March 2011 Archives by author

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Starting: Tue Mar 1 00:12:53 CET 2011
Ending: Thu Mar 31 23:52:58 CEST 2011
Messages: 933

[gmx-users] about -CN triple bond Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] Re: Nitrogen box Mark Abraham
[gmx-users] .tdr file not created Mark Abraham
[gmx-users] .tdr file not created Mark Abraham
[gmx-users] index file groups Mark Abraham
[gmx-users] mpi run in Gromacs Mark Abraham
[gmx-users] Re: adding ff parameter of modified residue to charmm ff Mark Abraham
[gmx-users] REMD simulation of peptide-membrane system Mark Abraham
[gmx-users] How to find average protein structure. Mark Abraham
[gmx-users] different RMSD graphs after using pbc mol Mark Abraham
[gmx-users] calcium diffuses away from the protein during MD Mark Abraham
[gmx-users] trajectory output from g_select ? Mark Abraham
[gmx-users] MD of a crystall structure Mark Abraham
[gmx-users] Re: adding ff parameter of modified residue to charmm ff Mark Abraham
[gmx-users] trajectory output from g_select ? Mark Abraham
[gmx-users] trajectory output from g_select ? Mark Abraham
[gmx-users] number of DD cells Mark Abraham
[gmx-users] Dihedral Restraints Mark Abraham
[gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration Mark Abraham
[gmx-users] Warning: 1-4 interaction Mark Abraham
[gmx-users] # Protein non-integer charge‏ Mark Abraham
[gmx-users] RMSD truncation Restart simulation problems Mark Abraham
[gmx-users] g_RMS: Mismatch of atom number between topology and reference structure Mark Abraham
[gmx-users] Re-compile Gromacs Program? Mark Abraham
[gmx-users] Disable non-bonded interactions between molecules Mark Abraham
[gmx-users] QMMM Mark Abraham
[gmx-users] Unsupported box diagonal Mark Abraham
[gmx-users] using one thermostat for entire system ?? Mark Abraham
[gmx-users] Instantaneous Square Displacement Mark Abraham
[gmx-users] g_energy inconsistent results Mark Abraham
[gmx-users] RMSD truncation Restart simulation problems Mark Abraham
[gmx-users] parallel running Mark Abraham
[gmx-users] g_rms and g_cluster Mark Abraham
[gmx-users] Density of water, Dispcorr and rmsd Mark Abraham
[gmx-users] Definition of helicity Mark Abraham
[gmx-users] secondary structure propensities of residues Mark Abraham
[gmx-users] Zero Potential of Mean Force with g_wham Mark Abraham
[gmx-users] Treatment of protein termini when there are missing residues Mark Abraham
[gmx-users] Regarding Gromacs Application in more than 10 node cluster Mark Abraham
[gmx-users] .cpt and .trr files Mark Abraham
[gmx-users] terminated but not completely Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] Energy calculation Mark Abraham
[gmx-users] ffamber99.hdb Mark Abraham
[gmx-users] Coulomb interactions Mark Abraham
[gmx-users] Re: installation of gromacs (Dommert Florian) Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] isopeptide bond Mark Abraham
[gmx-users] Grandcanonical Ensemble Mark Abraham
[gmx-users] LINCS and number of nodes Mark Abraham
[gmx-users] Pressure Fluctuations Mark Abraham
[gmx-users] Energy calculation Mark Abraham
[gmx-users] installation of gromacs Mark Abraham
[gmx-users] Post simulation energy calculation of Ligand - Protein complex Mark Abraham
[gmx-users] Regarding editconf Mark Abraham
[gmx-users] installation of gromacs Mark Abraham
[gmx-users] installation of gromacs Mark Abraham
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx Mark Abraham
[gmx-users] C-terminal amidation of peptide Mark Abraham
[gmx-users] Re: compressing a system Mark Abraham
[gmx-users] Re: compressing a system Mark Abraham
[gmx-users] Hydroixde Ion Mark Abraham
[gmx-users] Gromacs on other Operating Systems Mark Abraham
[gmx-users] checking gen_seed Mark Abraham
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx Mark Abraham
[gmx-users] install problems cygwin Mark Abraham
[gmx-users] Alcohol Dehydrogenase MD simulation....Reg Mark Abraham
[gmx-users] unit of surface tension, KJ/mol? Mark Abraham
[gmx-users] how to differentiate crystal water and explicit waters in gromacs ??? Mark Abraham
[gmx-users] LINCS warning on galactose molecule Mark Abraham
[gmx-users] unit of surface tension, KJ/mol? Mark Abraham
[gmx-users] No cut-off Mark Abraham
[gmx-users] No cut-off Mark Abraham
[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI Mark Abraham
[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI Mark Abraham
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral Mark Abraham
[gmx-users] g_cluster segmentation fault Mark Abraham
[gmx-users] Re: Alcohol Dehydrogenase MD simulation....Reg Mark Abraham
[gmx-users] How can I convert Gromacs ouput to Desmond input file?? Mark Abraham
[gmx-users] amide partial charges Mark Abraham
[gmx-users] NADPH parameters Mark Abraham
[gmx-users] problem in energy minimization of the inflted system Mark Abraham
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral Mark Abraham
[gmx-users] No DD grid found Mark Abraham
[gmx-users] mdrun Mark Abraham
[gmx-users] flexible spc water model Mark Abraham
[gmx-users] Re: Resplica exchange with solute tempering (REST) Mark Abraham
[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family Mark Abraham
[gmx-users] PSF files from .top to .psf Mark Abraham
[gmx-users] distorted structure Mark Abraham
[gmx-users] Strange behavior from g_sas Mark Abraham
[gmx-users] How to merge 2 top-files Mark Abraham
[gmx-users] Strange behavior from g_sas Mark Abraham
[gmx-users] the total charge of system is not an integer Mark Abraham
[gmx-users] the total charge of system is not an integer Mark Abraham
[gmx-users] manually creating a topology file Mark Abraham
[gmx-users] gromacs/CPMD. Is LAM mandatory? Mark Abraham
[gmx-users] MD of a crystall structure Hernan Ahumada
[gmx-users] www site is temporarily down Rossen Apostolov
[gmx-users] New maintenance release: gromacs-4.5.4 Rossen Apostolov
[gmx-users] New version 4.5.4 of the Gromacs manual Rossen Apostolov
[gmx-users] Various web issues Rossen Apostolov
[gmx-users] Various web issues Rossen Apostolov
[gmx-users] Various web issues Rossen Apostolov
[gmx-users] Web site issues (Search, Redmine) Rossen Apostolov
[gmx-users] PSF files from .top to .psf Donovan B.T.
[gmx-users] tpic run option - potential energy meaning JAVIER CEREZO BASTIDA
[gmx-users] Carbohydrate simulation: problem with the terminal atoms Somaye Badieyan
[gmx-users] Problem when running in many nodes Tomy van Batis
[gmx-users] couple-moltype for two molecules Luca Bellucci
[gmx-users] couple-moltype for two molecules Luca Bellucci
[gmx-users] couple-moltype for two molecules Luca Bellucci
[gmx-users] Alternating electric fields in GROMACS Bert
[gmx-users] How to compile the template.c when GMX is builded with cmake Bert
[gmx-users] no output dgdl file Emanuel Birru
[gmx-users] no output dgdl file Emanuel Birru
[gmx-users] no output dgdl file Emanuel Birru
[gmx-users] no output dgdl file Emanuel Birru
[gmx-users] no output dgdl file Emanuel Birru
[gmx-users] no output dgdl file Emanuel Birru
[gmx-users] Re: adding ff parameter of modified residue to charmm ff Pär Bjelkmar
[gmx-users] thermostats, canonical distribution, and stochastic dynamics Michael Brunsteiner
[gmx-users] IMPLICIT SOLVENT IN AMBER Michael Brunsteiner
[gmx-users] pull forces Michael Brunsteiner
[gmx-users] .pdb file for DNA Alexander Bujotzek
[gmx-users] Dihedral Restraints Alexander Bujotzek
[gmx-users] Phd positions in SISSA Giovanni Bussi
[gmx-users] about -CN triple bond C.Y. Chang
[gmx-users] Energy calculation C.Y. Chang
[gmx-users] Energy calculation C.Y. Chang
[gmx-users] Energy calculation C.Y. Chang
[gmx-users] implicit solvent model: formulation of non-polar free energy Chi-cheng Chiu
[gmx-users] implicit solvent GB force table Chi-cheng Chiu
[gmx-users] Parameterization of a molecule containing a radical (oxygen) Simone Cirri
[gmx-users] Tables - two non-bonded interactions Vinícius Contessoto
[gmx-users] tpic run option - potential energy meaning João M. Damas
[gmx-users] thickness of interface Widya Desmarani
[gmx-users] g_dielectric Nilesh Dhumal
[gmx-users] dipole autocorrelation function at each fs Nilesh Dhumal
[gmx-users] g_dipole Nilesh Dhumal
[gmx-users] dipole moment autocorrelation function Nilesh Dhumal
[gmx-users] g_dipole: dipole moment autocorrelation function Nilesh Dhumal
[gmx-users] g_dipole: dipole moment autocorrelation function: Bug? Nilesh Dhumal
[gmx-users] g_dipole: dipole moment autocorrelation function: Bug? Nilesh Dhumal
[gmx-users] flexible spc water model Nilesh Dhumal
[gmx-users] flexible spc water model Nilesh Dhumal
[gmx-users] g_dipole: dipole moment autocorrelation function Nilesh Dhumal
[gmx-users] g_dipole: dipole moment autocorrelation function Nilesh Dhumal
[gmx-users] g_dipole: dipole moment autocorrelation function Nilesh Dhumal
[gmx-users] surface tension in gmx Elisabeth
[gmx-users] surface tension Elisabeth
[gmx-users] Re: surface tension Elisabeth
[gmx-users] unit of surface tension, KJ/mol? Elisabeth
[gmx-users] unit of surface tension, KJ/mol? Elisabeth
[gmx-users] unit of surface tension, KJ/mol? Elisabeth
[gmx-users] unit of surface tension, KJ/mol? Elisabeth
[gmx-users] unit of surface tension, KJ/mol? Elisabeth
[gmx-users] surface tension vs. system size Elisabeth
[gmx-users] heat capacity in 4.5.3 and 4.0.7 Elisabeth
[gmx-users] heat capacity in 4.5.3 and 4.0.7 Elisabeth
[gmx-users] index file Elisabeth
[gmx-users] Thermal expansion coeff. Elisabeth
[gmx-users] Heat of vap Elisabeth
[gmx-users] Heat of vap Elisabeth
[gmx-users] Heat of vap Elisabeth
[gmx-users] installation of gromacs Diego Enry
[gmx-users] installation of gromacs Diego Enry
[gmx-users] installation of gromacs Diego Enry
[gmx-users] parallel running Esztermann, Ansgar
[gmx-users] parallel running Esztermann, Ansgar
[gmx-users] parallel running Esztermann, Ansgar
[gmx-users] No DD grid found André Ferreira
[gmx-users] No DD grid found André Ferreira
[gmx-users] installation of gromacs Dommert Florian
[gmx-users] Re: installation of gromacs (Dommert Florian) Dommert Florian
[gmx-users] installation of gromacs Dommert Florian
[gmx-users] g_tcaf reference Dommert Florian
[gmx-users] g_tcaf reference Dommert Florian
[gmx-users] g_dipole: dipole moment autocorrelation function Dommert Florian
[gmx-users] g_dipole: dipole moment autocorrelation function Dommert Florian
[gmx-users] g_dipole: dipole moment autocorrelation function Dommert Florian
[gmx-users] gromacs/CPMD. Is LAM mandatory? Elena Formoso
[gmx-users] gromacs/CPMD. Is LAM mandatory? Elena Formoso
[gmx-users] gromacs/CPMD. Is LAM mandatory? Elena Formoso
[gmx-users] RE: Regarding DCCM analysis with g_covar available in user contributed section Ran Friedman
[gmx-users] Surface tension readings in NVT vs NPT simulations Denny Frost
[gmx-users] Surface tension readings in NVT vs NPT simulations Denny Frost
[gmx-users] Surface tension readings in NVT vs NPT simulations Denny Frost
[gmx-users] Surface tension readings in NVT vs NPT simulations Denny Frost
[gmx-users] Surface tension readings in NVT vs NPT simulations Denny Frost
[gmx-users] Surface tension readings in NVT vs NPT simulations Denny Frost
[gmx-users] OPLS-AA force field for Benzyl alcohol and Phenylethanol Cen-Feng Fu
[gmx-users] Re: OPLS-AA force field for Benzyl alcohol and Phenylethanol Cen-Feng Fu
[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water Patrick Fuchs
[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water Patrick Fuchs
[gmx-users] mdrun cannot append to file larger than 2Gb Warren Gallin
[gmx-users] Is there still interest in rigid-body simulation? Ignacio Fernández Galván
[gmx-users] mdrun-gpu Nathalia Garces
[gmx-users] Problems with a three domain protein in a membrane "Dr. Ramón Garduño-Juárez"
[gmx-users] Splitted DMPC bilayer "Dr. Ramón Garduño-Juárez"
[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT) Yulian Gavrilov
[gmx-users] IMPLICIT SOLVENT IN AMBER Yulian Gavrilov
[gmx-users] IMPLICIT SOLVENT IN AMBER Yulian Gavrilov
[gmx-users] IMPLICIT SOLVENT IN AMBER Yulian Gavrilov
[gmx-users] isopeptide bond Yulian Gavrilov
[gmx-users] isopeptide bond Yulian Gavrilov
[gmx-users] isopeptide bond Yulian Gavrilov
[gmx-users] isopeptide bond Yulian Gavrilov
[gmx-users] ffamber99.hdb Yulian Gavrilov
[gmx-users] isopeptide bond Yulian Gavrilov
[gmx-users] isopeptide bond Yulian Gavrilov
[gmx-users] Annealing of shell polarizable water model Ivan Gladich
[gmx-users] Annealing of shell polarizable water model Ivan Gladich
[gmx-users] Annealing of shell polarizable water model Ivan Gladich
[gmx-users] Annealing of shell polarizable water model Ivan Gladich
[gmx-users] Regarding Gromacs Application in more than 10 node cluster Kannan Govindarajan
[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein Oliver Grant
[gmx-users] Re: 4. Re: QMMM (Txema Mercero) Gerrit Groenhof
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 63 Gerrit Groenhof
[gmx-users] Re: Parameterization of a molecule containing a radical, (oxygen) (Justin A. Lemkul) Gerrit Groenhof
[gmx-users] Viscosity calculation problems (periodic perturbation method) Xiang Gu
[gmx-users] Re: Is there still interest in rigid-body simulation? Michael Hagan
[gmx-users] Effect of pH on catalytic side Monisha Hajra
[gmx-users] Effect of pH on catalytic side Monisha Hajra
[gmx-users] Effect of pH on catalytic side Monisha Hajra
[gmx-users] Error in GROMACS installation Monisha Hajra
[gmx-users] Error in GROMACS installation Monisha Hajra
[gmx-users] installation of gromacs Tim Harder
[gmx-users] QMMM Haresh
[gmx-users] QMMM Haresh
[gmx-users] How to merge 2 top-files Ghassen Hassani
[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI Adam Herbst
[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI Adam Herbst
[gmx-users] Is there still interest in rigid-body simulation? Adam Herbst
[gmx-users] checking gen_seed Kwee Hong
[gmx-users] checking gen_seed Kwee Hong
[gmx-users] g_wham PMF profile Jochen Hub
[gmx-users] Zero Potential of Mean Force with g_wham Jochen Hub
[gmx-users] need help on how to use gromacs to simulate polymer ADETUNJI BAMIDELE IBRAHIM
[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's Jordi Inglés
[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's Jordi Inglés
[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's Jordi Inglés
[gmx-users] Gromacs for carbohydrates Geethu Issac
[gmx-users] water residence time on a certain group of ligand Olga Ivchenko
[gmx-users] distorted structure Olga Ivchenko
[gmx-users] Unsupported box diagonal Sweta Iyer
[gmx-users] Problem with g_rdf plot Carla Jamous
[gmx-users] Polarizable halide (Iodide) Abhijeet Joshi
[gmx-users] Polarizable halide (Iodide) Abhijeet Joshi
[gmx-users] Pull Error message Jonathan KHAO
[gmx-users] C-terminal amidation of peptide anna Kalkbrenner
[gmx-users] Forces with Constraints Apoorv Kalyankar
[gmx-users] Spatially Varying External Force Apoorv Kalyankar
[gmx-users] Questions about implementing G56A_CARB parameters Jon Kapla
[gmx-users] Special parameters for certain 1-5 LJ pairs (56Acarbo) Jon Kapla
[gmx-users] No cut-off Itamar Kass
[gmx-users] AFM pulling simulations Laura Kingsley
[gmx-users] Alcohol Dehydrogenase MD simulation....Reg Kishore
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 160 Kishore
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 188 Kishore
[gmx-users] CUT-OFFs for GROMOS96 43a1...Reg Kishore
[gmx-users] g_cluster segmentation fault Craig Kitchen
[gmx-users] Re: g_cluster segmentation fault Craig Kitchen
[gmx-users] heat capacity etc. Thomas Koller
[gmx-users] RE: heat capacity etc. Thomas Koller
[gmx-users] RE: heat capacity etc. Thomas Koller
[gmx-users] heat capacity etc. Thomas Koller
[gmx-users] Re: heat capacity etc. (David van der Spoel) Thomas Koller
[gmx-users] RE: heat capacity etc. Thomas Koller
[gmx-users] RE: heat capacity etc. (Thomas Koller) Thomas Koller
[gmx-users] RE: heat capacity etc. (Thomas Koller) Thomas Koller
[gmx-users] installation of gromacs Thomas Koller
[gmx-users] Re: installation of gromacs (Dommert Florian) Thomas Koller
[gmx-users] Re: installation of gromacs (Dommert Florian) Thomas Koller
[gmx-users] installation of gromacs Thomas Koller
[gmx-users] installation of gromacs Thomas Koller
[gmx-users] installation of gromacs Thomas Koller
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 123 Thomas Koller
[gmx-users] New maintenance release: gromacs-4.5.4 Carsten Kutzner
[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI Carsten Kutzner
[gmx-users] The "correct" way to equilibrate a membrane / lipid bilayer w/water? Peter C. Lai
[gmx-users] IMPLICIT SOLVENT IN AMBER Per Larsson
[gmx-users] IMPLICIT SOLVENT IN AMBER Per Larsson
[gmx-users] RE: g_energy inconsistent results Per Larsson
[gmx-users] implicit solvent model: formulation of non-polar free energy Per Larsson
[gmx-users] implicit solvent GB force table Per Larsson
[gmx-users] 1/viscosity in g_energy Alif M Latif
[gmx-users] Git tutorial for gromacs Alif M Latif
[gmx-users] Thank You for 4.5.4 Alif M Latif
[gmx-users] question about g_tcaf Alif M Latif
[gmx-users] charge group radii- use maxwarn or increase rlist? Justin A. Lemkul
[gmx-users] .tdr file not created Justin A. Lemkul
[gmx-users] .tdr file not created Justin A. Lemkul
[gmx-users] about -CN triple bond Justin A. Lemkul
[gmx-users] Particle type 'B' in topology file? Justin A. Lemkul
[gmx-users] Problems with pull simulation output - VMD shows broken up groups Justin A. Lemkul
[gmx-users] Problems with pull simulation output - VMD shows broken up groups Justin A. Lemkul
[gmx-users] Re: adding ff parameter of modified residue to charmm ff Justin A. Lemkul
[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04 Justin A. Lemkul
[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04 Justin A. Lemkul
[gmx-users] number of DD cells Justin A. Lemkul
[gmx-users] number of DD cells Justin A. Lemkul
[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04 Justin A. Lemkul
[gmx-users] number of DD cells Justin A. Lemkul
[gmx-users] Diffusion Coefficient Justin A. Lemkul
[gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration Justin A. Lemkul
[gmx-users] Warning: 1-4 interaction Justin A. Lemkul
[gmx-users] Warning: 1-4 interaction Justin A. Lemkul
[gmx-users] zero SOL molecules Justin A. Lemkul
[gmx-users] g_RMS: Mismatch of atom number between topology and reference structure Justin A. Lemkul
[gmx-users] Dihedral angles distribution Justin A. Lemkul
[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT) Justin A. Lemkul
[gmx-users] Thermostat for equilibration Justin A. Lemkul
[gmx-users] Dihedral angles distribution Justin A. Lemkul
[gmx-users] membrane-protein tutorial Justin A. Lemkul
[gmx-users] select in pymol after trjconv Justin A. Lemkul
[gmx-users] # Protein non-integer charge‏ Justin A. Lemkul
[gmx-users] select in pymol after trjconv Justin A. Lemkul
[gmx-users] membrane-protein tutorial Justin A. Lemkul
[gmx-users] # Protein non-integer charge‏ Justin A. Lemkul
[gmx-users] select in pymol after trjconv Justin A. Lemkul
[gmx-users] membrane-protein tutorial Justin A. Lemkul
[gmx-users] where does the gromacs looks for the top data file. Justin A. Lemkul
[gmx-users] # Protein non-integer charge‏ Justin A. Lemkul
[gmx-users] where does the gromacs looks for the top data file. Justin A. Lemkul
[gmx-users] g_rmsf Justin A. Lemkul
[gmx-users] Membrane-protein tutorial Justin A. Lemkul
[gmx-users] Instantaneous Square Displacement Justin A. Lemkul
[gmx-users] parallel running Justin A. Lemkul
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Justin A. Lemkul
[gmx-users] creating a bilayer of dppc Justin A. Lemkul
[gmx-users] Definition of helicity Justin A. Lemkul
[gmx-users] Definition of helicity Justin A. Lemkul
[gmx-users] secondary structure propensities of residues Justin A. Lemkul
[gmx-users] Problem when running in many nodes Justin A. Lemkul
[gmx-users] Treatment of protein termini when there are missing residues Justin A. Lemkul
[gmx-users] disulfide bridge broken during EM Justin A. Lemkul
[gmx-users] Re: disulfide bridge broken during EM Justin A. Lemkul
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Justin A. Lemkul
[gmx-users] RMSD truncation Restart simulation problems Justin A. Lemkul
[gmx-users] Possible free energy bug? Justin A. Lemkul
[gmx-users] Viscosity calculation problems (periodic perturbation method) Justin A. Lemkul
[gmx-users] 2 Questions Justin A. Lemkul
[gmx-users] Possible free energy bug? Justin A. Lemkul
[gmx-users] Possible free energy bug? Justin A. Lemkul
[gmx-users] Possible free energy bug? Justin A. Lemkul
[gmx-users] modified atomtypes.atp and grompp Justin A. Lemkul
[gmx-users] Topology Justin A. Lemkul
[gmx-users] the problem of gromacs Justin A. Lemkul
[gmx-users] Regarding error during genion step before energy minimization Justin A. Lemkul
[gmx-users] Implicit Solvent seems to collapse molecule to origin Justin A. Lemkul
[gmx-users] Can gmx change a, b of 3D pbc box but remain c in constant-NPT MD? Justin A. Lemkul
[gmx-users] Possible free energy bug? Justin A. Lemkul
[gmx-users] trjorder, what and how does es count (amount solvent atoms or molecules)? Justin A. Lemkul
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Justin A. Lemkul
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Justin A. Lemkul
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Justin A. Lemkul
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Justin A. Lemkul
[gmx-users] Possible free energy bug? (NOT SOLVED) Justin A. Lemkul
[gmx-users] g_wham PMF profile Justin A. Lemkul
[gmx-users] Possible free energy bug? (NOT SOLVED) Justin A. Lemkul
[gmx-users] Re: installation of gromacs (Dommert Florian) Justin A. Lemkul
[gmx-users] Failure to preserve simulation temperature Justin A. Lemkul
[gmx-users] LINCS and number of nodes Justin A. Lemkul
[gmx-users] OPLS forcefield for Alkane and ethers? Justin A. Lemkul
[gmx-users] Replacing a residue and continuing a simulation run Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] g_order for DPC alkyl chain in the micelle Justin A. Lemkul
[gmx-users] Pressure Fluctuations Justin A. Lemkul
[gmx-users] Re: g_order for DPC alkyl chain in the micelle Justin A. Lemkul
[gmx-users] Pressure Fluctuations Justin A. Lemkul
[gmx-users] Website search down again Justin A. Lemkul
[gmx-users] Memory allocation - xpm2ps Justin A. Lemkul
[gmx-users] lipopeptide problem Justin A. Lemkul
[gmx-users] installation of gromacs Justin A. Lemkul
[gmx-users] including non standard amino acid CSD in topology file Justin A. Lemkul
[gmx-users] PMF for Carbohydrate-Protein Justin A. Lemkul
[gmx-users] lipopeptide problem Justin A. Lemkul
[gmx-users] 1/viscosity in g_energy Justin A. Lemkul
[gmx-users] Re: change in structure after simulation Justin A. Lemkul
[gmx-users] ATP+Mg Justin A. Lemkul
[gmx-users] LINCS and number of nodes Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 130 Justin A. Lemkul
[gmx-users] Re: Fwd: pdb2gmx problem recognising capping on Gromacs 4.5.2 Justin A. Lemkul
[gmx-users] C-terminal amidation of peptide Justin A. Lemkul
[gmx-users] Re: compressing a system Justin A. Lemkul
[gmx-users] Re: compressing a system Justin A. Lemkul
[gmx-users] Fw: g_membed tool Justin A. Lemkul
[gmx-users] Git tutorial for gromacs Justin A. Lemkul
[gmx-users] including non standard amino acid CSD in topology file Justin A. Lemkul
[gmx-users] compressing in presence of voids Justin A. Lemkul
[gmx-users] Gromacs on other Operating Systems Justin A. Lemkul
[gmx-users] Gromacs on other Operating Systems Justin A. Lemkul
[gmx-users] Annealing of shell polarizable water model Justin A. Lemkul
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx Justin A. Lemkul
[gmx-users] changing charged groups in CHARMM RNA Justin A. Lemkul
[gmx-users] changing charged groups in CHARMM RNA Justin A. Lemkul
[gmx-users] AFM pulling simulations Justin A. Lemkul
[gmx-users] Hydroixde Ion Justin A. Lemkul
[gmx-users] Various web issues Justin A. Lemkul
[gmx-users] Various web issues Justin A. Lemkul
[gmx-users] Hydroixde Ion Justin A. Lemkul
[gmx-users] Hydroixde Ion Justin A. Lemkul
[gmx-users] Parameterization of a molecule containing a radical (oxygen) Justin A. Lemkul
[gmx-users] unit of surface tension, KJ/mol? Justin A. Lemkul
[gmx-users] unit of surface tension, KJ/mol? Justin A. Lemkul
[gmx-users] unit of surface tension, KJ/mol? Justin A. Lemkul
[gmx-users] %hbond number problem Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] account for PBC Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] no output dgdl file Justin A. Lemkul
[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI Justin A. Lemkul
[gmx-users] ethanol and dmso files Justin A. Lemkul
[gmx-users] Problems with a three domain protein in a membrane Justin A. Lemkul
[gmx-users] Problems with a three domain protein in a membrane Justin A. Lemkul
[gmx-users] The "correct" way to equilibrate a membrane / lipid bilayer w/water? Justin A. Lemkul
[gmx-users] units for atomic coordinates in traj.xtc? nm? Justin A. Lemkul
[gmx-users] Citation for NICS Justin A. Lemkul
[gmx-users] flexible spc water model Justin A. Lemkul
[gmx-users] Automated RMSD Calculations Justin A. Lemkul
[gmx-users] Re: Alcohol Dehydrogenase MD simulation....Reg Justin A. Lemkul
[gmx-users] mdrun cannot append to file larger than 2Gb Justin A. Lemkul
[gmx-users] RMSD Calculation Justin A. Lemkul
[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family Justin A. Lemkul
[gmx-users] dihedral angles Justin A. Lemkul
[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family Justin A. Lemkul
[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family Justin A. Lemkul
[gmx-users] No DD grid found Justin A. Lemkul
[gmx-users] flexible spc water model Justin A. Lemkul
[gmx-users] Gromacs for carbohydrates Justin A. Lemkul
[gmx-users] oligoglycines Justin A. Lemkul
[gmx-users] Placing ions at a required distance Justin A. Lemkul
[gmx-users] re: Gromos96 43A1 Justin A. Lemkul
[gmx-users] Placing ions at a required distance Justin A. Lemkul
[gmx-users] PSF files from .top to .psf Justin A. Lemkul
[gmx-users] Atomtype CCL4 not found Justin A. Lemkul
[gmx-users] Atomtype CCL4 not found Justin A. Lemkul
[gmx-users] Atomtype CCL4 not found Justin A. Lemkul
[gmx-users] pullx.xvg format Justin A. Lemkul
[gmx-users] pullx.xvg format Justin A. Lemkul
[gmx-users] Effect of pH on catalytic side Justin A. Lemkul
[gmx-users] Check for bad contacts and/or reduce the timestep. Justin A. Lemkul
[gmx-users] Error in GROMACS installation Justin A. Lemkul
[gmx-users] SO4 Justin A. Lemkul
[gmx-users] Error in GROMACS installation Justin A. Lemkul
[gmx-users] index file Justin A. Lemkul
[gmx-users] g_energy -ravg option Justin A. Lemkul
[gmx-users] Splitted DMPC bilayer Justin A. Lemkul
[gmx-users] Heat of vap Justin A. Lemkul
[gmx-users] Help on umbrella sampling Justin A. Lemkul
[gmx-users] Help with Umbrella Sampling Justin A. Lemkul
[gmx-users] Umbrella sampling Justin A. Lemkul
[gmx-users] CUT-OFFs for GROMOS96 43a1...Reg Justin A. Lemkul
[gmx-users] Heat of vap Justin A. Lemkul
[gmx-users] adding a new residue in the ff Justin A. Lemkul
[gmx-users] Heat of vap Justin A. Lemkul
[gmx-users] adding a new residue in the ff Justin A. Lemkul
[gmx-users] Taking difference of forces in two trajectories Justin A. Lemkul
[gmx-users] Free energy calculation and position restraint Da-Wei Li
[gmx-users] REMD simulation of peptide-membrane system Jianguo Li
[gmx-users] Re: adding ff parameter of modified residue to charmm ff Jianguo Li
[gmx-users] parallel running Jianguo Li
[gmx-users] Zero Potential of Mean Force with g_wham Jianguo Li
[gmx-users] Re: g_hbond output Jianguo Li
[gmx-users] Re: g_hbond output Jianguo Li
[gmx-users] C-terminal amidation of peptide Jianguo Li
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 153 Xiaohu Li
[gmx-users] Diffusion Coefficient Chih-Ying Lin
[gmx-users] Re-compile Gromacs Program? Chih-Ying Lin
[gmx-users] select in pymol after trjconv ZHAO Lina
[gmx-users] select in pymol after trjconv ZHAO Lina
[gmx-users] select in pymol after trjconv ZHAO Lina
[gmx-users] select in pymol after trjconv ZHAO Lina
[gmx-users] where does the gromacs looks for the top data file. ZHAO Lina
[gmx-users] where does the gromacs looks for the top data file. ZHAO Lina
[gmx-users] secondary structure propensities of residues ZHAO Lina
[gmx-users] terminated but not completely ZHAO Lina
[gmx-users] g_hbond output ZHAO Lina
[gmx-users] Re: g_hbond output ZHAO Lina
[gmx-users] Re: g_hbond output ZHAO Lina
[gmx-users] make_ndx ZHAO Lina
[gmx-users] Re: make_ndx ZHAO Lina
[gmx-users] Invitation to connect on LinkedIn ram prasad via LinkedIn
[gmx-users] Invitation to connect on LinkedIn Ramachandran Gnanasekaran via LinkedIn
[gmx-users] surface tension in gmx Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] spectral density calculation with GROMACS ZHANG Lu
[gmx-users] couple-moltype for two molecules Luca
[gmx-users] How to find average protein structure. Daniel Adriano Silva M
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx Daniel Adriano Silva M
[gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration Kavyashree M
[gmx-users] Q's regarding cutoff, charge groups, thermocouple and equlibration Kavyashree M
[gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration Kavyashree M
[gmx-users] Thermostat for equilibration Kavyashree M
[gmx-users] Thermostat for equilibration Kavyashree M
[gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration Kavyashree M
[gmx-users] Density of water, Dispcorr and rmsd Kavyashree M
[gmx-users] Pressure Fluctuations Kavyashree M
[gmx-users] Pressure Fluctuations Kavyashree M
[gmx-users] Pressure Fluctuations Kavyashree M
[gmx-users] Pressure Fluctuations Kavyashree M
[gmx-users] OPLS forcefield for Alkane and ethers? Sanku M
Re: [gmx-users] New maintenance release: gromacs-4.5.4 Ye MEI
[gmx-users] Fw: How can I use trjorder ? mina Madah
[gmx-users] how to differentiate crystal water and explicit waters in gromacs ??? Praveen Kumar Madala
[gmx-users] Web site issues (Search, Redmine) Lutz Maibaum
[gmx-users] g_RMS: Mismatch of atom number between topology and reference structure Sergio Manzetti
[gmx-users] Citation for NICS Sergio Manzetti
[gmx-users] Citation for NICS Sergio Manzetti
[gmx-users] disulfide bridge broken during EM Anna Marabotti
[gmx-users] Re: disulfide bridge broken during EM Anna Marabotti
[gmx-users] .cpt and .trr files Anna Marabotti
[gmx-users] LINCS warning on galactose molecule Anna Marabotti
[gmx-users] adding a new residue in the ff Anna Marabotti
[gmx-users] mpi run in Gromacs Erik Marklund
[gmx-users] pdb structure file at particular time(ps) Erik Marklund
[gmx-users] V-Rescale Reference Erik Marklund
[gmx-users] Re: g_hbond output Erik Marklund
[gmx-users] Re: g_hbond output Erik Marklund
[gmx-users] mdrun the pr.trr Erik Marklund
[gmx-users] No cut-off Erik Marklund
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral Erik Marklund
[gmx-users] Effect of pH on catalytic side Erik Marklund
[gmx-users] Effect of pH on catalytic side Erik Marklund
[gmx-users] creating a bilayer of dppc Igor Marques
[gmx-users] g_membed tool Igor Marques
[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04 Joanne Martin
[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04 Joanne Martin
[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04 Joanne Martin
[gmx-users] Taking difference of forces in two trajectories Sikandar Mashayak
[gmx-users] Taking difference of forces in two trajectories Sikandar Mashayak
[gmx-users] Implicit Solvent seems to collapse molecule to origin Andrew Mauro
[gmx-users] Support GTS 450 Aleksei Medvedev
[gmx-users] Regarding error during genion step before energy minimization Meenakshi
[gmx-users] pullx.xvg format Gavin Melaugh
[gmx-users] pullx.xvg format Gavin Melaugh
[gmx-users] Umbrella sampling Gavin Melaugh
[gmx-users] Umbrella sampling Gavin Melaugh
[gmx-users] Umbrella sampling Gavin Melaugh
[gmx-users] Umbrella sampling Gavin Melaugh
[gmx-users] Umbrella Sampling Gavin Melaugh
[gmx-users] Umbrella sampling Gavin Melaugh
[gmx-users] Umbrella Sampling Gavin Melaugh
[gmx-users] QMMM Txema Mercero
[gmx-users] charge group radii- use maxwarn or increase rlist? Moeed
[gmx-users] number of DD cells Moeed
[gmx-users] number of DD cells Moeed
[gmx-users] Warning: 1-4 interaction Moeed
[gmx-users] Warning: 1-4 interaction Moeed
[gmx-users] heat capacity etc. Moeed
[gmx-users] Re: question about gromacs (4.5) installation Moeed
[gmx-users] Re: question about gromacs (4.5) installation Moeed
[gmx-users] Warning: 1-4 interaction Moeed
[gmx-users] LINCS and number of nodes Moeed
[gmx-users] LINCS and number of nodes Moeed
[gmx-users] compressing a system Moeed
[gmx-users] Re: compressing a system Moeed
[gmx-users] Re: compressing a system Moeed
[gmx-users] compressing in presence of voids Moeed
[gmx-users] no output dgdl file Moeed
[gmx-users] no output dgdl file Moeed
[gmx-users] no output dgdl file Moeed
[gmx-users] RMSD truncation Restart simulation problems Henri Mone
[gmx-users] RMSD truncation Restart simulation problems Henri Mone
[gmx-users] RMSD truncation Restart simulation problems Henri Mone
[gmx-users] trjorder, what and how does es count (amount solvent atoms or molecules)? Henri Mone
[gmx-users] Density of methanol too low Jesús Carrete Montaña
[gmx-users] surface tension in gmx André Farias de Moura
[gmx-users] surface tension in gmx André Farias de Moura
[gmx-users] Re: surface tension André Farias de Moura
[gmx-users] Re: surface tension André Farias de Moura
[gmx-users] Re: surface tension André Farias de Moura
[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water André Farias de Moura
[gmx-users] g_gyrate options Juliette N.
[gmx-users] Hydroixde Ion SHIVANGI NANGIA
[gmx-users] Hydroixde Ion SHIVANGI NANGIA
[gmx-users] Hydroixde Ion SHIVANGI NANGIA
[gmx-users] Hydroixde Ion SHIVANGI NANGIA
[gmx-users] Gromacs on other Operating Systems Nancy
[gmx-users] Gromacs on other Operating Systems Nancy
[gmx-users] Automated RMSD Calculations Nancy
[gmx-users] Automated RMSD Calculations Nancy
[gmx-users] Best Program for Simulating Lipid Bilayers in Water Nancy
[gmx-users] RMSD Calculation Nancy
[gmx-users] mpi run in Gromacs Selina Nawaz
[gmx-users] .pdb file for DNA Paulo Netz
[gmx-users] re: Gromos96 43A1 Frank Neuhaus
[gmx-users] namd in gromacs Francesco Oteri
[gmx-users] versions Francesco Oteri
[gmx-users] versions Francesco Oteri
[gmx-users] calcium diffuses away from the protein during MD Sunita Patel
[gmx-users] calcium diffuses away from the protein during MD XAvier Periole
[gmx-users] GROMACS 4.5 and MARTINI Force Field Installation XAvier Periole
[gmx-users] Umbrella sampling XAvier Periole
[gmx-users] Umbrella sampling XAvier Periole
[gmx-users] Umbrella sampling XAvier Periole
Antw: [gmx-users] Citation for NICS Emanuel Peter
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 217 Raghuvir R S Pissurlenkar
[gmx-users] Help with Umbrella Sampling Raghuvir R S Pissurlenkar
[gmx-users] g_order for DPC alkyl chain in the micelle Ángel Piñeiro
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 106 Ángel Piñeiro
[gmx-users] g_order for DPC alkyl chain in the micelle Ángel Piñeiro
[gmx-users] Dihedral Restraints Sai Pooja
[gmx-users] dihedral angles Sai Pooja
[gmx-users] Resplica exchange with solute tempering (REST) Sai Pooja
[gmx-users] Re: Resplica exchange with solute tempering (REST) Sai Pooja
[gmx-users] Re: Resplica exchange with solute tempering (REST) Sai Pooja
[gmx-users] Re: Resplica exchange with solute tempering (REST) Sai Pooja
[gmx-users] mdrun-gpu Szilárd Páll
[gmx-users] Tweeking MDP file options to run on GPU Szilárd Páll
[gmx-users] no output dgdl file Szilárd Páll
[gmx-users] no output dgdl file Szilárd Páll
[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's Szilárd Páll
[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's Szilárd Páll
[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's Szilárd Páll
[gmx-users] PMF for Carbohydrate-Protein Sai Kumar Ramadugu
[gmx-users] angular velocity autocorrelation Vigneshwar Ramakrishnan
[gmx-users] modified atomtypes.atp and grompp Rausch, Felix
AW: [gmx-users] modified atomtypes.atp and grompp Rausch, Felix
AW: [gmx-users] lipopeptide problem Rausch, Felix
[gmx-users] Atomtype CCL4 not found Rausch, Felix
[gmx-users] GROMACS 4.5 and MARTINI Force Field Installation Edroaldo Lummertz da Rocha
[gmx-users] AFM pulling simulations X Rules
[gmx-users] AFM pulling simulations X Rules
[gmx-users] AFM pulling simulations X Rules
[gmx-users] Re: pull forces Thomas Schlesier
[gmx-users] g_energy inconsistent results Ehud Schreiber
[gmx-users] RE: g_energy inconsistent results Ehud Schreiber
[gmx-users] namd in gromacs Roland Schulz
[gmx-users] Gromacs on other Operating Systems Roland Schulz
[gmx-users] Thank You for 4.5.4 Roland Schulz
[gmx-users] New maintenance release: gromacs-4.5.4 Roland Schulz
[gmx-users] install problems cygwin Roland Schulz
[gmx-users] Replacing a residue and continuing a simulation run J. Nathan Scott
[gmx-users] gromacs/CPMD. Is LAM mandatory? Christian Seifert
[gmx-users] problem with REMD run continuation Giovanni Settanni
[gmx-users] Memory allocation - xpm2ps Shi, Chuanyin
[gmx-users] Memory allocation - xpm2ps Shi, Chuanyin
[gmx-users] Possible free energy bug? Michael Shirts
[gmx-users] autocorrelation time of dVpot/dlambda? Michael Shirts
[gmx-users] Post simulation energy calculation of Ligand - Protein complex Rahul ShubhraMandal
[gmx-users] QMMM Jack Shultz
[gmx-users] ffamber99.hdb Alexey Shvetsov
[gmx-users] converting ILDN parameters to RB Alan Wilter Sousa da Silva
[gmx-users] converting ILDN parameters to RB Alan Wilter Sousa da Silva
[gmx-users] # Protein non-integer charge‏ Marcelo Silva
[gmx-users] # Protein non-integer charge‏ Marcelo Silva
[gmx-users] V-Rescale Reference Ricardo O. S. Soares
Res: [gmx-users] V-Rescale Reference Ricardo O. S. Soares
[gmx-users] Polarizable halide (Iodide) David van der Spoel
[gmx-users] Polarizable halide (Iodide) David van der Spoel
[gmx-users] Re: Polarizable halide (Iodide) David van der Spoel
[gmx-users] g_dipole David van der Spoel
[gmx-users] heat capacity etc. David van der Spoel
[gmx-users] heat capacity etc. David van der Spoel
[gmx-users] Re: heat capacity etc. (David van der Spoel) David van der Spoel
[gmx-users] RE: heat capacity etc. David van der Spoel
[gmx-users] RE: heat capacity etc. (Thomas Koller) David van der Spoel
[gmx-users] Surface tension readings in NVT vs NPT simulations David van der Spoel
[gmx-users] versions David van der Spoel
[gmx-users] versions David van der Spoel
[gmx-users] RE: heat capacity etc. (Thomas Koller) David van der Spoel
[gmx-users] Surface tension readings in NVT vs NPT simulations David van der Spoel
[gmx-users] Surface tension readings in NVT vs NPT simulations David van der Spoel
[gmx-users] Surface tension readings in NVT vs NPT simulations David van der Spoel
[gmx-users] Surface tension readings in NVT vs NPT simulations David van der Spoel
[gmx-users] Surface tension readings in NVT vs NPT simulations David van der Spoel
[gmx-users] g_wham PMF profile David van der Spoel
[gmx-users] OPLS forcefield for Alkane and ethers? David van der Spoel
[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ? David van der Spoel
[gmx-users] Density of methanol too low David van der Spoel
[gmx-users] OPLS-AA force field for Benzyl alcohol and Phenylethanol David van der Spoel
[gmx-users] Re: OPLS-AA force field for Benzyl alcohol and Phenylethanol David van der Spoel
[gmx-users] Nucleosides OPLS-AA David van der Spoel
[gmx-users] Nucleosides OPLS-AA David van der Spoel
[gmx-users] Annealing of shell polarizable water model David van der Spoel
[gmx-users] heat capacity in 4.5.3 and 4.0.7 David van der Spoel
[gmx-users] g_clustsize and monomers David van der Spoel
[gmx-users] heat capacity in 4.5.3 and 4.0.7 David van der Spoel
[gmx-users] g_clustsize and monomers David van der Spoel
[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family David van der Spoel
[gmx-users] Alternating electric fields in GROMACS David van der Spoel
[gmx-users] g_dipole: dipole moment autocorrelation function David van der Spoel
[gmx-users] g_dipole: dipole moment autocorrelation function David van der Spoel
[gmx-users] Heat of vap David van der Spoel
[gmx-users] g_dipole: dipole moment autocorrelation function David van der Spoel
[gmx-users] converting ILDN parameters to RB David van der Spoel
[gmx-users] converting ILDN parameters to RB David van der Spoel
[gmx-users] Heat of vap David van der Spoel
[gmx-users] Heat of vap David van der Spoel
[gmx-users] Problems with pull simulation output - VMD shows broken up groups Natalie Stephenson
[gmx-users] Problems with pull simulation output - VMD shows broken up groups Natalie Stephenson
[gmx-users] Re: Polarizable halide (Iodide) Mikhail Stukan
[gmx-users] amide partial charges XUEMING TANG
[gmx-users] DENIZ-senin yapacagina benzer birsey yapmis, residue eklemis.. Emine Deniz Tekin
[gmx-users] lipopeptide problem Emine Deniz Tekin
[gmx-users] lipopeptide problem Emine Deniz Tekin
[gmx-users] Strange behavior from g_sas Terry
[gmx-users] Strange behavior from g_sas Terry
[gmx-users] Zero Potential of Mean Force with g_wham Susana Tomasio
[gmx-users] Zero Potential of Mean Force with g_wham Susana Tomasio
[gmx-users] Zero Potential of Mean Force with g_wham Susana Tomasio
[gmx-users] manually creating a topology file Nishith Saurav Topno
[gmx-users] Tables - two non-bonded interactions Gareth Tribello
[gmx-users] Coulomb interactions Swarnendu Tripathi
[gmx-users] Coulomb interactions Swarnendu Tripathi
[gmx-users] No cut-off Swarnendu Tripathi
[gmx-users] No cut-off Swarnendu Tripathi
[gmx-users] No cut-off Swarnendu Tripathi
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian
[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault Steve Vivian
[gmx-users] Failure to preserve simulation temperature NG HUI WEN
[gmx-users] Membrane Protein Tutorial Dallas Warren
[gmx-users] QMMM Dallas Warren
[gmx-users] Fw: g_membed tool Dallas Warren
[gmx-users] Fw: g_membed tool Dallas Warren
[gmx-users] compressing in presence of voids Dallas Warren
[gmx-users] trjconv problem Tsjerk Wassenaar
[gmx-users] Vectors in non-cubic box Tsjerk Wassenaar
[gmx-users] Vectors in non-cubic box Tsjerk Wassenaar
[gmx-users] Replacing a residue and continuing a simulation run Tsjerk Wassenaar
[gmx-users] g_rms & g-rmsd Tsjerk Wassenaar
[gmx-users] Simulation of slow folding proteins Tsjerk Wassenaar
[gmx-users] question about g_tcaf Tsjerk Wassenaar
[gmx-users] g_tcaf reference Tsjerk Wassenaar
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral Tsjerk Wassenaar
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral Tsjerk Wassenaar
[gmx-users] RMSD Calculation Tsjerk Wassenaar
[gmx-users] oligoglycines Tsjerk Wassenaar
[gmx-users] Re: Which structure to be used during covariance analysis Tsjerk Wassenaar
[gmx-users] the total charge of system is not an integer Tsjerk Wassenaar
[gmx-users] the total charge of system is not an integer Tsjerk Wassenaar
[gmx-users] adding a new residue in the ff Tsjerk Wassenaar
[gmx-users] using one thermostat for entire system ?? Jennifer Williams
[gmx-users] Instantaneous Square Displacement Jennifer Williams
[gmx-users] using one thermostat for entire system ?? Jennifer Williams
[gmx-users] Instantaneous Square Displacement Jennifer Williams
[gmx-users] units for atomic coordinates in traj.xtc? nm? Jennifer Williams
[gmx-users] autocorrelation time of dVpot/dlambda? Shun Zhu
[gmx-users] autocorrelation time of dVpot/dlambda? Shun Zhu
[gmx-users] Possible free energy bug? Matthew Zwier
[gmx-users] Possible free energy bug? Matthew Zwier
[gmx-users] creating a bilayer of dppc delara aghaie
[gmx-users] g_wham PMF profile anna
[gmx-users] Polarizable halide (Iodide) aldi asmadi
[gmx-users] Surface tension readings in NVT vs NPT simulations aldi asmadi
[gmx-users] Help on umbrella sampling raghuvir at bcpindia.org
[gmx-users] Particle type 'B' in topology file? cdalgicdir
[gmx-users] g_clustsize and monomers devicerandom
[gmx-users] g_clustsize and monomers devicerandom
[gmx-users] g_clustsize and monomers devicerandom
[gmx-users] pdb structure file at particular time(ps) ajaniharesh at gmail.com
[gmx-users] How to find average protein structure. ajaniharesh at gmail.com
[gmx-users] OPLS force field for RNA nucleotides for protein RNA simulation maria goranovic
[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ? maria goranovic
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx maria goranovic
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx maria goranovic
[gmx-users] Nucleosides OPLS-AA maria goranovic
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx maria goranovic
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx maria goranovic
[gmx-users] changing charged groups in CHARMM RNA maria goranovic
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx maria goranovic
[gmx-users] changing charged groups in CHARMM RNA maria goranovic
[gmx-users] changing charged groups in CHARMM RNA maria goranovic
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx maria goranovic
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral maria goranovic
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral maria goranovic
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral maria goranovic
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral maria goranovic
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral maria goranovic
[gmx-users] the problem of gromacs zengyq at graduate.org
[gmx-users] Fatal error: ci = -1 should be in 0 zengyq at graduate.org
[gmx-users] mdrun the pr.trr zengyq at graduate.org
[gmx-users] %hbond number problem gromacs564
[gmx-users] %hbond number problem gromacs564
[gmx-users] Re: adding ff parameter of modified residue to charmm ff bharat gupta
[gmx-users] Re: adding ff parameter of modified residue to charmm ff bharat gupta
[gmx-users] Re: adding ff parameter of modified residue to charmm ff bharat gupta
[gmx-users] Re: change in structure after simulation bharat gupta
[gmx-users] Re: Simulation of slow folding proteins bharat gupta
[gmx-users] Treatment of protein termini when there are missing residues jo hanna
[gmx-users] .pdb file for DNA majid hasan
[gmx-users] trajectory output from g_select ? jkhao at ifr88.cnrs-mrs.fr
[gmx-users] Definition of helicity cd231 at ipc.uni-karlsruhe.de
[gmx-users] Definition of helicity cd231 at ipc.uni-karlsruhe.de
[gmx-users] trajectory output from g_select ? jonathan
[gmx-users] trajectory output from g_select ? jonathan
[gmx-users] trajectory output from g_select ? jonathan
[gmx-users] Re: Nitrogen box sarah k
[gmx-users] zero SOL molecules sarah k
[gmx-users] How to calculate parameters for gbsa.itp kala
[gmx-users] Tweeking MDP file options to run on GPU kala
[gmx-users] .tdr file not created sakthi kumaran
[gmx-users] .tdr file not created sakthi kumaran
[gmx-users] .tdr file not created sakthi kumaran
[gmx-users] Generating toplogy chitrala kumaraswamynaidu
[gmx-users] Topology chitrala kumaraswamynaidu
[gmx-users] g_membed tool Mohana lakshmi
[gmx-users] Fw: g_membed tool Mohana lakshmi
[gmx-users] Fw: g_membed tool Mohana lakshmi
[gmx-users] Umbrella Sampling and WHAM battistia at libero.it
[gmx-users] g_wham PMF profile battistia at libero.it
[gmx-users] g_wham PMF profile battistia at libero.it
[gmx-users] Vectors in non-cubic box afsaneh maleki
[gmx-users] Vectors in non-cubic box afsaneh maleki
[gmx-users] Disable non-bonded interactions between molecules ruehle at mpip-mainz.mpg.de
[gmx-users] Is there still interest in rigid-body simulation? ms
[gmx-users] Placing ions at a required distance shivangi nangia
[gmx-users] Placing ions at a required distance shivangi nangia
[gmx-users] Placing ions at a required distance shivangi nangia
[gmx-users] Check for bad contacts and/or reduce the timestep. shivangi nangia
[gmx-users] Check for bad contacts and/or reduce the timestep. shivangi nangia
[gmx-users] g_rms and g_cluster shahid nayeem
[gmx-users] membrane-protein tutorial mohsen ramezanpour
[gmx-users] membrane-protein tutorial mohsen ramezanpour
[gmx-users] membrane-protein tutorial mohsen ramezanpour
[gmx-users] membrane-protein tutorial mohsen ramezanpour
[gmx-users] Membrane-protein tutorial mohsen ramezanpour
[gmx-users] parallel running mohsen ramezanpour
[gmx-users] parallel running mohsen ramezanpour
[gmx-users] parallel running mohsen ramezanpour
[gmx-users] parallel running mohsen ramezanpour
[gmx-users] parallel running mohsen ramezanpour
[gmx-users] parallel running mohsen ramezanpour
[gmx-users] Membrane Protein Tutorial mohsen ramezanpour
[gmx-users] membrane-protein mohsen ramezanpour
[gmx-users] membrane protein mohsen ramezanpour
[gmx-users] versions mohsen ramezanpour
[gmx-users] versions mohsen ramezanpour
[gmx-users] versions mohsen ramezanpour
[gmx-users] terminated but not completely mohsen ramezanpour
[gmx-users] Grandcanonical Ensemble mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Pulling mohsen ramezanpour
[gmx-users] Pulling mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Fwd: membrane protein mohsen ramezanpour
[gmx-users] Fwd: membrane-protein mohsen ramezanpour
[gmx-users] Pulling mohsen ramezanpour
[gmx-users] g_rms & g-rmsd mohsen ramezanpour
[gmx-users] pick in pull.xvg mohsen ramezanpour
[gmx-users] g_rms & g-rmsd mohsen ramezanpour
[gmx-users] g_sham mohsen ramezanpour
[gmx-users] plot of force via time mohsen ramezanpour
[gmx-users] plot of force via time mohsen ramezanpour
[gmx-users] Dihedral angles distribution sa
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 40 sa
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 41 sa
[gmx-users] g_order for DPC alkyl chain in the micelle sa
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 106 sa
[gmx-users] g_order for DPC alkyl chain in the micelle sa
[gmx-users] Re: g_order for DPC alkyl chain in the micelle sa
[gmx-users] g_order for DPC alkyl chain in the micelle sa
[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family sa
[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family sa
[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family sa
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 196 sa
[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family sa
[gmx-users] RE: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family sa
[gmx-users] 2 Questions simon sham
[gmx-users] g_rmsf simon sham
[gmx-users] SO4 simon sham
[gmx-users] g_energy -ravg option simon sham
[gmx-users] Error during PUMED installation for GROMACS-4.5.3 bipin singh
[gmx-users] Regarding DCCM analysis with g_covar available in user contributed section bipin singh
[gmx-users] Regarding editconf bipin singh
[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar) bipin singh
[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar) bipin singh
[gmx-users] Which structure to be used during covariance analysis bipin singh
[gmx-users] Re: Which structure to be used during covariance analysis bipin singh
[gmx-users] Re: Which structure to be used during covariance analysis bipin singh
[gmx-users] Error during PUMED installation for GROMACS-4.5.3 andrea spitaleri
[gmx-users] including non standard amino acid CSD in topology file ashutosh srivastava
[gmx-users] including non standard amino acid CSD in topology file ashutosh srivastava
[gmx-users] install problems cygwin vijaya subramanian
[gmx-users] install problems cygwin vijaya subramanian
[gmx-users] problem in energy minimization of the inflted system Parul tew
[gmx-users] g_rmsf vferrario at units.it
[gmx-users] g_rmsf vferrario at units.it
[gmx-users] using one thermostat for entire system ?? chris.neale at utoronto.ca
[gmx-users] Zero Potential of Mean Force with g_wham chris.neale at utoronto.ca
[gmx-users] g_wham PMF profile chris.neale at utoronto.ca
[gmx-users] Pulling chris.neale at utoronto.ca
[gmx-users] Umberella sampling chris.neale at utoronto.ca
[gmx-users] Pulling chris.neale at utoronto.ca
[gmx-users] Umberella sampling chris.neale at utoronto.ca
[gmx-users] pick in pull.xvg chris.neale at utoronto.ca
[gmx-users] plot of force via time chris.neale at utoronto.ca
[gmx-users] g_sham chris.neale at utoronto.ca
[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water chris.neale at utoronto.ca
[gmx-users] Simulation of slow folding proteins chris.neale at utoronto.ca
[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water chris.neale at utoronto.ca
[gmx-users] Umbrella sampling chris.neale at utoronto.ca
[gmx-users] Umbrella Sampling chris.neale at utoronto.ca
[gmx-users] Umbrella Sampling chris.neale at utoronto.ca
[gmx-users] oplsaa galactose nishap.patel at utoronto.ca
[gmx-users] Nucleosides OPLS-AA nishap.patel at utoronto.ca
[gmx-users] Nucleosides OPLS-AA nishap.patel at utoronto.ca
[gmx-users] Nucleosides OPLS-AA nishap.patel at utoronto.ca
[gmx-users] Carbohydrate simulation: problem with the terminal atoms nishap.patel at utoronto.ca
[gmx-users] oligoglycines nishap.patel at utoronto.ca
[gmx-users] oligoglycines nishap.patel at utoronto.ca
[gmx-users] oligoglycines nishap.patel at utoronto.ca
[gmx-users] account for PBC ahmet yıldırım
[gmx-users] ethanol and dmso files ahmet yıldırım
[gmx-users] Atomtype CCL4 not found ahmet yıldırım
[gmx-users] Atomtype CCL4 not found ahmet yıldırım
[gmx-users] Atomtype CCL4 not found ahmet yıldırım
[gmx-users] Atomtype CCL4 not found ahmet yıldırım
[gmx-users] the total charge of system is not an integer ahmet yıldırım
[gmx-users] the total charge of system is not an integer ahmet yıldırım
[gmx-users] isopeptide bond zeppelin zeppelin
[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT) zeppelin zeppelin
[gmx-users] mdrun michael zhenin
[gmx-users] trjconv problem Алексей Раевский
[gmx-users] (no subject) Алексей Раевский
[gmx-users] ATP+Mg Алексей Раевский
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 130 Алексей Раевский
[gmx-users] different RMSD graphs after using pbc mol גדעון לפידות
[gmx-users] Can gmx change a, b of 3D pbc box but remain c in constant-NPT MD? 英雄不再寂寞
[gmx-users] How can I convert Gromacs ouput to Desmond input file?? 김현식

Last message date: Thu Mar 31 23:52:58 CEST 2011
Archived on: Thu Nov 14 12:10:32 CET 2013

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