June 2014 Archives by author

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Starting: Sun Jun 1 00:01:56 CEST 2014
Ending: Mon Jun 30 22:03:43 CEST 2014
Messages: 612

[gmx-users] Broken molecule across periodic boundary: "The sum of the two largest charge group radii (xxx) is larger than rlist (xxx)" yunshi11 .
[gmx-users] Broken molecule across periodic boundary: "The sum of the two largest charge group radii (xxx) is larger than rlist (xxx)" yunshi11 .
[gmx-users] help needed Mark Abraham
[gmx-users] Simplified picture: comments invited Mark Abraham
[gmx-users] Confusion about itp file generated by topolbuild Mark Abraham
[gmx-users] Eror: No parallel Ewald use PME instead! Mark Abraham
[gmx-users] Remove rotation around the center of mass Mark Abraham
[gmx-users] Remove rotation around the center of mass Mark Abraham
[gmx-users] Eror: No parallel Ewald use PME instead! Mark Abraham
[gmx-users] No such moleculetype ZN Mark Abraham
[gmx-users] Out of disk space Mark Abraham
[gmx-users] Remove rotation around the center of mass Mark Abraham
[gmx-users] Remove rotation around the center of mass Mark Abraham
[gmx-users] Intra molecular force correction for SPME Mark Abraham
[gmx-users] Eror: No parallel Ewald use PME instead! Mark Abraham
[gmx-users] Out of disk space Mark Abraham
[gmx-users] the water box become much larger in high temporature replicas after replica exchange simulation Mark Abraham
[gmx-users] Need some help with membrane simulation Mark Abraham
[gmx-users] 答复: the water box become much larger in high temporature replicas after replica exchange simulation Mark Abraham
[gmx-users] Intra molecular force correction for SPME Mark Abraham
[gmx-users] Intra molecular force correction for SPME Mark Abraham
[gmx-users] hardware problem of GPU? Mark Abraham
[gmx-users] Need some help with membrane simulation Mark Abraham
[gmx-users] hardware problem of GPU? Mark Abraham
[gmx-users] hardware problem of GPU? Mark Abraham
[gmx-users] hardware problem of GPU? Mark Abraham
[gmx-users] Why does the list keep unsubscribing me? Mark Abraham
[gmx-users] Tc grps, one group or two? Mark Abraham
[gmx-users] Why does the list keep unsubscribing me? Mark Abraham
[gmx-users] peculiar water behavior Mark Abraham
[gmx-users] interaction potential parameters and the forcefield.itp file Mark Abraham
[gmx-users] How to rotate box in editconf Mark Abraham
[gmx-users] interaction potential parameters and the forcefield.itp file Mark Abraham
[gmx-users] g_cluster for ligand clustering Mark Abraham
[gmx-users] g_cluster for ligand clustering Mark Abraham
[gmx-users] Too many LINCS warnings Mark Abraham
[gmx-users] Using specbond.dat in pdb2gmx Mark Abraham
[gmx-users] Using specbond.dat in pdb2gmx Mark Abraham
[gmx-users] tunepme does not start Mark Abraham
[gmx-users] tunepme does not start Mark Abraham
[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes Mark Abraham
[gmx-users] maximum number of specbonds? Mark Abraham
[gmx-users] Using specbond.dat in pdb2gmx Mark Abraham
[gmx-users] More suitable force field and water model Mark Abraham
[gmx-users] question about installation of gmx on Cray linux Mark Abraham
[gmx-users] Fwd: segmentation fault on gpus Mark Abraham
[gmx-users] Hamiltonian Replica Exchange Mark Abraham
[gmx-users] Carbon monoxide topology Mark Abraham
[gmx-users] no domain decomposition Mark Abraham
[gmx-users] Query regarding Domain decomposition Mark Abraham
[gmx-users] Query regarding Domain decomposition Mark Abraham
[gmx-users] REMD: A small bug in repl_ex.c and a related question Mark Abraham
[gmx-users] help with poor performance on gromacs on Cray linux Mark Abraham
[gmx-users] GROMACS 5.0 official release Mark Abraham
[gmx-users] hardware problem of GPU? Albert
[gmx-users] hardware problem of GPU? Albert
[gmx-users] hardware problem of GPU? Albert
[gmx-users] why deltaG=0? Albert
[gmx-users] why deltaG=0? Albert
[gmx-users] hardware problem of GPU? Albert
[gmx-users] hardware problem of GPU? Albert
[gmx-users] Eror: No parallel Ewald use PME instead! Ali Alizadeh
[gmx-users] Eror: No parallel Ewald use PME instead! Ali Alizadeh
[gmx-users] Eror: No parallel Ewald use PME instead! Ali Alizadeh
[gmx-users] Eror: No parallel Ewald use PME instead! Ali Alizadeh
[gmx-users] Eror: No parallel Ewald use PME instead! Ali Alizadeh
[gmx-users] New Molecule Topology Todor Antonijevic
[gmx-users] New Molecule Topology Todor Antonijevic
[gmx-users] How to calculate Box Vectors in the last line of the .gro file? Todor Antonijevic
[gmx-users] Welcome to the "gromacs.org_gmx-users" mailing list (Digest mode) Shahnaz Ashrafpour
[gmx-users] Adding residue at two end of DNA Mehdi Bagherpour
[gmx-users] isothermal-isometric ensemble on gromacs Antonio Baptista
[gmx-users] How to exit cluster during the simulation Batdorj Batsaikhan
[gmx-users] How to exit cluster during the simulation Batdorj Batsaikhan
[gmx-users] How to extend Amber FF parameters of Lipids Batdorj Batsaikhan
[gmx-users] How to fix protein went out water? Batdorj Batsaikhan
[gmx-users] How to fix protein went out water? Batdorj Batsaikhan
[gmx-users] Net charge neutrality during thermodynamic integration Leandro Bortot
[gmx-users] Simulation of wild and mutant types of HSA protein Francesco Carbone
[gmx-users] from coarse-grained to all atoms Francesco Carbone
[gmx-users] the water box become much larger in high temporature replicas after replica exchange simulation Dr. Vitaly Chaban
[gmx-users] Reactive force field Dr. Vitaly Chaban
[gmx-users] Martini in Gromacs Dr. Vitaly Chaban
[gmx-users] how many groups shall I use to control the temperature? Dr. Vitaly Chaban
[gmx-users] How to exit cluster during the simulation Dr. Vitaly Chaban
[gmx-users] Regarding lipid topology Dr. Vitaly Chaban
[gmx-users] More suitable force field and water model Dr. Vitaly Chaban
[gmx-users] NPT MD and Berendsen Dr. Vitaly Chaban
[gmx-users] Charges & non-bonded interaction values usage in different force fields Dr. Vitaly Chaban
[gmx-users] Carbon monoxide topology Dr. Vitaly Chaban
[gmx-users] EDLC simulation using Gromacs Dr. Vitaly Chaban
[gmx-users] CNT with BN co doping Dr. Vitaly Chaban
[gmx-users] How to calculate Box Vectors in the last line of the .gro file? Dr. Vitaly Chaban
[gmx-users] Questions regarding converting .GRO files to .TOP files Dr. Vitaly Chaban
[gmx-users] CNT with BN co doping Dr. Vitaly Chaban
[gmx-users] REMD: A small bug in repl_ex.c and a related question Suman Chakrabarty
[gmx-users] topology file Andy Chao
[gmx-users] EDLC simulation using Gromacs Andy Chao
[gmx-users] Questions regarding converting .GRO files to .TOP files Andy Chao
[gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 128 Andy Chao
[gmx-users] CHARMM36 and carbohydrates Timothy Click
[gmx-users] Problem with T-coupling. Udaya Dahal
[gmx-users] -inf potential with TPIC João M. Damas
[gmx-users] -inf potential with TPIC João M. Damas
[gmx-users] dssp Uma Devi
[gmx-users] dssp Uma Devi
[gmx-users] DSSP -regarding Uma Devi
[gmx-users] Reactive force field Nilesh Dhumal
[gmx-users] Reactive force field Nilesh Dhumal
[gmx-users] Velocities from checkpoint Nilesh Dhumal
[gmx-users] Numbering coordinate file Mihaela Drenscko
[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids Melsa Rose Ducut
[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids Melsa Rose Ducut
[gmx-users] specbond identified by pdb2gmx but not added to topology Vedat Durmaz
[gmx-users] specbond identified by pdb2gmx but not added to topology Vedat Durmaz
[gmx-users] (no subject) Vedat Durmaz
[gmx-users] (no subject) Vedat Durmaz
[gmx-users] (no subject) Vedat Durmaz
[gmx-users] Hamiltonian Replica Exchange Thomas Evangelidis
[gmx-users] Hamiltonian Replica Exchange Thomas Evangelidis
[gmx-users] helix crossing angle Natalia Alveal F.
[gmx-users] Interaction energy between helices Natalia Alveal F.
[gmx-users] Hbonds per residue Natalia Alveal F.
[gmx-users] Interaction energy between helices Natalia Alveal F.
[gmx-users] Out of disk space Carlos Familia
[gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 61 Andrey Frolov
[gmx-users] ligand topology for opls.aa Andrey Frolov
[gmx-users] g_cluster Neha Gandhi
[gmx-users] Martini in Gromacs Neha Gandhi
[gmx-users] Adding polyatomic ions using genion or genbox .. Alberto Sergio Garay
[gmx-users] Water-Zinc interactions Vito Genna
[gmx-users] Water-Zinc interactions Vito Genna
[gmx-users] About pdb2gmx and cyclic peptides Ivan Gladich
[gmx-users] About pdb2gmx and cyclic peptides Ivan Gladich
[gmx-users] Angle constraints independent on bond constraints Fabian Gottwald
[gmx-users] How to rotate box in editconf Rini Gupta
[gmx-users] the water box become much larger in high temporature replicas after replica exchange simulation #ZHANG HAIPING#
[gmx-users] 答复: the water box become much larger in high temporature replicas after replica exchange simulation #ZHANG HAIPING#
[gmx-users] ligand_protein binding free energy caculation using gromacs #ZHANG HAIPING#
[gmx-users] (no subject) #ZHANG HAIPING#
[gmx-users] 答复: ligand_protein binding free energy caculation using gromacs #ZHANG HAIPING#
[gmx-users] 答复: (no subject) #ZHANG HAIPING#
[gmx-users] continue a crashed run, but change the output frequency #ZHANG HAIPING#
[gmx-users] how to set number of exchange attempts in replica exchange simulation #ZHANG HAIPING#
[gmx-users] pH based calculation João Henriques
[gmx-users] Error in Umbrella sampling Maziya Ibrahim
[gmx-users] Polymers James
[gmx-users] Polymers James
[gmx-users] NPT MD and Berendsen Francis Jing
[gmx-users] How to exit cluster during the simulation Monoj Mon Kalita
[gmx-users] Atom was not found Monoj Mon Kalita
[gmx-users] g_gyrate or g_polystat Argyrios Karatrantos
[gmx-users] Regarding protein folding kinetics Singam Karthick
[gmx-users] folding kinetics from SMD simulation Singam Karthick
[gmx-users] dssp Gurunath Katagi
[gmx-users] Hydrogen bond existence map Nidhi Katyal
[gmx-users] g_hbond Nidhi Katyal
[gmx-users] Need some help with membrane simulation Ali Khan
[gmx-users] Need some help with membrane simulation Ali Khan
[gmx-users] Need some help with membrane simulation Ali Khan
[gmx-users] Need some help with membrane simulation Ali Khan
[gmx-users] Need some help with membrane simulation Ali Khan
[gmx-users] Need some help with membrane simulation Ali Khan
[gmx-users] g_clustsize Raisa Kociurzynski
[gmx-users] How to fix protein went out water? Thales Kronenberger
[gmx-users] Indicators of protein stability Pappu Kumar
[gmx-users] pH based calculation Praveen Kumar
[gmx-users] Error in mdrun Praveen Kumar
[gmx-users] Hamiltonian Replica Exchange HANNIBAL LECTER
[gmx-users] crystal, nrexcl Justin Lemkul
[gmx-users] About free enrgy calculation Justin Lemkul
[gmx-users] MD for extracellular and transmembrane system Justin Lemkul
[gmx-users] need you help - New user Justin Lemkul
[gmx-users] Prevent protein rotation - rectangular box Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Water-Zinc interactions Justin Lemkul
[gmx-users] Problem with T-coupling. Justin Lemkul
[gmx-users] Prevent protein rotation - rectangular box Justin Lemkul
[gmx-users] Prevent protein rotation - rectangular box Justin Lemkul
[gmx-users] rlist for implicit water Justin Lemkul
[gmx-users] Non-bonded Interactions Justin Lemkul
[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids Justin Lemkul
[gmx-users] Confusion about itp file generated by topolbuild Justin Lemkul
[gmx-users] Simulation of wild and mutant types of HSA protein Justin Lemkul
[gmx-users] isothermal-isometric ensemble on gromacs Justin Lemkul
[gmx-users] rlist for implicit water Justin Lemkul
[gmx-users] Non-bonded interactions Justin Lemkul
[gmx-users] Error in mdrun Justin Lemkul
[gmx-users] No such moleculetype ZN Justin Lemkul
[gmx-users] g_membed itp file Justin Lemkul
[gmx-users] Confusion about itp file generated by topolbuild Justin Lemkul
[gmx-users] Prevent protein rotation - rectangular box Justin Lemkul
[gmx-users] Eror: No parallel Ewald use PME instead! Justin Lemkul
[gmx-users] No such moleculetype for ZN Justin Lemkul
[gmx-users] No such moleculetype ZN Justin Lemkul
[gmx-users] help gm1 Justin Lemkul
[gmx-users] Prevent protein rotation - rectangular box Justin Lemkul
[gmx-users] Need some help with membrane simulation Justin Lemkul
[gmx-users] Need some help with membrane simulation Justin Lemkul
[gmx-users] Need some help with membrane simulation Justin Lemkul
[gmx-users] problem with membrane simulation Justin Lemkul
[gmx-users] ligand_protein binding free energy caculation using gromacs Justin Lemkul
[gmx-users] specbond identified by pdb2gmx but not added to topology Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] why deltaG=0? Justin Lemkul
[gmx-users] charge groups Justin Lemkul
[gmx-users] why deltaG=0? Justin Lemkul
[gmx-users] Some confusion related to extending a simulation Justin Lemkul
[gmx-users] charge groups Justin Lemkul
[gmx-users] Regarding membrane construction Justin Lemkul
[gmx-users] Problem in NVT equilibration Justin Lemkul
[gmx-users] helix crossing angle Justin Lemkul
[gmx-users] Regarding membrane construction Justin Lemkul
[gmx-users] -inf potential with TPIC Justin Lemkul
[gmx-users] charge groups Justin Lemkul
[gmx-users] Regarding membrane construction Justin Lemkul
[gmx-users] Martini in Gromacs Justin Lemkul
[gmx-users] -inf potential with TPIC Justin Lemkul
[gmx-users] -inf potential with TPIC Justin Lemkul
[gmx-users] -inf potential with TPIC Justin Lemkul
[gmx-users] C36 cyclopropanated lipids in Gromacs Justin Lemkul
[gmx-users] C36 cyclopropanated lipids in Gromacs Justin Lemkul
[gmx-users] GROMOS96 user guide Justin Lemkul
[gmx-users] virtual site independent from other structure Justin Lemkul
[gmx-users] Regarding membrane construction Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] Interaction energy between helices Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Energy minimisation step in Lipid protein simulation Justin Lemkul
[gmx-users] how many groups shall I use to control the temperature? Justin Lemkul
[gmx-users] -inf potential with TPIC Justin Lemkul
[gmx-users] Energy minimisation step in Lipid protein simulation Justin Lemkul
[gmx-users] Interaction energy between helices Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] Adding polyatomic ions using genion or genbox .. Justin Lemkul
[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes Justin Lemkul
[gmx-users] peculiar water behavior Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] How to extend Amber FF parameters of Lipids Justin Lemkul
[gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] How to fix protein went out water? Justin Lemkul
[gmx-users] How to fix protein went out water? Justin Lemkul
[gmx-users] peculiar water behavior Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] peculiar water behavior Justin Lemkul
[gmx-users] CHARMM36 and carbohydrates Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] grompp Justin Lemkul
[gmx-users] min in vacuum Justin Lemkul
[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes Justin Lemkul
[gmx-users] grompp Justin Lemkul
[gmx-users] problem with Charmm36 ff Justin Lemkul
[gmx-users] Atom was not found Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] problem with Charmm36 ff Justin Lemkul
[gmx-users] pdb2gmx Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] problem with Charmm36 ff Justin Lemkul
[gmx-users] genbox solvate insert_molecules Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] EnMin & constraints: Hamletic doubt Justin Lemkul
[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position Justin Lemkul
[gmx-users] More suitable force field and water model Justin Lemkul
[gmx-users] pdb2gmx Justin Lemkul
[gmx-users] EnMin & constraints: Hamletic doubt Justin Lemkul
[gmx-users] Velocities from checkpoint Justin Lemkul
[gmx-users] .rtp files Justin Lemkul
[gmx-users] Using specbond.dat in pdb2gmx Justin Lemkul
[gmx-users] g_hbond Justin Lemkul
[gmx-users] More suitable force field and water model Justin Lemkul
[gmx-users] EnMin & constraints: Hamletic doubt Justin Lemkul
[gmx-users] EnMin & constraints: Hamletic doubt Justin Lemkul
[gmx-users] continue a crashed run, but change the output frequency Justin Lemkul
[gmx-users] EnMin & constraints: Hamletic doubt Justin Lemkul
[gmx-users] pdb2gmx Justin Lemkul
[gmx-users] Intramolecular interactions Justin Lemkul
[gmx-users] help with poor performance on gromacs on Cray linux Justin Lemkul
[gmx-users] Pressure scaling more than 1% please help new user Justin Lemkul
[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters Justin Lemkul
[gmx-users] Fwd: segmentation fault on gpus Justin Lemkul
[gmx-users] Error in Umbrella sampling Justin Lemkul
[gmx-users] Fwd: segmentation fault on gpus Justin Lemkul
[gmx-users] Fwd: segmentation fault on gpus Justin Lemkul
[gmx-users] Fwd: segmentation fault on gpus Justin Lemkul
[gmx-users] proteins break up in simulation Justin Lemkul
[gmx-users] topology file Justin Lemkul
[gmx-users] Unit of force constants and adding new residue. Justin Lemkul
[gmx-users] pdb2gmx Justin Lemkul
[gmx-users] no domain decomposition Justin Lemkul
[gmx-users] mdrun error Justin Lemkul
[gmx-users] Energy minimization has stopped, but the forces have not converged Justin Lemkul
[gmx-users] cholesterol bond rotation Justin Lemkul
[gmx-users] hbond correspondence between hbond.log and hbmap.xpm Justin Lemkul
[gmx-users] About pdb2gmx and cyclic peptides Justin Lemkul
[gmx-users] how to set number of exchange attempts in replica exchange simulation Justin Lemkul
[gmx-users] Possible trjconv malfunction? Justin Lemkul
[gmx-users] Can i change the dihedral angle during MD Justin Lemkul
[gmx-users] Possible trjconv malfunction? Justin Lemkul
[gmx-users] grompp does not find atomtype Justin Lemkul
[gmx-users] grompp does not find atomtype Justin Lemkul
[gmx-users] Strange error message when trying to preprocess a cyclotide in GROMACS Justin Lemkul
[gmx-users] help with poor performance on gromacs on Cray linux Justin Lemkul
[gmx-users] Carbon monoxide topology- Charges & non-bonded interaction values usage Justin Lemkul
[gmx-users] grompp does not find atomtype Justin Lemkul
[gmx-users] grompp does not find atomtype Justin Lemkul
[gmx-users] How to calculate Box Vectors in the last line of the .gro file? Justin Lemkul
[gmx-users] Questions regarding converting .GRO files to .TOP files Justin Lemkul
[gmx-users] grompp does not find atomtype Justin Lemkul
[gmx-users] ionic liquids Justin Lemkul
[gmx-users] C36 cyclopropanated lipids in Gromacs Ariel Leong
[gmx-users] C36 cyclopropanated lipids in Gromacs Ariel Leong
[gmx-users] C36 cyclopropanated lipids in Gromacs Ariel Leong
[gmx-users] Calculating shifted VDW energies Michael Lerner
[gmx-users] Calculating shifted VDW energies Michael Lerner
[gmx-users] lipid bilayer of POPC and cholesterol available for download? Gunther Lukat
[gmx-users] AMBER99SB-ILDNP and AMBER99SB*-ILDNP Grom Macs
[gmx-users] crystal, nrexcl Chetan Mahajan
[gmx-users] help needed Chetan Mahajan
[gmx-users] help needed Chetan Mahajan
[gmx-users] Simplified picture: comments invited Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] peculiar water behavior Chetan Mahajan
[gmx-users] Interpreting energy drift Chetan Mahajan
[gmx-users] NPT MD and Berendsen Chetan Mahajan
[gmx-users] NPT MD and Berendsen Chetan Mahajan
[gmx-users] NPT MD and Berendsen Chetan Mahajan
[gmx-users] NPT MD and Berendsen Chetan Mahajan
[gmx-users] no domain decomposition Chetan Mahajan
[gmx-users] no domain decomposition Chetan Mahajan
[gmx-users] gromacs genbox SPC water population Chetan Mahajan
[gmx-users] gromacs genbox SPC water population Chetan Mahajan
[gmx-users] gromacs genbox SPC water population Chetan Mahajan
[gmx-users] dssp Erik Marklund
[gmx-users] Hbonds per residue Erik Marklund
[gmx-users] Hydrogen bond existence map Erik Marklund
[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters Nikolaos Michelarakis
[gmx-users] pH simulation Lovika Moudgil
[gmx-users] pH simulation Lovika Moudgil
[gmx-users] mdrun error Lovika Moudgil
[gmx-users] mdrun error Lovika Moudgil
[gmx-users] dynamic selection memory allocation problem Teemu Murtola
[gmx-users] dynamic selection memory allocation problem Teemu Murtola
[gmx-users] dynamic selection memory allocation problem Teemu Murtola
[gmx-users] Possible trjconv malfunction? Christopher Neale
[gmx-users] Possible trjconv malfunction? Christopher Neale
[gmx-users] Prevent protein rotation - rectangular box Steven Neumann
[gmx-users] Prevent protein rotation - rectangular box Steven Neumann
[gmx-users] Prevent protein rotation - rectangular box Steven Neumann
[gmx-users] Prevent protein rotation - rectangular box Steven Neumann
[gmx-users] Prevent protein rotation - rectangular box Steven Neumann
[gmx-users] Prevent protein rotation - rectangular box Steven Neumann
[gmx-users] question about topolbuild Hui Wen Ng
[gmx-users] question about topolbuild Hui Wen Ng
[gmx-users] How to exit cluster during the simulation Thomas C. O'Connor
[gmx-users] Simulation of wild and mutant types of HSA protein Negar Parvizi
[gmx-users] Simulation of wild and mutant types of HSA protein Negar Parvizi
[gmx-users] charge groups Negar Parvizi
[gmx-users] Fw: charge groups Negar Parvizi
[gmx-users] charge groups Negar Parvizi
[gmx-users] GROMOS96 user guide Negar Parvizi
[gmx-users] .rtp files Negar Parvizi
[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids Thomas Piggot
[gmx-users] problem with Charmm36 ff Thomas Piggot
[gmx-users] optimize cpu with gpu node for gromacs Szilárd Páll
[gmx-users] optimize cpu with gpu node for gromacs Szilárd Páll
[gmx-users] Fwd: segmentation fault on gpus Szilárd Páll
[gmx-users] Hamiltonian Replica Exchange Szilárd Páll
[gmx-users] Hamiltonian Replica Exchange Szilárd Páll
[gmx-users] Hamiltonian Replica Exchange Szilárd Páll
[gmx-users] Thanks to the developers heroic efforts! Szilárd Páll
[gmx-users] Calculating the interaction energy as well individual energy? RJ
[gmx-users] grompp Meenakshi Rajput
[gmx-users] grompp Meenakshi Rajput
[gmx-users] More suitable force field and water model Mohsen Ramezanpour
[gmx-users] More suitable force field and water model Mohsen Ramezanpour
[gmx-users] More suitable force field and water model Mohsen Ramezanpour
[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS Rashmi
[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS Rashmi
[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS Rashmi
[gmx-users] g_sham segmentation fault Soumya Lipsa Rath
[gmx-users] I am still being regularly unsubscribed from the gromacs.org mailing list Bruce D. Ray
[gmx-users] Regarding membrane construction Venkat Reddy
[gmx-users] Regarding membrane construction Venkat Reddy
[gmx-users] Problem in NVT equilibration Venkat Reddy
[gmx-users] Problem in NVT equilibration Venkat Reddy
[gmx-users] Regarding membrane construction Venkat Reddy
[gmx-users] Regarding membrane construction Venkat Reddy
[gmx-users] Regarding membrane construction Venkat Reddy
[gmx-users] (no subject) Venkat Reddy
[gmx-users] Regarding membrane construction Venkat Reddy
[gmx-users] Regarding lipid topology Venkat Reddy
[gmx-users] grompp Venkat Reddy
[gmx-users] isothermal-isometric ensemble on gromacs Carlos Navarrro Retamal
[gmx-users] How to exit cluster during the simulation Carlos Navarrro Retamal
[gmx-users] Charges & non-bonded interaction values usage in different force fields Rj
[gmx-users] hbond correspondence between hbond.log and hbmap.xpm Zheng Ruan
[gmx-users] Why does the list keep unsubscribing me? X Rules
[gmx-users] Why does the list keep unsubscribing me? X Rules
[gmx-users] Why does the list keep unsubscribing me? X Rules
[gmx-users] Why does the list keep unsubscribing me? X Rules
[gmx-users] (no subject) AMNINDER SINGH
[gmx-users] packing lipid around protein Catarina Santos
[gmx-users] Mixed 1-4 scaling factors Liel Sapir
[gmx-users] Possible trjconv malfunction? Nathan Scott
[gmx-users] Possible trjconv malfunction? Nathan Scott
[gmx-users] Possible trjconv malfunction? Nathan Scott
[gmx-users] Possible trjconv malfunction? Nathan Scott
[gmx-users] Water-Zinc interactions Steve Seibold
[gmx-users] Acpyte with opls-aa Saman Shahriyari
[gmx-users] ligand topology for opls.aa Saman Shahriyari
[gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc Saman Shahriyari
[gmx-users] Confusion about itp file generated by topolbuild Bikramjit Sharma
[gmx-users] Fw: Confusion about itp file generated by topolbuild Bikramjit Sharma
[gmx-users] Confusion about itp file generated by topolbuild Bikramjit Sharma
[gmx-users] Net charge neutrality during thermodynamic integration Michael Shirts
[gmx-users] NPT MD and Berendsen Michael Shirts
[gmx-users] Intramolecular interactions Robson da Silva
[gmx-users] Error in mdrun Harshkumar Singh
[gmx-users] Error in mdrun Harshkumar Singh
[gmx-users] Energy minimization has stopped, but the forces have not converged Iris Nira Smith
[gmx-users] compile single src file Eric Smoll
[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS David van der Spoel
[gmx-users] g_clustsize David van der Spoel
[gmx-users] EnMin & constraints: Hamletic doubt Nicola Staffolani
[gmx-users] EnMin & constraints: Hamletic doubt Nicola Staffolani
[gmx-users] EnMin & constraints: Hamletic doubt Nicola Staffolani
[gmx-users] EnMin & constraints: Hamletic doubt Nicola Staffolani
[gmx-users] EnMin & constraints: Hamletic doubt Nicola Staffolani
[gmx-users] EnMin & constraints: Hamletic doubt Nicola Staffolani
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Using specbond.dat in pdb2gmx Matthew Stancea
[gmx-users] Strange error message when trying to preprocess a cyclotide in GROMACS Matthew Stancea
[gmx-users] virtual site independent from other structure Linlin Sun
[gmx-users] (no subject) Balasubramanian Suriyanarayanan
[gmx-users] Problem in NVT equilibration Balasubramanian Suriyanarayanan
[gmx-users] Problem in NVT equilibration Balasubramanian Suriyanarayanan
[gmx-users] NVT equilibration - error message Balasubramanian Suriyanarayanan
[gmx-users] (no subject) Balasubramanian Suriyanarayanan
[gmx-users] Packing lipid around protein Balasubramanian Suriyanarayanan
[gmx-users] (no subject) Balasubramanian Suriyanarayanan
[gmx-users] packing lipid around protein Balasubramanian Suriyanarayanan
[gmx-users] (no subject) Balasubramanian Suriyanarayanan
[gmx-users] packing lipid around protein Balasubramanian Suriyanarayanan
[gmx-users] Energy minimisation step in Lipid protein simulation Balasubramanian Suriyanarayanan
[gmx-users] energy minimisation step in lipid protein simulation Balasubramanian Suriyanarayanan
[gmx-users] energy minimisation step in protein lipid simulation Balasubramanian Suriyanarayanan
[gmx-users] (no subject) Balasubramanian Suriyanarayanan
[gmx-users] energy minimisation in lipid protein simulation Balasubramanian Suriyanarayanan
[gmx-users] (no subject) Balasubramanian Suriyanarayanan
[gmx-users] Energy minimisation step in Lipid protein simulation Balasubramanian Suriyanarayanan
[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids Piggot T.
[gmx-users] Need some help with membrane simulation Piggot T.
[gmx-users] GROMOS96 user guide Piggot T.
[gmx-users] need you help - New user MUSYOKA THOMMAS
[gmx-users] help with poor performance on gromacs on Cray linux Tom
[gmx-users] question about installation of gmx on Cray linux Tom
[gmx-users] help with poor performance on gromacs on Cray linux Tom
[gmx-users] help with poor performance on gromacs on Cray linux Tom
[gmx-users] need you help - New user Urszula Uciechowska
[gmx-users] need you help - New user Urszula Uciechowska
[gmx-users] rlist for implicit water Urszula Uciechowska
[gmx-users] rlist for implicit water Urszula Uciechowska
[gmx-users] min in vacuum Urszula Uciechowska
[gmx-users] Pressure scaling more than 1% please help new user Urszula Uciechowska
[gmx-users] Gromacs & GPU no longer working together Rafael I. Silverman y de la Vega
[gmx-users] Gromacs & GPU no longer working together Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] -inf potential with TPIC Rafael I. Silverman y de la Vega
[gmx-users] tunepme does not start Soren Wacker
[gmx-users] tunepme does not start Soren Wacker
[gmx-users] genbox solvate insert_molecules Soren Wacker
[gmx-users] maximum number of specbonds? Soren Wacker
[gmx-users] maximum number of specbonds? Soren Wacker
[gmx-users] Thanks to the developers heroic efforts! Mirco Wahab
[gmx-users] Soln to visualised long molecule bonds across box in VMD Dallas Warren
[gmx-users] Numbering coordinate file Dallas Warren
[gmx-users] Polymers Tsjerk Wassenaar
[gmx-users] Polymers Tsjerk Wassenaar
[gmx-users] dssp Tsjerk Wassenaar
[gmx-users] truncated octahedron box vector angles and number of waters Tsjerk Wassenaar
[gmx-users] g_clustsize Tsjerk Wassenaar
[gmx-users] Velocities from checkpoint Tsjerk Wassenaar
[gmx-users] EDLC simulation using Gromacs Tsjerk Wassenaar
[gmx-users] cholesterol bond rotation Michael Weiner
[gmx-users] cholesterol bond rotation Michael Weiner
[gmx-users] Intra molecular force correction for SPME Sumith YD
[gmx-users] Intra molecular force correction for SPME Sumith YD
[gmx-users] Intra molecular force correction for SPME Sumith YD
[gmx-users] Fwd: Fw: Confusion about itp file generated by topolbuild Sushma Yadav
[gmx-users] Confusion about itp file generated by topolbuild Sushma Yadav
[gmx-users] Martini in Gromacs Zhi Yue
[gmx-users] Hydrogen bond existence map andrea
[gmx-users] Free energy change upon residue mutation in protein tomas bastys
[gmx-users] Fwd: segmentation fault on gpus ram bio
[gmx-users] Fwd: segmentation fault on gpus ram bio
[gmx-users] Fwd: segmentation fault on gpus ram bio
[gmx-users] Fwd: segmentation fault on gpus ram bio
[gmx-users] Fwd: segmentation fault on gpus ram bio
[gmx-users] pdb2gmx mirko busato
[gmx-users] pdb2gmx mirko busato
[gmx-users] pdb2gmx mirko busato
[gmx-users] pdb2gmx mirko busato
[gmx-users] g_cluster for ligand clustering mbalint at caesar.elte.hu
[gmx-users] Unit of force constants and adding new residue. Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] grompp does not find atomtype Dawid das
[gmx-users] confusion of forward and backward FEP in Gromacs-4.6.5 dbaogen
[gmx-users] confusion of forward and backward FEP in Gromacs-4.6.5 dbaogen
[gmx-users] topolbuild marzieh dehghan
[gmx-users] pH simulation rajat desikan
[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes sucharita dey
[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS sucharita dey
[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS sucharita dey
[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes sucharita dey
[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes sucharita dey
[gmx-users] MD for extracellular and transmembrane system rahul dhakne
[gmx-users] optimize cpu with gpu node for gromacs rahul dhakne
[gmx-users] exchange kinetic dina dusti
[gmx-users] dynamic selection memory allocation problem gigo
[gmx-users] dynamic selection memory allocation problem gigo
[gmx-users] dynamic selection memory allocation problem gigo
[gmx-users] dynamic selection memory allocation problem gigo
[gmx-users] Remove rotation around the center of mass gmail
[gmx-users] Remove rotation around the center of mass gmail
[gmx-users] Some confusion related to extending a simulation bharat gupta
[gmx-users] Salt Bridge bharat gupta
[gmx-users] problem with membrane simulation free882 at inwind.it
[gmx-users] interaction potential parameters and the forcefield.itp file akari karin
[gmx-users] interaction potential parameters and the forcefield.itp file akari karin
[gmx-users] CNT with BN co doping akari karin
[gmx-users] CNT with BN co doping akari karin
[gmx-users] Query regarding Domain decomposition suhani nagpal
[gmx-users] Query regarding Domain decomposition suhani nagpal
[gmx-users] Query regarding Domain decomposition suhani nagpal
[gmx-users] g_dielectric errors for getting frequency dependent dielectric constants 550931258 at qq.com
[gmx-users] truncated octahedron box vector angles and number of waters gromacs query
[gmx-users] (no subject) fatemeh ramezani
[gmx-users] Mdrun kill despite the use of nohup fatemeh ramezani
[gmx-users] Need some help with membrane simulation lloyd riggs
[gmx-users] specbond identified by pdb2gmx but not added to topology lloyd riggs
[gmx-users] specbond identified by pdb2gmx but not added to topology lloyd riggs
[gmx-users] About free enrgy calculation vidhya sankar
[gmx-users] g_rmsdist ignores -equiv option sebastian.buchenberg
[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position neeru sharma
[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position neeru sharma
[gmx-users] Calculating dielectric constant using g_dipoles and g_dielectric bipin singh
[gmx-users] Regarding the difference between g_dipoles and g_dielectric calculations bipin singh
[gmx-users] about thermal intergation calculations mircial at sjtu.edu.cn
[gmx-users] hydrogen bond analysis sunyeping
[gmx-users] proteins break up in simulation sunyeping
[gmx-users] No such moleculetype ZN elham tazikeh
[gmx-users] (no subject) elham tazikeh
[gmx-users] No such moleculetype for ZN elham tazikeh
[gmx-users] No such moleculetype ZN elham tazikeh
[gmx-users] problem with Charmm36 ff Esteban.Pedrueza at uv.es
[gmx-users] problem with Charmm36 ff Esteban.Pedrueza at uv.es
[gmx-users] problem with Charmm36 ff Esteban.Pedrueza at uv.es
[gmx-users] help gm1 leonardo villalba
[gmx-users] lipid bilayer of POPC and cholesterol available for download? william wang
[gmx-users] lipid bilayer of POPC and cholesterol available for download william wang
[gmx-users] Can i change the dihedral angle during MD xiao
[gmx-users] g_membed itp file h.alizadeh at znu.ac.ir
[gmx-users] g_membed itp file h.alizadeh at znu.ac.ir
[gmx-users] Too many LINCS warnings h.alizadeh at znu.ac.ir
[gmx-users] Atom was not found h.alizadeh at znu.ac.ir
[gmx-users] Fwd: ion mutation in FEP SEMRAN İPEK
[gmx-users] ZN-His coordinate bond 陈功
[gmx-users] Regarding membrane construction 陈功
[gmx-users] Regarding membrane construction 陈功
[gmx-users] Tc grps, one group or two? 陈功
[gmx-users] Tc grps, one group or two? 陈功
[gmx-users] how many groups shall I use to control the temperature? 陈功
[gmx-users] how many groups shall I use to control the temperature? 陈功
[gmx-users] How to exit cluster during the simulation 陈功
[gmx-users] Non-bonded Interactions 라지브간디
[gmx-users] Non-bonded interactions 라지브간디
[gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 103 라지브간디
[gmx-users] Re:Carbon monoxide topology- Charges & non-bonded interaction values usage 라지브간디

Last message date: Mon Jun 30 22:03:43 CEST 2014
Archived on: Mon Jun 30 22:03:43 CEST 2014

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