lemkul
[gmx-users] Define a new group for protein-ligand complex system Justin Lemkul
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Justin Lemkul
[gmx-users] error while executing do_dssp program Justin Lemkul
[gmx-users] Jump in temperature each time a new simulation is started. Justin Lemkul
[gmx-users] error while executing do_dssp program Justin Lemkul
[gmx-users] Errors about dihidral angle type 9 in free energy perturbation Jianguo Li
[gmx-users] Errors about dihidral angle type 9 in free energy perturbation Jianguo Li
[gmx-users] Errors about dihidral angle type 9 in free energy perturbation Jianguo Li
[gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file? Jianguo Li
[gmx-users] Problem with gmx-users mail list subscription Elena Lilkova
[gmx-users] Protein distance with respect to box walls James Lord
[gmx-users] g_mindist James Lord
[gmx-users] Different box volumes from gmxdump and g_energy Johnny Lu
[gmx-users] Different box volumes from gmxdump and g_energy Johnny Lu
[gmx-users] Different box volumes from gmxdump and g_energy Johnny Lu
[gmx-users] Different box volumes from gmxdump and g_energy Johnny Lu
[gmx-users] Precision of xtc-precision Johnny Lu
[gmx-users] Question on installation Johnny Lu
[gmx-users] Dihedral angle calculation in Gromacs Johnny Lu
[gmx-users] xeon-phi and double precision Johnny Lu
[gmx-users] trjconv precision lost from double to single conversion Johnny Lu
[gmx-users] trjconv precision lost from double to single conversion Johnny Lu
[gmx-users] trjconv precision lost from double to single conversion Johnny Lu
[gmx-users] pmetune and restarting Johnny Lu
[gmx-users] with 5.0: file INSTALL cannot find gmx Johnny Lu
[gmx-users] with 5.0: file INSTALL cannot find gmx Johnny Lu
[gmx-users] with 5.0: file INSTALL cannot find gmx Johnny Lu
[gmx-users] Stop protein diffusion in simulation box to make a movie Johnny Lu
[gmx-users] Need to Sort Out Johnny Lu
[gmx-users] trjconv during transfer of .trr Johnny Lu
[gmx-users] trjconv during transfer of .trr Johnny Lu
[gmx-users] trjconv during transfer of .trr Johnny Lu
[gmx-users] 0 +- 0.5 bar ok? Johnny Lu
[gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed Johnny Lu
[gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed Johnny Lu
[gmx-users] Ions drifting Johnny Lu
[gmx-users] compiling for xeon phi Johnny Lu
[gmx-users] GTX 980 benchmark Johnny Lu
[gmx-users] CG MD Simulation of DNA and PAMAM dendrimers Johnny Lu
[gmx-users] Ions drifting Johnny Lu
[gmx-users] Ions drifting Johnny Lu
[gmx-users] Ions drifting Johnny Lu
[gmx-users] AMD GPUs Johnny Lu
[gmx-users] Element naming format in .pdb file Johnny Lu
[gmx-users] ProDrg Magnus Lundborg
[gmx-users] Converting Amber parameters to gromacs parameters Magnus Lundborg
[gmx-users] fluid flow Katie Maerzke
[gmx-users] Simulating Carbon nanotubes as finite systems in GROMACS Sergio Manzetti
[gmx-users] CNT simulation Sergio Manzetti
[gmx-users] CNT simulation Sergio Manzetti
[gmx-users] conformational entropy Daniel Margul
[gmx-users] using g_hbond between index gps of specific interest Erik Marklund
[gmx-users] using g_hbond between index gps of specific interest Erik Marklund
[gmx-users] Structure downloads Erik Marklund
[gmx-users] PMF and RDF Erik Marklund
[gmx-users] PMF and RDF Erik Marklund
[gmx-users] Protein distance with respect to box walls Erik Marklund
[gmx-users] Steered molecular dynamics Erik Marklund
[gmx-users] g_hbond not running Erik Marklund
[gmx-users] g_hbond not running Erik Marklund
[gmx-users] g_hbond not running Erik Marklund
[gmx-users] g_mindist Erik Marklund
[gmx-users] Implicit and explicit solvation Erik Marklund
[gmx-users] Continuing inturepted REMD simulation Nizar Masbukhin
[gmx-users] Continuing inturepted REMD simulation Nizar Masbukhin
[gmx-users] error while executing do_dssp program Nizar Masbukhin
[gmx-users] error while executing do_dssp program Nizar Masbukhin
[gmx-users] Working on a GPU cluster with GROMACS 5 Ebert Maximilian
[gmx-users] Silica monolayer with Martini force field André Farias de Moura
[gmx-users] Question about water freezing when in contact to a solid surface (ramon) André Farias de Moura
[gmx-users] how to remove water molecule inside micelle? André Farias de Moura
[gmx-users] ProDrg Naba
[gmx-users] Renumber atom ids and charge group in topology (.itp) Nash, Anthony
[gmx-users] Renumber atom ids and charge group in topology (.itp) Nash, Anthony
[gmx-users] Renumber atom ids and charge group in topology (.itp) Nash, Anthony
[gmx-users] Umbrella sampling along a dihedral angle Nash, Anthony
[gmx-users] Umbrella sampling along a dihedral angle Nash, Anthony
[gmx-users] Umbrella sampling along a dihedral angle Nash, Anthony
[gmx-users] Umbrella sampling along a dihedral angle Nash, Anthony
[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ? Christopher Neale
[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ? Christopher Neale
[gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified Christopher Neale
[gmx-users] Amber missing psi dihedral at cationic N-terminus of protein/peptide? Christopher Neale
[gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified Christopher Neale
[gmx-users] How to change the multiplicity of a dihedral in FEP in Gromacs Christopher Neale
[gmx-users] Structure downloads Norman, Lucy
[gmx-users] Gromacs error regarding default gromos bond type and angle type Negar Parvizi
[gmx-users] Fw: Gromacs error regarding default gromos bond type and angle type Negar Parvizi
[gmx-users] Maximun time-step recommended in the grompp part for each system Mario Fernández Pendás
[gmx-users] Maximun time-step recommended in the grompp part for each system Mario Fernández Pendás
[gmx-users] Maximun time-step recommended in the grompp part for each system Mario Fernández Pendás
[gmx-users] Maximun time-step recommended in the grompp part for each system Mario Fernández Pendás
[gmx-users] martinize.py: option for partly have elastic network on partly in the protein XAvier Periole
[gmx-users] adding hydrogen atoms into a POPC membrane Thomas Piggot
[gmx-users] Performance of GPU Workstation (GPU selection) Szilárd Páll
[gmx-users] Performance of GPU Workstation (GPU selection) Szilárd Páll
[gmx-users] multinode issue Szilárd Páll
[gmx-users] multinode issue Szilárd Páll
[gmx-users] gromacs on GPU Szilárd Páll
[gmx-users] GXT690 vs GTX Titan black Szilárd Páll
[gmx-users] GXT690 vs GTX Titan black Szilárd Páll
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Szilárd Páll
[gmx-users] GTX 980 benchmark Szilárd Páll
[gmx-users] GTX 980 benchmark Szilárd Páll
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Szilárd Páll
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Szilárd Páll
[gmx-users] AMD GPUs Szilárd Páll
[gmx-users] AMD GPUs Szilárd Páll
[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09 Szilárd Páll
[gmx-users] malloc error at mdrun step Kalyan Reddy
[gmx-users] RDF does not reach 1 for bulk Venkat Reddy
[gmx-users] adding hydrogen atoms into a POPC membrane Carlos Navarro Retamal
[gmx-users] adding hydrogen atoms into a POPC membrane Carlos Navarro Retamal
[gmx-users] mdp file coarse grained simulation with cutoff-scheme =?utf-8?Q?=3D_?=Verlet Carlos Navarro Retamal
[gmx-users] mdp file coarse grained simulation with cutoff-scheme =?utf-8?Q?=3D_?=Verlet Carlos Navarro Retamal
[gmx-users] adding hydrogen atoms into a POPC membrane Carlos Navarro Retamal
[gmx-users] Converting Amber parameters to gromacs parameters Carlos Navarro Retamal
[gmx-users] Installing GTX 980 on linux - which distro should i use? Carlos Navarro Retamal
[gmx-users] Installing GTX 980 on linux - which distro should i se? Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3) Carlos Navarro Retamal
[gmx-users] Regarding parallel run in Gromacs 5.0 Bikash Ranjan Sahoo
[gmx-users] Regarding Gromacs parallel run Bikash Ranjan Sahoo
[gmx-users] Regarding parallel run in Gromacs 5.0 Bikash Ranjan Sahoo
[gmx-users] Regarding Gromacs 5.0 parallel installation Bikash Ranjan Sahoo
[gmx-users] Free energy calculation by MM_PBSA Bikash Ranjan Sahoo
[gmx-users] Regarding Gromacs 5.0.3 parallel computation Bikash Ranjan Sahoo
[gmx-users] Installation problem with Gromacs 5.0.2 Bikash Ranjan Sahoo
[gmx-users] Regarding Gromacs 5.0.3 parallel computation Bikash Ranjan Sahoo
[gmx-users] How to define the covalent bonds between ligand and protein Bikash Ranjan Sahoo
[gmx-users] fatal erroe in prorein-ligand comlex Bikash Ranjan Sahoo
[gmx-users] Segmentation fault error Seyed Mojtaba Rezaei Sani
[gmx-users] Segmentation fault error Seyed Mojtaba Rezaei Sani
[gmx-users] Segmentation fault error Seyed Mojtaba Rezaei Sani
[gmx-users] avx2 with gcc 4.8.3 Roland Schulz
[gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed Roland Schulz
[gmx-users] Umbrella Sampling continuation Lalita Shaki
[gmx-users] Question on installation Igor Shchechkin
[gmx-users] Protein distance with respect to box walls Smith, Micholas D.
[gmx-users] All-atom vs United-atom force fields and hydrogen bonds Smith, Micholas D.
[gmx-users] content of trr / xtc files + -b/-e flag question + tpr question Eric Smoll
[gmx-users] trjconv during transfer of .trr Eric Smoll
[gmx-users] Naughty Vacuum Bubble in our Vesicle! Björn Sommer
[gmx-users] Problems with CO2-water simulation David van der Spoel
[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995) David van der Spoel
[gmx-users] Questions about CO2. David van der Spoel
[gmx-users] Jump in temperature each time a new simulation is started. Dan Sponseller
[gmx-users] Regarding Gromacs 5.0.3 parallel computation Téletchéa Stéphane
[gmx-users] Regarding Gromacs 5.0.3 parallel computation Téletchéa Stéphane
[gmx-users] Regarding Gromacs 5.0.3 parallel computation Téletchéa Stéphane
[gmx-users] Installing GTX 980 on linux - which distro should i use? Téletchéa Stéphane
[gmx-users] (no subject) Prajisha Sujaya
[gmx-users] Can we calculate rmsd from after energy minimization? Seera Suryanarayana
[gmx-users] Why the rmsd value has been varied from different hardware for same protein? Seera Suryanarayana
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 1 Seera Suryanarayana
[gmx-users] MMPBSA & GMXPBSA 2.1 Tom
[gmx-users] PCA of crystal structures Ullmann, Thomas
[gmx-users] Install gromacs 5.0.2,ERROR Hooman Vahidi
[gmx-users] GXT690 vs GTX Titan black Mirco Wahab
[gmx-users] GXT690 vs GTX Titan black Mirco Wahab
[gmx-users] read trr file Tsjerk Wassenaar
[gmx-users] read trr file Tsjerk Wassenaar
[gmx-users] read trr file Tsjerk Wassenaar
[gmx-users] Problems with CO2-water simulation Tsjerk Wassenaar
[gmx-users] Problems with CO2-water simulation Tsjerk Wassenaar
[gmx-users] Problems with CO2-water simulation Tsjerk Wassenaar
[gmx-users] running solvate twice... Tsjerk Wassenaar
[gmx-users] adding hydrogen atoms into a POPC membrane Tsjerk Wassenaar
[gmx-users] Ions drifting Tsjerk Wassenaar
[gmx-users] Question about water freezing when in contact to a solid surface (ramon) Tsjerk Wassenaar
[gmx-users] minimal distance between periodic images Tsjerk Wassenaar
[gmx-users] Protein split with mindist Tsjerk Wassenaar
[gmx-users] initial velocities Tsjerk Wassenaar
[gmx-users] initial velocities Tsjerk Wassenaar
[gmx-users] extracting velocities Tsjerk Wassenaar
[gmx-users] extracting velocities Tsjerk Wassenaar
[gmx-users] Projection of trajectory onto PCs Tsjerk Wassenaar
[gmx-users] BN parameters in MD Kester Wong
[gmx-users] How to plot a droplet radius profile as a function of z-direction? Kester Wong
[gmx-users] How to plot a droplet radius profile as a function of z-directio Kester Wong
[gmx-users] PTM force field Jianqing Xu
[gmx-users] PTM force field Jianqing Xu
[gmx-users] PTM force field Jianqing Xu
[gmx-users] Pressure in gromacs Sushma Yadav
[gmx-users] Remove rotation from rmsd Mikhail Yustanov
[gmx-users] how to scale epsilon parameters of Lennard-Jones term in .top file Shuangyan Zhou
[gmx-users] charmm to gromacs Jernej Zidar
[gmx-users] MDP parameters for OPLS-aa + Verlet cutoff scheme Jernej Zidar
[gmx-users] Force Field for protein in water neha bharti
[gmx-users] Implicit and explicit solvation neha bharti
[gmx-users] g_hbond not running antoni borysik
[gmx-users] g_hbond not running antoni borysik
[gmx-users] g_hbond not running antoni borysik
[gmx-users] constrained bonds marzieh dehghan
[gmx-users] adding a new residue into an existing force field? marzieh dehghan
[gmx-users] use of g_hbond soumadwip ghosh
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15 soumadwip ghosh
[gmx-users] use of g_hbond soumadwip ghosh
[gmx-users] using g_hbond between index gps of specific interest soumadwip ghosh
[gmx-users] Re : using g_hbond between index gps of specific interest soumadwip ghosh
[gmx-users] using g_hbond between index gps of specific soumadwip ghosh
[gmx-users] .itp file of choline molecule soumadwip ghosh
[gmx-users] .itp file of choline molecule soumadwip ghosh
[gmx-users] problem during energy minimization soumadwip ghosh
[gmx-users] use of g_densmap soumadwip ghosh
[gmx-users] Using g_densmap soumadwip ghosh
[gmx-users] calculation of H-bonds soumadwip ghosh
[gmx-users] RDF calculation. soumadwip ghosh
[gmx-users] Protein distance with respect to box walls amin at imtech.res.in
[gmx-users] minimal distance between periodic images jinxin
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 97 jinxin
[gmx-users] g_spatial pratibha kapoor
[gmx-users] length of beta sheet pratibha kapoor
[gmx-users] Projection of trajectory onto PCs tarak karmakar
[gmx-users] Force between two groups of atoms ibrahim khalil
[gmx-users] initial velocities mah maz
[gmx-users] initial velocities mah maz
[gmx-users] initial velocities mah maz
[gmx-users] extracting velocities mah maz
[gmx-users] extracting velocities mah maz
[gmx-users] extracting velocities mah maz
[gmx-users] box siz mah maz
[gmx-users] box siz mah maz
[gmx-users] box siz mah maz
[gmx-users] parametrization of GABA for charmm27 jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] martinize.py: option for partly have elastic network on partly in the protein shivangi nangia
[gmx-users] Pulling code asasa qsqs
[gmx-users] Pulling code asasa qsqs
[gmx-users] Pulling asasa qsqs
[gmx-users] dangling bond error no matter what pdb file I use asasa qsqs
[gmx-users] trr file time/frame information gromacs query
[gmx-users] trr file time/frame information gromacs query
[gmx-users] Add new residue to forcefield fatemeh ramezani
[gmx-users] Fw: Add new residue to oplsaa force field fatemeh ramezani
[gmx-users] Add new residue to oplsaa force field fatemeh ramezani
[gmx-users] Question about water freezing when in contact to a solid surface ramon
[gmx-users] Question about water freezing when in contact to a solid surface (ramon) ramon
[gmx-users] odd replica excahnge leila salimi
[gmx-users] odd replica excahnge leila salimi
[gmx-users] biasing potential replica exchang for polymer leila salimi
[gmx-users] conversion of amber outputs to gromacs shahab shariati
[gmx-users] PCA of crystal structures neeru sharma
[gmx-users] Regarding the generation of intermolecule disulphide bond between two monomer subunits bipin singh
[gmx-users] Regarding the generation of intermolecule disulphide bond between two monomer subunits bipin singh
[gmx-users] How to change the multiplicity of a dihedral in FEP in Gromacs bipin singh
[gmx-users] Regarding Null free energy values in Free energy perturbation (bond force constant perturbation) bipin singh
[gmx-users] Error during entropy calculation bipin singh
[gmx-users] Fatal error during entropy calculation using g_anaeig bipin singh
[gmx-users] MMPBSA & GMXPBSA 2.1 andrea spitaleri
[gmx-users] core dumped elham tazikeh
[gmx-users] charge distribution elham tazikeh
[gmx-users] core dumped elham tazikeh
[gmx-users] charge distribution elham tazikeh
[gmx-users] farticle demanding about Small-Molecule Topologies elham tazikeh
[gmx-users] pdb information elham tazikeh
[gmx-users] charge distribution elham tazikeh
[gmx-users] pdb information elham tazikeh
[gmx-users] charge distriburion elham tazikeh
[gmx-users] A small Questions of umbrella samping vg
[gmx-users] A small Questions of umbrella samping vg
[gmx-users] Ions drifting jani vinod
[gmx-users] Ions drifting jani vinod
[gmx-users] Ions drifting jani vinod
[gmx-users] Ions drifting jani vinod
[gmx-users] Ions drifting jani vinod
[gmx-users] Ions drifting jani vinod
[gmx-users] Ions drifting jani vinod
[gmx-users] Gromacs 5.0.1 restart simulation wh
[gmx-users] Gromacs 5.0.1 restart simulation wh
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 10 wh
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 11 wh
[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 12 wh
[gmx-users] Define Heavy Water xy21hb
[gmx-users] conformational entropy xy21hb
[gmx-users] ProDrg xy21hb
[gmx-users] pdb2gmx atom not found xy21hb
[gmx-users] Fw: pdb2gmx atom not found xy21hb
[gmx-users] Problems about the WALL used with NPT systems: possible bug? xu zhijun
[gmx-users] Problems about the WALL used with NPT systems: possible bug? xu zhijun
[gmx-users] Problems about the WALL used with NPT systems: possible bug? xu zhijun
[gmx-users] Possible bugs: Problems about the 12-6 WALL used with NPT systems. xu zhijun
[gmx-users] Protein distance with respect to box walls xu zhijun
[gmx-users] -vsite hydrogen h.alizadeh at znu.ac.ir
[gmx-users] ProDrg Hadházi Ádám
[gmx-users] GTX 980 benchmark Hadházi Ádám
[gmx-users] questions about normal mode analysis in gromacs 凌未风
[gmx-users] how to scale epsilon parameters of Lennard-Jones term in .top file 周双艳
[gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file? 周双艳
[gmx-users] read trr file 石锐
[gmx-users] read trr file 石锐

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