June 2011 Archives by author

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Starting: Wed Jun 1 00:23:12 CEST 2011
Ending: Thu Jun 30 20:20:52 CEST 2011
Messages: 819

[gmx-users] Problem with 512 membrane Du Jiangfeng (BIOCH)
[gmx-users] EM broke protein-lipid system Du Jiangfeng (BIOCH)
[gmx-users] Re: Indexing problem when using genconf Ryan S Davis (rsdavis1)
[gmx-users] Windows 7 Chathurika Abeyrathne
[gmx-users] Autocorrelation of dipole moment Chathurika Abeyrathne
[gmx-users] Autocorrelation of dipole moment Chathurika Abeyrathne
[gmx-users] scaling non-bonded interactions Mark Abraham
[gmx-users] gmx4.5.4 installation help Mark Abraham
[gmx-users] g_rdf query Mark Abraham
[gmx-users] error: Only triclinic boxes... Mark Abraham
[gmx-users] option -pbc in trjconv Mark Abraham
[gmx-users] option -pbc in trjconv Mark Abraham
[gmx-users] FFT plan mismatch with mdrun_mpi Mark Abraham
[gmx-users] Why does the -append option exist? Mark Abraham
[gmx-users] g_rotacf Mark Abraham
[gmx-users] g_rotacf Mark Abraham
[gmx-users] Re: Indexing problem when using genconf Mark Abraham
[gmx-users] Why does the -append option exist? Mark Abraham
[gmx-users] Why does the -append option exist? Mark Abraham
[gmx-users] Why does the -append option exist? Mark Abraham
[gmx-users] Why does the -append option exist? Mark Abraham
[gmx-users] Negative pressure Mark Abraham
[gmx-users] problem in g_density Mark Abraham
[gmx-users] Gromacs-4.5.4 install error Mark Abraham
[gmx-users] reg PME usage Mark Abraham
[gmx-users] reg PME usage Mark Abraham
[gmx-users] Force field parameters for phosphorylated tyrosine Mark Abraham
[gmx-users] Water Potential Energy Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 84 Mark Abraham
[gmx-users] data points missing Mark Abraham
[gmx-users] Re: data points missing Mark Abraham
[gmx-users] g_sas index files/hydrogen bonds Mark Abraham
[gmx-users] rdf Mark Abraham
[gmx-users] local pressure calcuation for Gromacs-4.5 Mark Abraham
[gmx-users] Questions about GB parameters Mark Abraham
[gmx-users] Water Potential Energy Mark Abraham
[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ? Mark Abraham
[gmx-users] Position restraints Mark Abraham
[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA Mark Abraham
[gmx-users] an error for .tpr files Mark Abraham
[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA Mark Abraham
[gmx-users] Implicit solvent calculatiom Mark Abraham
[gmx-users] Gromacs to Amber trajectory Mark Abraham
[gmx-users] load imbalance Mark Abraham
[gmx-users] monitoring the water molecules Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97 Mark Abraham
[gmx-users] thermostats Mark Abraham
[gmx-users] Re: Gromacs error Mark Abraham
[gmx-users] What does it mean by saying mca: base: component_find: unable to open.... Mark Abraham
[gmx-users] Re: Gromacs error Mark Abraham
[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field Mark Abraham
[gmx-users] load imbalance Mark Abraham
[gmx-users] is lincs used with virtual hydrogens? Mark Abraham
[gmx-users] is lincs used with virtual hydrogens? Mark Abraham
[gmx-users] need tip3p.gro for charmm force field Mark Abraham
[gmx-users] Windows 7 Mark Abraham
[gmx-users] reg g_hbond Mark Abraham
[gmx-users] is lincs used with virtual hydrogens? Mark Abraham
[gmx-users] Re: LINCS WARNING relative constraint deviation Mark Abraham
[gmx-users] Re: LINCS WARNING relative constraint deviation Mark Abraham
[gmx-users] NVT equilibration of DMSO solvent (Charmm all-atom force field) Mark Abraham
[gmx-users] EM broke protein-lipid system Mark Abraham
[gmx-users] NMR chemical shift restraints Mark Abraham
[gmx-users] Re: Increase in charge after adding the ligand Mark Abraham
[gmx-users] Re: Error during executing the protein ligand tutorial Mark Abraham
[gmx-users] Re: Error during executing the protein ligand tutorial Mark Abraham
[gmx-users] minimum image violation Mark Abraham
[gmx-users] Re: Error during executing the protein ligand tutorial Mark Abraham
[gmx-users] Re: Error during executing the protein ligand tutorial Mark Abraham
[gmx-users] xvg plotting Mark Abraham
[gmx-users] Timing variability Mark Abraham
[gmx-users] T->A mutation for a dimer protein Mark Abraham
[gmx-users]Question about reduced unit for coarse grain Mark Abraham
[gmx-users] Re: T->A mutation for a dimer protein Mark Abraham
[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water? Mark Abraham
[gmx-users] Re: Re: T->A mutation for a dimer protein Mark Abraham
[gmx-users] Box-dimensions -g_energy_output Mark Abraham
[gmx-users] required topology stuff modification for GBSA Mark Abraham
[gmx-users] placing dihedral constraints Mark Abraham
[gmx-users] g_msd bug Mark Abraham
[gmx-users] Tabulated potential for metal-oxide Mark Abraham
[gmx-users] Directional Thermostat in GROMACS Mark Abraham
[gmx-users] R: gmx-users Digest, Vol 86, Issue 183 Mark Abraham
[gmx-users] Running Lyz in water Mark Abraham
[gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham) Mark Abraham
[gmx-users] error in running pdb2gmx command Mark Abraham
[gmx-users] CPHMD in GROMACS4.5 Mark Abraham
[gmx-users] Fwd: Parallellization problem Nuria Alegret
[gmx-users] binaries for mac os x 10.6 Clement Angkawidjaja
[gmx-users] Why does the -append option exist? Rossen Apostolov
[gmx-users] gromacs 2.1 Rossen Apostolov
[gmx-users] in preparation for 4.5.5 and 4.6 releases Rossen Apostolov
[gmx-users] extended deadline to July 1st: call for papers: IEEE eScience2011 Workshop on “Computing Advances in Life Sciences” Rossen Apostolov
[gmx-users] Fw: properdihedrals Prema Awati
[gmx-users] All-atom topologies for lipid head groups Ioannis Beis
[gmx-users] (no subject) Sven Benson
[gmx-users] Fw: properdihedrals Emanuel Birru
[gmx-users] FFT plan mismatch with mdrun_mpi Christian Blouin
[gmx-users] Gradually increasing the force constant during restrained MD runs Aditi Borkar
[gmx-users] pdb2gmx Could not find force field, when using -ff commandline parameter Keith Callenberg
[gmx-users] Enthalpy of vaporization Fabian Casteblanco
[gmx-users] Enthalpy of Vaporization Fabian Casteblanco
[gmx-users] Enthalpy of Vaporization Fabian Casteblanco
[gmx-users] Enthalpy of Vaporization Fabian Casteblanco
[gmx-users] Liquid/Gas Systems Fabian Casteblanco
[gmx-users] Heat Capacity Question Fabian Casteblanco
[gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb Javier Cerezo
[gmx-users] Regarding NPT Eq. Javier Cerezo
[gmx-users] Re: Fw: properdihedrals Dr. Vitaly V. Chaban
[gmx-users] Re: compression to study pressure effect Vitaly Chaban
[gmx-users] Re: compression to study pressure effect Vitaly Chaban
[gmx-users] Re: scaling non-bonded interactions Vitaly Chaban
[gmx-users] Re: scaling non-bonded interactions Vitaly Chaban
[gmx-users] Re: compression to study pressure effect Vitaly Chaban
[gmx-users] Re: Liquid/Gas Systems Vitaly Chaban
[gmx-users] Re: my apologize Vitaly Chaban
[gmx-users] Re: carbon nano tubes pdb file Vitaly Chaban
[gmx-users] mdrun -nc Hsin-Lin Chiang
[gmx-users] Re: mdrun -nc Hsin-Lin Chiang
[gmx-users] Can't unfold the protein Hsin-Lin Chiang
[gmx-users] Can't unfold the protein Hsin-Lin Chiang
[gmx-users] Why does the -append option exist? Amit Choubey
[gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey
[gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey
[gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey
[gmx-users] local pressure v4.5 issues Amit Choubey
[gmx-users] Re: local pressure v4.5 issues Amit Choubey
[gmx-users] Re: local pressure v4.5 issues Amit Choubey
[gmx-users] gmx4.5.4 installation help Chandan Choudhury
[gmx-users] gmx4.5.4 installation help Chandan Choudhury
[gmx-users] gromacs 2.1 Bogdan Costescu
[gmx-users] implicit solvent LINCS errors Michael Daily
[gmx-users] oplsaa vs. charmm Michael Daily
[gmx-users] implicit solvent LINCS errors Michael D. Daily
[gmx-users] ED - Projecting on an eigenvector Sarath Chandra Dantu
[gmx-users] Rotational autocorrelation function of molecules using g_rotacf Andrew DeYoung
[gmx-users] nonormalize option in g_rotacf Andrew DeYoung
[gmx-users] Re: nonormalize option in g_rotacf Andrew DeYoung
[gmx-users] g_dipoles + tpbconv Nilesh Dhumal
[gmx-users] (no subject) Nilesh Dhumal
[gmx-users] Lennard Jones interactions Nilesh Dhumal
[gmx-users] Lennard Jones interactions Nilesh Dhumal
[gmx-users] Lennard Jones interactions Nilesh Dhumal
[gmx-users] rdf Nilesh Dhumal
[gmx-users] rdf Nilesh Dhumal
[gmx-users] g_dist Nilesh Dhumal
[gmx-users] g_velacc Nilesh Dhumal
[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation Anna Duncan
[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation Anna Duncan
[gmx-users] Position restraints Tom Dupree
[gmx-users] simulating a protein homodimer Stephen Edgcomb
[gmx-users] compression to study pressure effect Elisabeth
[gmx-users] error: Only triclinic boxes... Elisabeth
[gmx-users] error: Only triclinic boxes... Elisabeth
[gmx-users] error: Only triclinic boxes... Elisabeth
[gmx-users] error: Only triclinic boxes... Elisabeth
[gmx-users] energy file with g_dipoles Asmaa Elsheshiny
[gmx-users] effect of slab geometry correction on Coulomb energies for interface systems Ozge Engin
[gmx-users] flexibility Thomas Evangelidis
[gmx-users] oplsaa vs. charmm Thomas Evangelidis
[gmx-users] oplsaa vs. charmm Thomas Evangelidis
[gmx-users] NMR chemical shift restraints Thomas Evangelidis
[gmx-users] Generation of configurations for Umbrella Sampling Rebeca García Fandiño
[gmx-users] restraints in PMF (Justin's tutorial) Rebeca García Fandiño
[gmx-users] restraints in PMF (Justin's tutorial) Rebeca García Fandiño
[gmx-users] restraints in PMF (Justin's tutorial) Rebeca García Fandiño
[gmx-users] Calculate distance between two atoms Amjad Farooq
[gmx-users] viscosity Dommert Florian
[gmx-users] RE: Essential dynamics - concepts (Kavyashree M) Ran Friedman
[gmx-users] Re: oplsaa vs. charmm (Thomas Evangelidis) Ran Friedman
[gmx-users] RE: Including quadrupole-charge interaction in GROMACS (WU Yanbin) Ran Friedman
[gmx-users] monitoring the water molecules Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Regarding ffG43a1p force field Ramachandran G
[gmx-users] Question about g_bar output Warren Gallin
[gmx-users] Question about g_bar output Warren Gallin
[gmx-users] Negative pressure Francisco Garcia
[gmx-users] trjconv and g_filter Yulian Gavrilov
[gmx-users] g_rdf query Anirban Ghosh
[gmx-users] CPHMD in GROMACS4.5 Anirban Ghosh
[gmx-users] g_msd uncertainty Ivan Gladich
[gmx-users] Water Potential Energy Rini Gupta
Re: Re: [gmx-users] Water Potential Energy Rini Gupta
[gmx-users] .gro to .pqr Mona Habibi
[gmx-users] .gro to .pqr Mona Habibi
[gmx-users] an error for .tpr files Maria Hamilton
[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27 Leonhard Henkes
[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27 Leonhard Henkes
[gmx-users] Is there still interest in rigid-body simulation? Adam Herbst
[gmx-users] pulling code Adam Herbst
[gmx-users] error bars g_wham Jochen Hub
[gmx-users] Dissociation of Ligand-reg ITHAYARAJA
[gmx-users] Re: Dissociation of Ligand-reg ITHAYARAJA
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97 ITHAYARAJA
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97 ITHAYARAJA
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97 ITHAYARAJA
[gmx-users] Directional Thermostat in GROMACS Apoorv Kalyankar
[gmx-users] top2psf.pl Faezeh Kargar
[gmx-users] Implicit solvent calculatiom Netaly Khazanov
[gmx-users] Including a solvation model after converting from AMBER to GROMACS Massih Khorvash
[gmx-users] proper tau_t value with SD Hyunjin Kim
[gmx-users] Position restraints with multiple identical molecules Craig Kitchen
[gmx-users] Position restraints with multiple identical molecules Craig Kitchen
[gmx-users] Position restraints with multiple identical molecules Craig Kitchen
[gmx-users] viscosity Thomas Koller
[gmx-users] load imbalance E. Nihal Korkmaz
[gmx-users] cross correlations E. Nihal Korkmaz
[gmx-users] load imbalance E. Nihal Korkmaz
[gmx-users] LINCS WARNING relative constraint deviation E. Nihal Korkmaz
[gmx-users] Re: LINCS WARNING relative constraint deviation E. Nihal Korkmaz
[gmx-users] Re: LINCS WARNING relative constraint deviation E. Nihal Korkmaz
[gmx-users] implicit solvent system set up E. Nihal Korkmaz
[gmx-users] plateau in msd (glass transition); ref_t Anja Kuhnhold
[gmx-users] plateau in msd (glass transition); ref_t Anja Kuhnhold
[gmx-users] scaling non-bonded interactions Kukol, Andreas
[gmx-users] Re: scaling non-bonded interactions Kukol, Andreas
[gmx-users] question about trajcat command: Merge files Kukol, Andreas
[gmx-users] scaling non-bonded interactions Kukol, Andreas
[gmx-users] 1,4 hydrogen pairtypes in CHARMM36 Peter C. Lai
[gmx-users] http gromacs.org down? Peter C. Lai
[gmx-users] Force field parameters for phosphorylated tyrosine Peter C. Lai
[gmx-users] Fatal Error: The largest charge group contains 140 atoms. The maximum is 32 Lalit
[gmx-users] Questions about GB parameters Per Larsson
[gmx-users] Questions about GB parameters Per Larsson
[gmx-users] Liquid/Gas Systems Jussi Lehtola
[gmx-users] Why does the -append option exist? Jussi Lehtola
[gmx-users] Comparing single with double precision runs Jussi Lehtola
[gmx-users] flexibility Justin A. Lemkul
[gmx-users] Steered Molecular dynamics Justin A. Lemkul
[gmx-users] .gro to .pqr Justin A. Lemkul
[gmx-users] .gro to .pqr Justin A. Lemkul
[gmx-users] .gro to .pqr Justin A. Lemkul
[gmx-users] compression to study pressure effect Justin A. Lemkul
[gmx-users] scaling non-bonded interactions Justin A. Lemkul
[gmx-users] Re: scaling non-bonded interactions Justin A. Lemkul
[gmx-users] Re: scaling non-bonded interactions Justin A. Lemkul
[gmx-users] scaling non-bonded interactions Justin A. Lemkul
[gmx-users] question about trajcat command: Merge files Justin A. Lemkul
[gmx-users] scaling non-bonded interactions Justin A. Lemkul
[gmx-users] Re: question about trajcat command: Merge files Justin A. Lemkul
[gmx-users] Enthalpy of vaporization Justin A. Lemkul
[gmx-users] Fatal error: Not enough memory. Failed to realloc Justin A. Lemkul
[gmx-users] Protein ligand segmentation fault Justin A. Lemkul
[gmx-users] Enthalpy of Vaporization Justin A. Lemkul
[gmx-users] error: Only triclinic boxes... Justin A. Lemkul
[gmx-users] g_dipoles + tpbconv Justin A. Lemkul
[gmx-users] Enthalpy of Vaporization Justin A. Lemkul
[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation Justin A. Lemkul
[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation Justin A. Lemkul
[gmx-users] error: Only triclinic boxes... Justin A. Lemkul
[gmx-users] error: Only triclinic boxes... Justin A. Lemkul
[gmx-users] Solvating dodecahedron Justin A. Lemkul
[gmx-users] Liquid/Gas Systems Justin A. Lemkul
[gmx-users] selecting atoms---MD analysis Justin A. Lemkul
[gmx-users] Re: compression to study pressure effect Justin A. Lemkul
[gmx-users] Solvating dodecahedron Justin A. Lemkul
[gmx-users] Combining part files after using -noappend Justin A. Lemkul
[gmx-users] About publication Justin A. Lemkul
[gmx-users] trjconv and g_filter Justin A. Lemkul
[gmx-users] top2psf.pl Justin A. Lemkul
[gmx-users] Fatal Error: The largest charge group contains 140 atoms. The maximum is 32 Justin A. Lemkul
[gmx-users] proper tau_t value with SD Justin A. Lemkul
[gmx-users] carbon nano tubes pdb file Justin A. Lemkul
[gmx-users] reg hydrophobicx interaction Justin A. Lemkul
[gmx-users] Gauche dihedrals fraction Justin A. Lemkul
[gmx-users] Rotational autocorrelation function of molecules using g_rotacf Justin A. Lemkul
[gmx-users] Why does the -append option exist? Justin A. Lemkul
[gmx-users] reg linear interpolation Justin A. Lemkul
[gmx-users] Re: distance/direction PMF Justin A. Lemkul
[gmx-users] Re: distance/direction PMF Justin A. Lemkul
[gmx-users] g_hbond/g_sas - how is it calculated? Justin A. Lemkul
[gmx-users] Re: distance/direction PMF Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Re: distance/direction PMF Justin A. Lemkul
[gmx-users] Question about umbrella sampling "pull-geometry" option Justin A. Lemkul
[gmx-users] a question about position restraint time for long alkyl chain molecules Justin A. Lemkul
[gmx-users] a question about position restraint time for long alkyl chain molecules Justin A. Lemkul
[gmx-users] Re: distance/direction PMF Justin A. Lemkul
[gmx-users] oplsaa vs. charmm Justin A. Lemkul
[gmx-users] Umbrella sampling of phosphate ion binding Justin A. Lemkul
[gmx-users] Umbrella sampling of phosphate ion binding Justin A. Lemkul
[gmx-users] Umbrella sampling of phosphate ion binding Justin A. Lemkul
[gmx-users] Umbrella sampling of phosphate ion binding Justin A. Lemkul
[gmx-users] Umbrella sampling of phosphate ion binding Justin A. Lemkul
[gmx-users] Re:Umbrella sampling of phosphate ion binding (Dallas Warren) Justin A. Lemkul
[gmx-users] All-atom topologies for lipid head groups Justin A. Lemkul
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Justin A. Lemkul
[gmx-users] creating topology using g_x2top Justin A. Lemkul
[gmx-users] RE: Re:Umbrella sampling of phosphate ion binding (Dallas Warren) Justin A. Lemkul
[gmx-users] local pressure calcuation for Gromacs-4.5 Justin A. Lemkul
[gmx-users] local pressure calcuation for Gromacs-4.5 Justin A. Lemkul
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Justin A. Lemkul
[gmx-users] Invalid angle type 0 error during minimization. Justin A. Lemkul
[gmx-users] Atoms in the .top are not numbered consecutively from 1 Justin A. Lemkul
[gmx-users] Lennard Jones interactions Justin A. Lemkul
[gmx-users] Lennard Jones interactions Justin A. Lemkul
[gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb Justin A. Lemkul
[gmx-users] error during equilibriation Justin A. Lemkul
[gmx-users] reg SA cum SMD Justin A. Lemkul
[gmx-users] Re: error during equilibriation Justin A. Lemkul
[gmx-users] Re: error during equilibriation Justin A. Lemkul
[gmx-users] Regarding calculation of Salt bridge between specific group of atoms Justin A. Lemkul
[gmx-users] SA and smd Justin A. Lemkul
[gmx-users] reg ionic strength effect on the given protein Justin A. Lemkul
[gmx-users] Re: Largest charge group radii for Van der Waals; Largest Justin A. Lemkul
[gmx-users] g_energy Justin A. Lemkul
[gmx-users] nonormalize option in g_rotacf Justin A. Lemkul
[gmx-users] Dissociation of Ligand-reg Justin A. Lemkul
[gmx-users] MD - analysis Justin A. Lemkul
[gmx-users] g_confrms and superimposed structures Justin A. Lemkul
[gmx-users] MD - analysis Justin A. Lemkul
[gmx-users] g_confrms and superimposed structures Justin A. Lemkul
[gmx-users] MD - analysis Justin A. Lemkul
[gmx-users] MD - analysis Justin A. Lemkul
[gmx-users] g_confrms and superimposed structures Justin A. Lemkul
[gmx-users] Force field parameters for phosphorylated tyrosine Justin A. Lemkul
[gmx-users] Reducing density using -vdwd option for a new solvent in the system Justin A. Lemkul
[gmx-users] Re: Force field parameters for phosphorylated Justin A. Lemkul
[gmx-users] ionic strength and PME Justin A. Lemkul
[gmx-users] helix dihedral constraint Justin A. Lemkul
[gmx-users] MD - analysis Justin A. Lemkul
[gmx-users] Re: Dissociation of Ligand-reg Justin A. Lemkul
[gmx-users] Problem with 512 membrane Justin A. Lemkul
[gmx-users] mdrun -nc Justin A. Lemkul
[gmx-users] Questions about GB parameters Justin A. Lemkul
[gmx-users] Reducing density using -vdwd option for a new solvent in the system Justin A. Lemkul
[gmx-users] simulating a protein homodimer Justin A. Lemkul
[gmx-users] trjconv with superposition Justin A. Lemkul
[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ? Justin A. Lemkul
[gmx-users] initial temperature ridiculously high Justin A. Lemkul
[gmx-users] Reducing density using -vdwd option for a new solvent in the system Justin A. Lemkul
[gmx-users] CHARMM forcefield Justin A. Lemkul
[gmx-users] local pressure calcuation for Gromacs-4.5 Justin A. Lemkul
[gmx-users] Position restraints with multiple identical molecules Justin A. Lemkul
[gmx-users] Group DRG not found in indexfile Justin A. Lemkul
[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found Justin A. Lemkul
[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found Justin A. Lemkul
[gmx-users] load imbalance Justin A. Lemkul
[gmx-users] Re: doubt about your Umbrella Sampling tutorial Justin A. Lemkul
[gmx-users] minimum image violation Justin A. Lemkul
[gmx-users] error bars g_wham Justin A. Lemkul
[gmx-users] Re: Error during executing the protein ligand tutorial Justin A. Lemkul
[gmx-users] implicit solvent system set up Justin A. Lemkul
[gmx-users] How to calculate RMSD per residue with Gromacs ? Justin A. Lemkul
[gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial) Justin A. Lemkul
[gmx-users] query regarding g_ras command Justin A. Lemkul
[gmx-users] query regarding g_ras command Justin A. Lemkul
[gmx-users] Questions about GB parameters Justin A. Lemkul
[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water? Justin A. Lemkul
[gmx-users] PMF and appending simulation: -pf and -px flags (gromacs 4.0.7) Justin A. Lemkul
[gmx-users] DPPC temperatur setting Justin A. Lemkul
[gmx-users] Questions about GB parameters Justin A. Lemkul
[gmx-users] restraints in PMF (Justin's tutorial) Justin A. Lemkul
[gmx-users] restraints in PMF (Justin's tutorial) Justin A. Lemkul
[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field) Justin A. Lemkul
[gmx-users] DPPC temperatur setting Justin A. Lemkul
[gmx-users] Relaxed frozen groups Justin A. Lemkul
[gmx-users]Question about reduced unit for coarse grain Justin A. Lemkul
[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water? Justin A. Lemkul
[gmx-users]Question about reduced unit for coarse grain Justin A. Lemkul
[gmx-users] Re: Gromacs Query. Justin A. Lemkul
[gmx-users] DPPC temperatur setting Justin A. Lemkul
[gmx-users] Re: Relaxed frozen groups Justin A. Lemkul
[gmx-users] pdb2gmx Could not find force field, when using -ff commandline parameter Justin A. Lemkul
[gmx-users] Re: 1-4 cut off error during EM Justin A. Lemkul
[gmx-users] Re: 1-4 cut off error during EM Justin A. Lemkul
[gmx-users] Re: Box-dimensions -g_energy_output Justin A. Lemkul
[gmx-users] lattice Coulomb energy between energy groups Justin A. Lemkul
[gmx-users] Re: Box-dimensions -g_energy_output Justin A. Lemkul
[gmx-users] lattice Coulomb energy between energy groups Justin A. Lemkul
[gmx-users] Re: Box-dimensions -g_energy_output Justin A. Lemkul
[gmx-users] Re: Box-dimensions -g_energy_output Justin A. Lemkul
[gmx-users] Re: Box-dimensions -g_energy_output Justin A. Lemkul
[gmx-users] Regarding g_dist -dist option Justin A. Lemkul
[gmx-users] About the %SS values in the output of do_dssp Justin A. Lemkul
[gmx-users] Simulation of Primed DNA Justin A. Lemkul
[gmx-users] print inter and intra energy Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Periodic Images - clarification Justin A. Lemkul
[gmx-users] Periodic Images - clarification Justin A. Lemkul
[gmx-users] missing topology file adn creating a new one Justin A. Lemkul
[gmx-users] Comparing MD ensembles with exp. NOE restraints --> bus error Justin A. Lemkul
[gmx-users] minimization problem (Martini simulation) Justin A. Lemkul
[gmx-users] g_covar : segmentation fault Justin A. Lemkul
[gmx-users] The RMSD of a metal ion Justin A. Lemkul
[gmx-users] minimization problem (Martini simulation) Justin A. Lemkul
[gmx-users] pull direction of steered MD in Gromacs Justin A. Lemkul
[gmx-users] about periodic image violations Justin A. Lemkul
[gmx-users] Broken protein chain. Justin A. Lemkul
[gmx-users] reg ionic strngth Justin A. Lemkul
[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27 Justin A. Lemkul
[gmx-users] How to protonate a gmx trajectory? Justin A. Lemkul
[gmx-users] building a new molecule which does not exist in gmx data base Justin A. Lemkul
[gmx-users] trjorder and index Justin A. Lemkul
[gmx-users] converting psf file to gromacs .itp file Justin A. Lemkul
[gmx-users] Re: Running Lyz in water Justin A. Lemkul
[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27 Justin A. Lemkul
[gmx-users] error in running pdb2gmx command Justin A. Lemkul
[gmx-users] Question about g_bar output Justin A. Lemkul
[gmx-users] Question about g_bar output Justin A. Lemkul
[gmx-users] the effect of the ligand on each residue Justin A. Lemkul
[gmx-users] the effect of the ligand on each residue Justin A. Lemkul
[gmx-users] Regarding PDB file Justin A. Lemkul
[gmx-users] Calculate distance between two atoms Justin A. Lemkul
[gmx-users] Programs to add residues Michael Lerner
[gmx-users] scaling non-bonded interactions Da-Wei Li
[gmx-users] scaling non-bonded interactions Da-Wei Li
[gmx-users] oplsaa vs. charmm Da-Wei Li
[gmx-users] oplsaa vs. charmm Da-Wei Li
[gmx-users] Gravity force in equation of motion Jianguo Li
[gmx-users] gmx4.5.4 installation help Jianguo Li
[gmx-users] local pressure calcuation for Gromacs-4.5 Jianguo Li
[gmx-users] Re: local pressure v4.5 issues Jianguo Li
[gmx-users] How to calculate RMSD per residue with Gromacs ? Chih-Ying Lin
[gmx-users] Invitation to connect on LinkedIn srajan jain via LinkedIn
[gmx-users] Invitation to connect on LinkedIn Gideon Lapidoth via LinkedIn
[gmx-users] Invitation to connect on LinkedIn Ting Zhou via LinkedIn
[gmx-users] Invitation to connect on LinkedIn Ting Zhou via LinkedIn
[gmx-users] Invitation to connect on LinkedIn Zhao Lifeng via LinkedIn
[gmx-users] g_covar Kavyashree M
[gmx-users] g_covar Kavyashree M
[gmx-users] option -pbc in trjconv Kavyashree M
[gmx-users] option -pbc in trjconv Kavyashree M
[gmx-users] Essential dynamics - concepts Kavyashree M
[gmx-users] Essential dynamics - concepts Kavyashree M
[gmx-users] Essential dynamics - concepts Kavyashree M
[gmx-users] RE: Essential dynamics - concepts (Kavyashree M) Kavyashree M
[gmx-users] Essential dynamics - concepts Kavyashree M
[gmx-users] ED-analysis Kavyashree M
[gmx-users] ED-analysis Kavyashree M
[gmx-users] ED-analysis Kavyashree M
[gmx-users] MD - analysis Kavyashree M
[gmx-users] MD - analysis Kavyashree M
[gmx-users] MD - analysis Kavyashree M
[gmx-users] MD - analysis Kavyashree M
[gmx-users] MD - analysis Kavyashree M
[gmx-users] data points missing Kavyashree M
[gmx-users] Re: data points missing Kavyashree M
[gmx-users] minimum image violation Kavyashree M
[gmx-users] minimum image violation Kavyashree M
[gmx-users] cosine content Kavyashree M
[gmx-users] Trajectory and ED - (not old question again) Kavyashree M
[gmx-users] Box-dimensions -g_energy_output Kavyashree M
[gmx-users] Re: Trajectory and ED - (not old question again) Kavyashree M
[gmx-users] Re: Trajectory and ED - (not old question again) Kavyashree M
[gmx-users] Re: Trajectory and ED - (not old question again) Kavyashree M
[gmx-users] Re: Trajectory and ED - (not old question again) Kavyashree M
[gmx-users] Re: Trajectory and ED - (not old question again) Kavyashree M
[gmx-users] Re: Box-dimensions -g_energy_output Kavyashree M
[gmx-users] Re: Box-dimensions -g_energy_output Kavyashree M
[gmx-users] Re: Box-dimensions -g_energy_output Kavyashree M
[gmx-users] Re: Box-dimensions -g_energy_output Kavyashree M
[gmx-users] Re: Box-dimensions -g_energy_output Kavyashree M
[gmx-users] Re: Box-dimensions -g_energy_output Kavyashree M
[gmx-users] ED - Projecting on an eigenvector Kavyashree M
[gmx-users] ED - Projecting on an eigenvector Kavyashree M
[gmx-users] ED - Projecting on an eigenvector Kavyashree M
[gmx-users] Periodic Images - clarification Kavyashree M
[gmx-users] Periodic Images - clarification Kavyashree M
[gmx-users] Periodic Images - clarification Kavyashree M
[gmx-users] Periodic Images - clarification Kavyashree M
[gmx-users] Periodic Images - clarification Kavyashree M
[gmx-users] Broken protein chain. Kavyashree M
[gmx-users] Broken protein chain. Kavyashree M
[gmx-users] Dreiding force field in Gromacs ? Sanku M
[gmx-users] g_rdf: how to change grid spacing for structure factor Sanku M
[gmx-users] g_rdf problem Sanku M
[gmx-users] Transition path sampling Sanku M
[gmx-users] helix dihedral constraint Sanku M
[gmx-users] dipole-dipole interaction energy Sanku M
[gmx-users] trjorder and index Sanku M
[gmx-users] plateau in msd (glass transition); ref_t Lutz Maibaum
[gmx-users] about periodic images violation Anna Marabotti
[gmx-users] R: gmx-users Digest, Vol 86, Issue 183 Anna Marabotti
[gmx-users] about periodic image violations Anna Marabotti
[gmx-users] energy conservation Erik Marklund
[gmx-users] Regarding H-bond autocorrelation Erik Marklund
[gmx-users] Regarding H-bond autocorrelation Erik Marklund
[gmx-users] Including quadrupole-charge interaction in GROMACS Erik Marklund
[gmx-users] Including quadrupole-charge interaction in GROMACS Erik Marklund
[gmx-users] Regarding H-bond autocorrelation Erik Marklund
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Igor Marques
[gmx-users] g_hbond/g_sas - how is it calculated? Marzinek, Jan
[gmx-users] g_sas index files/hydrogen bonds Marzinek, Jan
[gmx-users] AFM Simulation Michael McGovern
[gmx-users] energy conservation Gavin Melaugh
[gmx-users] pull_vec Gavin Melaugh
[gmx-users] fatal error Gavin Melaugh
[gmx-users] distance/direction PMF Gavin Melaugh
[gmx-users] Re: distance/direction PMF Gavin Melaugh
[gmx-users] Re: distance/direction PMF Gavin Melaugh
[gmx-users] Re: distance/direction PMF Gavin Melaugh
[gmx-users] Re: distance/direction PMF Gavin Melaugh
[gmx-users] Re: distance/direction PMF Gavin Melaugh
[gmx-users] convergence Gavin Melaugh
[gmx-users] Re: convergence Gavin Melaugh
[gmx-users] error bars g_wham Gavin Melaugh
[gmx-users] lattice Coulomb energy between energy groups Gavin Melaugh
[gmx-users] lattice Coulomb energy between energy groups Gavin Melaugh
[gmx-users] question about trajcat command: Merge files Miguel Quiliano Meza
[gmx-users] Re: question about trajcat command: Merge files Miguel Quiliano Meza
[gmx-users] Re: Re: question about trjcat command: Merge files Miguel Quiliano Meza
[gmx-users] Autocorrelation of dipole moment André Farias de Moura
[gmx-users] Autocorrelation of dipole moment André Farias de Moura
[gmx-users] g_energy Juliette N.
[gmx-users] Problem in followin MARTINI tutorial Naba
[gmx-users] Programs to add residues Chris Neale
[gmx-users] .gro to .pqr Francesco Oteri
[gmx-users] Why does the -append option exist? Francesco Oteri
[gmx-users] standard deviation about rmsd and rmsf values Francesco Oteri
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Why does the -append option exist? Dimitar Pachov
[gmx-users] Lennard Jones interactions Andrew Paluch
[gmx-users] Lennard Jones interactions Andrew Paluch
[gmx-users] Lennard Jones interactions Andrew Paluch
[gmx-users] Gromacs to Amber trajectory Raja Pandian
[gmx-users] Gromacs to Amber trajectory Raja Pandian
[gmx-users] Problem in followin MARTINI tutorial XAvier Periole
[gmx-users] implicit solvent LINCS errors Joshua L. Phillips
[gmx-users] implicit solvent LINCS errors Joshua L. Phillips
[gmx-users] gmx4.5.4 installation help Joshua L. Phillips
[gmx-users] mdrun -nc Joshua L. Phillips
AW: Re: [gmx-users] where can I download POPC membrane file? Thomas Piggot
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Thomas Piggot
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Thomas Piggot
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Thomas Piggot
[gmx-users] All-atom topologies for lipid head groups Thomas Piggot
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC Thomas Piggot
[gmx-users] classic Ewald pressure tensor Elizabeth Ploetz
[gmx-users] g_covar : segmentation fault Poojari, Chetan
[gmx-users] Why does the -append option exist? Sander Pronk
[gmx-users] Installation of gromacs-gpu on windows Szilárd Páll
[gmx-users] selecting atoms---MD analysis Mr Bernard Ramos
[gmx-users] placing dihedral constraints Mr Bernard Ramos
[gmx-users] g_covar eigenval.xvg Tom Rodgers
[gmx-users] micelle clustering sulatha M. S
[gmx-users] g_density Matthias Schmidt
[gmx-users] Combining part files after using -noappend Zack Scholl
[gmx-users] Programs to add residues Zack Scholl
[gmx-users] Relaxed frozen groups Zack Scholl
[gmx-users] Re: Relaxed frozen groups Zack Scholl
[gmx-users] Why does the -append option exist? Roland Schulz
[gmx-users] Why does the -append option exist? Roland Schulz
[gmx-users] Why does the -append option exist? Roland Schulz
[gmx-users] gromacs 2.1 Roland Schulz
[gmx-users] is lincs used with virtual hydrogens? Roland Schulz
[gmx-users] is lincs used with virtual hydrogens? Roland Schulz
[gmx-users] force on protein by solvent SebastianWaltz
[gmx-users] rerun confusion SebastianWaltz
[gmx-users] How to protonate a gmx trajectory? Yun Shi
[gmx-users] trjconv with superposition Liu Shiyong
[gmx-users] cross correlations Alexey Shvetsov
[gmx-users] cross correlations Alexey Shvetsov
[gmx-users] Comparing MD ensembles with exp. NOE restraints --> bus error Thereza Soares
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 183 Thereza Soares
[gmx-users] Gauche dihedrals fraction Sławomir Stachura
[gmx-users] g_msd bug Sławomir Stachura
[gmx-users] g_msd bug Sławomir Stachura
[gmx-users] g_msd bug Sławomir Stachura
[gmx-users] a question about position restraint time for long alkyl chain molecules XUEMING TANG
[gmx-users] a question about position restraint time for long alkyl chain molecules XUEMING TANG
[gmx-users] a question about position restraint time for long alkyl chain molecules XUEMING TANG
[gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial) Shay Teaching
[gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial) Shay Teaching
[gmx-users] PMF and appending simulation: -pf and -px flags (gromacs 4.0.7) Shay Teaching
[gmx-users] umbrella sampling pull_group0 adn pull_group1 Shay Teaching
[gmx-users] strain Emine Deniz Tekin
[gmx-users] Atom OXT in residue ASP 18 was not found in rtp entry ASP with 9 atoms while sorting atoms. Emine Deniz Tekin
[gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb Tom
[gmx-users] Re: Largest charge group radii for Van der Waals; Largest Tom
[gmx-users] pull direction of steered MD in Gromacs Tom
[gmx-users] xvg plotting Nicole Varvarigou
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 84 Ravi Kumar Venkatraman
[gmx-users] Regarding NPT Eq. Ravi Kumar Venkatraman
[gmx-users] Running Lyz in water Ravi Kumar Venkatraman
[gmx-users] Re: Running Lyz in water Ravi Kumar Venkatraman
[gmx-users] Regarding PDB file Ravi Kumar Venkatraman
[gmx-users] Umbrella sampling of phosphate ion binding Dallas Warren
[gmx-users] Umbrella sampling of phosphate ion binding Dallas Warren
[gmx-users] Re: Gromacs error Dallas Warren
[gmx-users] Re: Increase in charge after adding the ligand Dallas Warren
[gmx-users] Re: Increase in charge after adding the ligand Dallas Warren
[gmx-users] xvg plotting Dallas Warren
[gmx-users] flexibility Tsjerk Wassenaar
[gmx-users] g_covar Tsjerk Wassenaar
[gmx-users] Solvating dodecahedron Tsjerk Wassenaar
[gmx-users] Essential dynamics - concepts Tsjerk Wassenaar
[gmx-users] Essential dynamics - concepts Tsjerk Wassenaar
[gmx-users] Essential dynamics - concepts Tsjerk Wassenaar
[gmx-users] ED-analysis Tsjerk Wassenaar
[gmx-users] ED-analysis Tsjerk Wassenaar
[gmx-users] standard deviation about rmsd and rmsf values Tsjerk Wassenaar
[gmx-users] cross correlations Tsjerk Wassenaar
[gmx-users] cross correlations Tsjerk Wassenaar
[gmx-users] radius of gyration - compactness Tsjerk Wassenaar
[gmx-users] adius of gyration - compactness Tsjerk Wassenaar
[gmx-users] radius of gyration - compactness - accessible surface area Tsjerk Wassenaar
[gmx-users] radius of gyration - compactness - accessible surface area Tsjerk Wassenaar
[gmx-users] Re: Trajectory and ED - (not old question again) Tsjerk Wassenaar
[gmx-users] Re: Trajectory and ED - (not old question again) Tsjerk Wassenaar
[gmx-users] Re: Trajectory and ED - (not old question again) Tsjerk Wassenaar
[gmx-users] cross correlations Tsjerk Wassenaar
[gmx-users] ED - Projecting on an eigenvector Tsjerk Wassenaar
[gmx-users] cross correlations Tsjerk Wassenaar
[gmx-users] Periodic Images - clarification Tsjerk Wassenaar
[gmx-users] Periodic Images - clarification Tsjerk Wassenaar
[gmx-users] g_msd bug Tsjerk Wassenaar
[gmx-users] about periodic images violation Tsjerk Wassenaar
[gmx-users] micelle clustering Tsjerk Wassenaar
[gmx-users] pdb2gmx Tsjerk Wassenaar
[gmx-users] Question about umbrella sampling "pull-geometry" option WU Yanbin
[gmx-users] Question about umbrella sampling through a nanotube WU Yanbin
[gmx-users] Including quadrupole-charge interaction in GROMACS WU Yanbin
[gmx-users] Including quadrupole-charge interaction in GROMACS WU Yanbin
[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found Ye Yang
[gmx-users]gmx4.5.4 genion problem: No line with moleculetype 'SOL' found Ye Yang
[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found Ye Yang
[gmx-users]Question about reduced unit for coarse grain Ye Yang
[gmx-users]Question about reduced unit for coarse grain Ye Yang
[gmx-users]Question about reduced unit for coarse grain Ye Yang
[gmx-users]Question about reduced unit for coarse grain Ye Yang
[gmx-users]Question about reduced unit for coarse grain Ye Yang
[gmx-users]Question about reduced unit for coarse grain Ye Yang
[gmx-users] Re: T->A mutation for a dimer protein Lishan Yao
[gmx-users] Re: Re: T->A mutation for a dimer protein Lishan Yao
[gmx-users] Re: Re: Re: T->A mutation for a dimer protein Lishan Yao
[gmx-users]Question about reduced unit for coarse grain Yang Ye
[gmx-users] required topology stuff modification for GBSA Makoto Yoneya
[gmx-users] required topology stuff modification for GBSA Makoto Yoneya
[gmx-users] required topology stuff modification for GBSA Makoto Yoneya
[gmx-users] implicit solvent and generic interaction Makoto Yoneya
[gmx-users] initial temperature ridiculously high GZ Zhang
[gmx-users] Fwd: Parallellization problem Matthew Zwier
AW: Re: [gmx-users] where can I download POPC membrane file? albert
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 209 shiva birgani
[gmx-users] problem in g_density cdalgicdir
[gmx-users] Re: problem in g_density cdalgicdir
[gmx-users] minimization problem politr at fh.huji.ac.il
[gmx-users] minimization problem (Martini simulation) politr at fh.huji.ac.il
[gmx-users] minimization problem (Martini simulation) politr at fh.huji.ac.il
[gmx-users] minimization problem (Martini simulation) politr at fh.huji.ac.il
[gmx-users] protonated histidine with Martini politr at fh.huji.ac.il
[gmx-users] Comparing single with double precision runs Kalavera at gmx.net
[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27 Kalavera at gmx.net
[gmx-users] writing trajectory with water molecules within a distance from protein maria goranovic
[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ? maria goranovic
[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ? maria goranovic
[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA maria goranovic
[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA maria goranovic
[gmx-users] Steered Molecular dynamics bharat gupta
[gmx-users] Umbrella sampling of phosphate ion binding bharat gupta
[gmx-users] Umbrella sampling of phosphate ion binding bharat gupta
[gmx-users] Umbrella sampling of phosphate ion binding bharat gupta
[gmx-users] Umbrella sampling of phosphate ion binding bharat gupta
[gmx-users] Umbrella sampling of phosphate ion binding bharat gupta
[gmx-users] Umbrella sampling of phosphate ion binding bharat gupta
[gmx-users] Force field parameters for phosphorylated tyrosine bharat gupta
[gmx-users] Force field parameters for phosphorylated tyrosine bharat gupta
[gmx-users] Re: Gromacs error bharat gupta
[gmx-users] Re: Gromacs error bharat gupta
Fwd: [gmx-users] Re: Gromacs error bharat gupta
[gmx-users] Re: Gromacs error bharat gupta
[gmx-users] Re: Increase in charge after adding the ligand bharat gupta
[gmx-users] Re: Error during executing the protein ligand tutorial bharat gupta
[gmx-users] Re: Increase in charge after adding the ligand bharat gupta
[gmx-users] Re: Error during executing the protein ligand tutorial bharat gupta
[gmx-users] Re: Error during executing the protein ligand tutorial bharat gupta
[gmx-users] Re: Error during executing the protein ligand tutorial bharat gupta
[gmx-users] Re: Error during executing the protein ligand tutorial bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Regarding ffG43a1p force field bharat gupta
[gmx-users] Fwd: Regarding ffG43a1p force field bharat gupta
[gmx-users] Re: 1-4 cut off error during EM bharat gupta
[gmx-users] Re: 1-4 cut off error during EM bharat gupta
[gmx-users] Re: 1-4 cut off error during EM bharat gupta
[gmx-users] converting psf file to gromacs .itp file bharat gupta
[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water? xiaodong huang
[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water? xiaodong huang
[gmx-users] Re: Force field parameters for phosphorylated sarah k
[gmx-users] g_confrms and superimposed structures leila karami
[gmx-users] g_confrms and superimposed structures leila karami
[gmx-users] g_confrms and superimposed structures leila karami
[gmx-users] g_confrms and superimposed structures leila karami
[gmx-users] xvg plotting leila karami
[gmx-users] Tabulated potential for metal-oxide manana koberidze
[gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham) manana koberidze
[gmx-users] binaries for mac os x 10.6 lina
[gmx-users] g_hbond/g_sas - how is it calculated? lina
[gmx-users] entropy from eigenfrequency nahren manuel
[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field udaya kiran marelli
[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field udaya kiran marelli
[gmx-users] NVT equilibration of DMSO solvent (Charmm all-atom force field) udaya kiran marelli
[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field) udaya kiran marelli
[gmx-users] micelle clustering gregory megariotis
[gmx-users] DPPC temperatur setting marco miele
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 138 marco miele
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 143 marco miele
[gmx-users] T->A mutation for a dimer protein yaolisha at msu.edu
[gmx-users] print inter and intra energy balaji nagarajan
[gmx-users] Fatal error: Not enough memory. Failed to realloc shivangi nangia
[gmx-users] Solvating dodecahedron shivangi nangia
[gmx-users] Reducing density using -vdwd option for a new solvent in the system shivangi nangia
[gmx-users] Reducing density using -vdwd option for a new solvent in the system shivangi nangia
[gmx-users] Reducing density using -vdwd option for a new solvent in the system shivangi nangia
[gmx-users] Reducing density using -vdwd option for a new solvent in the system shivangi nangia
[gmx-users] Regarding g_dist -dist option shivangi nangia
[gmx-users] building a new molecule which does not exist in gmx data base shivangi nangia
[gmx-users] query regarding g_ras command rashi parihar
[gmx-users] query regarding g_ras command rashi parihar
[gmx-users] error in running pdb2gmx command rashi parihar
[gmx-users] error in running pdb2gmx command rashi parihar
[gmx-users] (no subject) arezoo rahmanpour
[gmx-users] carbon nano tubes pdb file sreelakshmi ramesh
[gmx-users] creating topology using g_x2top sreelakshmi ramesh
[gmx-users] Invalid angle type 0 error during minimization. sreelakshmi ramesh
[gmx-users] Atoms in the .top are not numbered consecutively from 1 sreelakshmi ramesh
[gmx-users] error during equilibriation sreelakshmi ramesh
[gmx-users] Re: error during equilibriation sreelakshmi ramesh
[gmx-users] Re: error during equilibriation sreelakshmi ramesh
[gmx-users] need tip3p.gro for charmm force field sreelakshmi ramesh
[gmx-users] missing topology file adn creating a new one sreelakshmi ramesh
[gmx-users] umbrella sampling pull_group0 adn pull_group1 sreelakshmi ramesh
[gmx-users] Gravity force in equation of motion mohsen ramezanpour
[gmx-users] Gravity force in equation of motion mohsen ramezanpour
[gmx-users] Re:Umbrella sampling of phosphate ion binding (Dallas Warren) lloyd riggs
[gmx-users] RE: Re:Umbrella sampling of phosphate ion binding (Dallas Warren) lloyd riggs
[gmx-users] About the %SS values in the output of do_dssp sa
[gmx-users] Re: About the %SS values in the output of do_dssp sa
[gmx-users] About publication vidhya sankar
[gmx-users] reg hydrophobicx interaction vidhya sankar
[gmx-users] reg linear interpolation vidhya sankar
[gmx-users] reg SA cum SMD vidhya sankar
[gmx-users] Re: reg SA cum SMD vidhya sankar
[gmx-users] SA and smd vidhya sankar
[gmx-users] reg ionic strength effect on the given protein vidhya sankar
[gmx-users] reg PME usage vidhya sankar
[gmx-users] reg electrostatics interaction vidhya sankar
[gmx-users] reg PME usage vidhya sankar
[gmx-users] ionic strength and PME vidhya sankar
[gmx-users] reg g_hbond vidhya sankar
[gmx-users] reg ionic strngth vidhya sankar
[gmx-users] Order Parameters simon sham
[gmx-users] g_rotacf simon sham
[gmx-users] CHARMM forcefield simon sham
[gmx-users] g_hbond simon sham
[gmx-users] g_hbond simon sham
[gmx-users] The RMSD of a metal ion simon sham
[gmx-users] pdb2gmx simon sham
[gmx-users] standard deviation about rmsd and rmsf values shahab shariati
[gmx-users] radius of gyration - compactness shahab shariati
[gmx-users] adius of gyration - compactness shahab shariati
[gmx-users] radius of gyration - compactness - accessible surface area shahab shariati
[gmx-users] radius of gyration - compactness - accessible surface area shahab shariati
[gmx-users] radius of gyration - compactness - accessible surface area shahab shariati
[gmx-users] Regarding calculation of Salt bridge between specific group of atoms bipin singh
[gmx-users] Regarding calculation of Salt bridge between specific group of atoms bipin singh
[gmx-users] Regarding H-bond autocorrelation bipin singh
[gmx-users] Regarding H-bond autocorrelation bipin singh
[gmx-users] Regarding H-bond autocorrelation bipin singh
[gmx-users] Regarding H-bond autocorrelation bipin singh
[gmx-users] Regarding H-bond autocorrelation bipin singh
[gmx-users] cross correlations bipin singh
[gmx-users] Regarding g_dist -dist option bipin singh
[gmx-users] Regarding g_dist -dist option bipin singh
[gmx-users] cross correlations bipin singh
[gmx-users] cross correlations bipin singh
[gmx-users] Simulation of Primed DNA raghav singh
[gmx-users] xvg plotting andrea spitaleri
[gmx-users] Transition path sampling felmerino at uchile.cl
[gmx-users] Can't unfold the protein felmerino at uchile.cl
[gmx-users] binaries for mac os x 10.6 chris.neale at utoronto.ca
[gmx-users] Why does the -append option exist? chris.neale at utoronto.ca
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC chris.neale at utoronto.ca
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC chris.neale at utoronto.ca
[gmx-users] gromacs 2.1 chris.neale at utoronto.ca
[gmx-users] Gradually increasing the force constant during restrained MD runs chris.neale at utoronto.ca
[gmx-users] Question about umbrella sampling through a nanotube chris.neale at utoronto.ca
[gmx-users] centering a bilayer at a cartesian coordinate chris.neale at utoronto.ca
[gmx-users] centering a bilayer at a cartesian coordinate chris.neale at utoronto.ca
[gmx-users] g_density chris.neale at utoronto.ca
[gmx-users] g_dist chris.neale at utoronto.ca
[gmx-users] Can't unfold the protein chris.neale at utoronto.ca
[gmx-users] Can't unfold the protein chris.neale at utoronto.ca
[gmx-users] g_hbond chris.neale at utoronto.ca
[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found chris.neale at utoronto.ca
[gmx-users] is lincs used with virtual hydrogens? chris.neale at utoronto.ca
[gmx-users] is lincs used with virtual hydrogens? chris.neale at utoronto.ca
[gmx-users] is lincs used with virtual hydrogens? chris.neale at utoronto.ca
[gmx-users] is lincs used with virtual hydrogens? chris.neale at utoronto.ca
[gmx-users] restraints in PMF (Justin's tutorial) chris.neale at utoronto.ca
[gmx-users] Timing variability chris.neale at utoronto.ca
[gmx-users] T->A mutation for a dimer protein chris.neale at utoronto.ca
[gmx-users] pulling code chris.neale at utoronto.ca
[gmx-users] gromacs 2.1 chris.neale at utoronto.ca
[gmx-users] gromacs 2.1 chris.neale at utoronto.ca
[gmx-users] g_msd bug chris.neale at utoronto.ca
[gmx-users] What does it mean by saying mca: base: component_find: unable to open.... xiaowu759
[gmx-users] Gromacs-4.5.4 install error xuji
[gmx-users] the effect of the ligand on each residue ahmet yıldırım
[gmx-users] the effect of the ligand on each residue ahmet yıldırım
[gmx-users] Installation of gromacs-gpu on windows Андрей Гончар
[gmx-users] Protein ligand segmentation fault גדעון לפידות

Last message date: Thu Jun 30 20:20:52 CEST 2011
Archived on: Thu Nov 14 12:11:08 CET 2013

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