September 2012 Archives by author

Messages sorted by: [ thread ] [ subject ] [ date ]
More info on this list...

Starting: Sat Sep 1 03:45:13 CEST 2012
Ending: Sun Sep 30 19:06:29 CEST 2012
Messages: 674

[gmx-users] charge calculation........ ABEL Stephane 175950
[gmx-users] doubt in minimization part Shine A
[gmx-users] Elastic network model Mark Abraham
[gmx-users] Re: Turning off electrostatics between groups using custom tables? Mark Abraham
[gmx-users] periodicity in msd calculation Mark Abraham
[gmx-users] On creating pdb file using dynamic indices from g_select Mark Abraham
[gmx-users] puzzling about ffnonbonded.itp Mark Abraham
[gmx-users] Ligand Internal energy Mark Abraham
[gmx-users] Ligand Internal energy Mark Abraham
[gmx-users] Ligand Internal energy Mark Abraham
[gmx-users] Calculating number of water molecules involves between dimer protein. Mark Abraham
[gmx-users] How to delete atoms during MD runs? Mark Abraham
[gmx-users] How to delete atoms during MD runs? Mark Abraham
[gmx-users] Variation of angles of simulation cell - regd Mark Abraham
[gmx-users] Variation of angles of simulation cell - regd Mark Abraham
[gmx-users] Charge Group Number in itp File (cgnr) Mark Abraham
[gmx-users] time constant in V-rescale algorithm Mark Abraham
[gmx-users] How to determin the simulation time Mark Abraham
[gmx-users] create topology other solvent Mark Abraham
[gmx-users] Different initial conditions for the membrane protein simulation Mark Abraham
[gmx-users] Published articles which have used Gromcas for their work Mark Abraham
[gmx-users] Calculating tertiary structure rotation Mark Abraham
[gmx-users] Fatal error during lipid bilayer minimization Mark Abraham
[gmx-users] About pdb2gmx for cyclic pepetide Mark Abraham
[gmx-users] Rotated protein Mark Abraham
[gmx-users] Rotated protein Mark Abraham
[gmx-users] lipid.itp file CHARMM FF Mark Abraham
[gmx-users] Resuming of calculation from last *.cpt Mark Abraham
[gmx-users] g_confrms Mark Abraham
[gmx-users] g_confrms Mark Abraham
[gmx-users] About topology construction for yclic pepetide Mark Abraham
[gmx-users] About topology construction for Cyclic peptide Mark Abraham
[gmx-users] charge calculation........ Mark Abraham
[gmx-users] Issue with genbox Mark Abraham
[gmx-users] Extracting bond information from topol.tpr file using template.c Mark Abraham
[gmx-users] Extracting bond information from topol.tpr file using template.c Mark Abraham
[gmx-users] How to a .gro file generated from this .top file? Mark Abraham
[gmx-users] Water molecules cannot be settled: V-rescale is the cause Mark Abraham
[gmx-users] distance calculation Mark Abraham
[gmx-users] How to produce the photodissociation in Gromacs? Mark Abraham
[gmx-users] distance calculation Mark Abraham
[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause Mark Abraham
[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause Mark Abraham
[gmx-users] specific dihedral plotting Mark Abraham
[gmx-users] Some tips for decreasing CPU time for mdrun -rerun Mark Abraham
[gmx-users] Re: v-rescale Mark Abraham
[gmx-users] Photodissociation through MD Mark Abraham
[gmx-users] Re: Possible bug in the temperature calculation from rerun Mark Abraham
[gmx-users] elastic network model - normal mode analysis Mark Abraham
[gmx-users] Fast exchanges for REMD Mark Abraham
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer David Ackerman
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer David Ackerman
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer David Ackerman
[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR Sonia Aguilera
[gmx-users] Notes and warning using grompp Sonia Aguilera
[gmx-users] Re: Notes and warnings using grompp Sonia Aguilera
[gmx-users] job restart error Albert
[gmx-users] job restart error Albert
[gmx-users] job restart error Albert
[gmx-users] how to measure distance between two helix? Albert
[gmx-users] strange continued jobs Albert
[gmx-users] strange continued jobs Albert
[gmx-users] does anybody knows how to use CTMD for gromacs trajectories? Albert
[gmx-users] why the output of g_saltbr is so large? Albert
[gmx-users] why the output of g_saltbr is so large? Albert
[gmx-users] how to assign protonation sate at pH-8? Albert
[gmx-users] umbrella sampling (PMF) position discrepancy Raphael Alhadeff
[gmx-users] umbrella sampling (PMF) position discrepancy Raphael Alhadeff
[gmx-users] umbrella sampling (PMF) position discrepancy Raphael Alhadeff
[gmx-users] The .pdb file compatible with structure of .itp file, Ali Alizadeh
[gmx-users] The .pdb file compatible with structure of .itp file, Ali Alizadeh
Fwd: [gmx-users] The .pdb file compatible with structure of .itp file, Ali Alizadeh
[gmx-users] Re: gmx-users Digest, Vol 101, Issue 17 Ali Alizadeh
[gmx-users] How to create two parallel wall? Ali Alizadeh
[gmx-users] How to generate a .itp file for molecules? Ali Alizadeh
[gmx-users] Re: gmx-users Digest, Vol 101, Issue 56 Ali Alizadeh
[gmx-users] Re: How to generate a .itp file for molecules Ali Alizadeh
[gmx-users] Is it possible adding new atomtype to force fields? Ali Alizadeh
[gmx-users] How to a .gro file generated from this .top file? Ali Alizadeh
[gmx-users] How to create a box of molecules with three layer? Ali Alizadeh
[gmx-users] Re: gmx-users Digest, Vol 101, Issue 67 Ali Alizadeh
[gmx-users] Re: gmx-users Digest, Vol 101, Issue 68 Ali Alizadeh
[gmx-users] select randomly some of my moleculesand replace them, Ali Alizadeh
[gmx-users] i have not atomtype K in my input files, Ali Alizadeh
[gmx-users] i can not simulate box of water, Ali Alizadeh
[gmx-users] grompp errors.. Ali Alizadeh
[gmx-users] make_ndx Ali Alizadeh
[gmx-users] Topology generated of a dimer protein Shima Arasteh
[gmx-users] Orientation of protein Shima Arasteh
[gmx-users] Orientation of protein Shima Arasteh
[gmx-users] Orientation of protein Shima Arasteh
[gmx-users] Rotated protein Shima Arasteh
[gmx-users] Rotated protein Shima Arasteh
[gmx-users] Rotated protein Shima Arasteh
[gmx-users] lipid.itp file CHARMM FF Shima Arasteh
[gmx-users] lipid-protein simulation Shima Arasteh
[gmx-users] lipid-protein simulation Shima Arasteh
[gmx-users] Rotated protein Shima Arasteh
[gmx-users] visualize trajectory Shima Arasteh
[gmx-users] hi Shima Arasteh
[gmx-users] GridMAT Shima Arasteh
[gmx-users] Visualizing the system Shima Arasteh
[gmx-users] Visualizing the system Shima Arasteh
[gmx-users] Visualizing the system Shima Arasteh
[gmx-users] Strong position restrain Shima Arasteh
[gmx-users] Strong position restrain Shima Arasteh
[gmx-users] InflateGro methodology Shima Arasteh
[gmx-users] InflateGro methodology Shima Arasteh
[gmx-users] packing lipids Shima Arasteh
[gmx-users] packing lipids Shima Arasteh
[gmx-users] packing lipids Shima Arasteh
[gmx-users] packing lipids Shima Arasteh
[gmx-users] energy minimization output Shima Arasteh
[gmx-users] Energy minimization Shima Arasteh
[gmx-users] Output of rotation Shima Arasteh
[gmx-users] Output of rotation Shima Arasteh
[gmx-users] adding mix solvent Masumeh Asman
[gmx-users] Residue 'UNK' not found in residue topology database SIMONE BROGI
[gmx-users] genion problem with divalent ions Leandro Bortot
[gmx-users] grompp warnings "Overriding atomtype ..." Leandro Bortot
[gmx-users] a question related to grompp command Acoot Brett
[gmx-users] on tpbconv Acoot Brett
[gmx-users] Energies in simulation and rerun using different core counts Richard Broadbent
[gmx-users] PDB and XYZ Structure Files in GROMACS Lara Bunte
[gmx-users] PDB and XYZ Structure Files in GROMACS Lara Bunte
[gmx-users] Energy Minimization of Alanin Lara Bunte
[gmx-users] Energy Minimization of Alanin Lara Bunte
[gmx-users] Equilibration Water around Alanin - Problem with Names Lara Bunte
[gmx-users] Theoretical questions about cut-offs and neighbor searching Lara Bunte
[gmx-users] Problems in mdrun - CHARMM27 Lara Bunte
[gmx-users] CHARMM27 Equilibrating Settings Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] About mdrun -nt number Lara Bunte
[gmx-users] Meaning of Table Size Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] About mdrun -nt number Lara Bunte
[gmx-users] About mdrun -nt number Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] Water molecule can not be settled - mdrun error Lara Bunte
[gmx-users] mails of other users in this mailing list Lara Bunte
[gmx-users] a box of water Turgay Cakmak
[gmx-users] a box of water Turgay Cakmak
[gmx-users] why traj.trr appears Dr. Vitaly Chaban
[gmx-users] Re: why traj.trr appears Dr. Vitaly Chaban
[gmx-users] What is gbsa.itp in oplsaa of gmx4.5.5? Wu Chaofu
[gmx-users] puzzling about ffnonbonded.itp Wu Chaofu
[gmx-users] Automatic calculations of forces in tabulated potentials? Wu Chaofu
[gmx-users] Some tips for decreasing CPU time for mdrun -rerun Wu Chaofu
[gmx-users] configurations of the two dimensional simulation Clare
[gmx-users] MD problem with nwall=2 Bogdan Costescu
[gmx-users] Is there a way to redirect utility output to the screen, rather than to a file? Andrew DeYoung
[gmx-users] Charge Group Number in itp File (cgnr) Andrew DeYoung
[gmx-users] Deuterium and the meaning of the atomic number parameter Andrew DeYoung
[gmx-users] Turning off charges of a particular atom type Andrew DeYoung
[gmx-users] Re: Turning off charges of a particular atom type Andrew DeYoung
[gmx-users] adding hydrogens to protein with pdb2gmx Marcelo Depolo
[gmx-users] adding hydrogens to protein with pdb2gmx Marcelo Depolo
[gmx-users] Ligand Internal energy Marcelo Depolo
[gmx-users] Ligand Internal energy Marcelo Depolo
[gmx-users] energy minimisation of carbon nanotubes. Marcelo Depolo
[gmx-users] .gro file format details Julio Dominguez
[gmx-users] Re: .gro file format details Julio Dominguez
[gmx-users] Ligand Internal energy Tom Dupree
[gmx-users] Re: Ligand Internal energy Tom Dupree
[gmx-users] Effect of refcoord_scaling Matthias Ernst
[gmx-users] Effect of refcoord_scaling Matthias Ernst
[gmx-users] Effect of refcoord_scaling Matthias Ernst
[gmx-users] Effect of refcoord_scaling Matthias Ernst
[gmx-users] genion problem with divalent ions Matthias Ernst
[gmx-users] pca-based MD Thomas Evangelidis
[gmx-users] pca-based MD Thomas Evangelidis
[gmx-users] PCA comparison between two simulations Thomas Evangelidis
[gmx-users] pca-based MD Thomas Evangelidis
[gmx-users] force field parameters Asaf Farhi
[gmx-users] force field parameters Asaf Farhi
FW: [gmx-users] force field parameters Asaf Farhi
[gmx-users] Regarding RMSD analysis result Felipe Pineda, PhD
[gmx-users] Regarding RMSD analysis result Felipe Pineda, PhD
[gmx-users] tau_t and tc_grps for v-rescale Felipe Pineda, PhD
[gmx-users] tau_t and tc_grps for v-rescale (2) Felipe Pineda, PhD
[gmx-users] Impropers in OPLS-AA Ignacio Fernández Galván
[gmx-users] Exclusions in TIP4P Ignacio Fernández Galván
[gmx-users] Hydrogen bond breaking process Rajiv Gandhi
[gmx-users] Hydrogen bond breaking process Rajiv Gandhi
[gmx-users] Hydrogen bond breaking process Rajiv Gandhi
[gmx-users] Calculating number of water molecules involves between dimer protein. Rajiv Gandhi
[gmx-users] Calculating secondary structure movements Rajiv Gandhi
[gmx-users] Resuming of calculation from last *.cpt Rajiv Gandhi
[gmx-users] How to produce the photodissociation in Gromacs? Rajiv Gandhi
[gmx-users] How to produce the photodissociation in Gromacs? Rajiv Gandhi
[gmx-users] Photodissociation through MD Rajiv Gandhi
[gmx-users] create topology other solvent Nur Syafiqah Abdul Ghani
[gmx-users] adding mix solvent Nur Syafiqah Abdul Ghani
[gmx-users] CfP: 3rd International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim13) part of the Symposium on Theory of Modeling and Simulation SCS SpringSim 2013) Daniele Gianni
[gmx-users] Intercalation DNA-Ethidium bromide Hovakim Grabski
[gmx-users] The Futility of Validating OPLS Parameters for an Organic Cation Chris Ing
[gmx-users] something wrong with BlueGene/P Bao Kai
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] g_tcaf segmentation fault Stelios Karozis
[gmx-users] excess use of suplhate ions Arunima Kumar
[gmx-users] g_tune_pme cannot be executed Carsten Kutzner
[gmx-users] g_tune_pme for multiple nodes Carsten Kutzner
[gmx-users] how to optimize performance of IBM Power 775? Carsten Kutzner
[gmx-users] Water molecules cannot be settled: V-rescale is the cause Ladasky
[gmx-users] Re: v-rescale Ladasky
[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause Ladasky
[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause Ladasky
[gmx-users] Re: v-rescale Ladasky
[gmx-users] Re: v-rescale Ladasky
[gmx-users] Domain decomposition error, is mdrun_mpi now obsolete? Ladasky
[gmx-users] CHARMM27 Equilibrating Settings Peter Lai
[gmx-users] Hydrogen bond breaking process Peter C. Lai
[gmx-users] Adding phosphate to protein Peter C. Lai
[gmx-users] Adding phosphate to protein Peter C. Lai
[gmx-users] Adding phosphate to protein Peter C. Lai
[gmx-users] Is there a way to redirect utility output to the screen, rather than to a file? Peter C. Lai
[gmx-users] MD problem with nwall=2 Peter C. Lai
[gmx-users] MD problem with nwall=2 Peter C. Lai
[gmx-users] Charmm for Proteins Peter C. Lai
[gmx-users] make index groups with make_ndx Peter C. Lai
[gmx-users] LINCS warning in md run Peter C. Lai
[gmx-users] Extracting bond information from topol.tpr file using template.c Peter C. Lai
[gmx-users] Extracting bond information from topol.tpr file using template.c Peter C. Lai
[gmx-users] Energy Minimization of Alanin Peter C. Lai
[gmx-users] Re: v-rescale Peter C. Lai
[gmx-users] Re: v-rescale Peter C. Lai
[gmx-users] Water molecule can not be settled - mdrun error Peter C. Lai
[gmx-users] TIP4P water model Peter C. Lai
[gmx-users] About Presence of Bond In Topology Peter C. Lai
[gmx-users] Visualizing the system Peter C. Lai
[gmx-users] About Bond in Topology Peter C. Lai
[gmx-users] About Bond in Topology Peter C. Lai
[gmx-users] Strong position restrain Peter C. Lai
[gmx-users] Domain decomposition error, is mdrun_mpi now obsolete? Peter C. Lai
[gmx-users] InflateGro methodology Peter C. Lai
[gmx-users] packing lipids Peter C. Lai
[gmx-users] About mdrun -nt number Peter C. Lai
[gmx-users] Water molecule can not be settled - mdrun error Peter C. Lai
[gmx-users] Water molecule can not be settled - mdrun error Peter C. Lai
[gmx-users] About mdrun -nt number Peter C. Lai
[gmx-users] About mdrun -nt number Peter C. Lai
[gmx-users] Water molecule can not be settled - mdrun error Peter C. Lai
[gmx-users] Water molecule can not be settled - mdrun error Peter C. Lai
[gmx-users] Installation in a SGI Cluster Peter C. Lai
[gmx-users] Do not want to add hydrogens to intial pdb structure Peter C. Lai
[gmx-users] Assignment of new velocities for multi-runs Peter C. Lai
[gmx-users] a question related to grompp command Peter C. Lai
[gmx-users] monomer to dimer Hossein Lanjanian
[gmx-users] monomer to dimer Hossein Lanjanian
[gmx-users] g_sas doubt -reg Justin Lemkul
[gmx-users] What is gbsa.itp in oplsaa of gmx4.5.5? Justin Lemkul
[gmx-users] au virtual site Justin Lemkul
[gmx-users] Hydrogen bond breaking process Justin Lemkul
[gmx-users] Hydrogen bond breaking process Justin Lemkul
[gmx-users] g_mindist - reg Justin Lemkul
[gmx-users] au virtual atom Justin Lemkul
[gmx-users] Re: g_mindist - reg Justin Lemkul
[gmx-users] question about aminoacids.rtp file when adding a new residue Justin Lemkul
[gmx-users] question about aminoacids.rtp file when adding a new residue Justin Lemkul
[gmx-users] adding hydrogens to protein with pdb2gmx Justin Lemkul
[gmx-users] adding hydrogens to protein with pdb2gmx Justin Lemkul
[gmx-users] job restart error Justin Lemkul
[gmx-users] job restart error Justin Lemkul
[gmx-users] minimisation with protonated residues Justin Lemkul
[gmx-users] minimisation with protonated residues Justin Lemkul
[gmx-users] The .pdb file compatible with structure of .itp file, Justin Lemkul
[gmx-users] The .pdb file compatible with structure of .itp file, Justin Lemkul
[gmx-users] a box of water Justin Lemkul
[gmx-users] .gro file format details Justin Lemkul
[gmx-users] error in producing top file for a structure Justin Lemkul
[gmx-users] error in producing top file for a structure Justin Lemkul
[gmx-users] genion problem with divalent ions Justin Lemkul
[gmx-users] Topology generated of a dimer protein Justin Lemkul
[gmx-users] how to measure distance between two helix? Justin Lemkul
[gmx-users] umbrella sampling (PMF) position discrepancy Justin Lemkul
[gmx-users] umbrella sampling (PMF) position discrepancy Justin Lemkul
[gmx-users] strange continued jobs Justin Lemkul
[gmx-users] No molecules were defined in the system/ No such molecule type Dio Justin Lemkul
[gmx-users] dihedraltypes amber forcefield Justin Lemkul
[gmx-users] Orientation of protein Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] Re: freeze value Justin Lemkul
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer Justin Lemkul
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer Justin Lemkul
[gmx-users] Re: About Bond breaking and usage of constraints Justin Lemkul
[gmx-users] Error regarding topology and coordinate files Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] Resuming of calculation from last *.cpt Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] Resuming of calculation from last *.cpt Justin Lemkul
[gmx-users] Reg pdb2gmx for Cyclic peptide Justin Lemkul
[gmx-users] Segmentation fault (core dumped error) Justin Lemkul
[gmx-users] Pdb2gmx for cyclic Peptide Justin Lemkul
[gmx-users] Re: No molecules were defined in the system/ No such molecule type Justin Lemkul
[gmx-users] Resuming of calculation from last *.cpt Justin Lemkul
[gmx-users] Resuming of calculation from last *.cpt Justin Lemkul
[gmx-users] Resuming of calculation from last *.cpt Justin Lemkul
[gmx-users] energy minimisation of carbon nanotubes. Justin Lemkul
[gmx-users] About EM for Cyclic Peptide Justin Lemkul
[gmx-users] Resuming of calculation from last *.cpt Justin Lemkul
[gmx-users] lipid-protein simulation Justin Lemkul
[gmx-users] lipid-protein simulation Justin Lemkul
[gmx-users] Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR Justin Lemkul
[gmx-users] visualize trajectory Justin Lemkul
[gmx-users] Regarding RMSD graph nalysis Justin Lemkul
[gmx-users] DNA MD PROBLEM Justin Lemkul
[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] Hbond-ETH-WATER Justin Lemkul
[gmx-users] why traj.trr appears Justin Lemkul
[gmx-users] Hbond-ETH-WATER Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] Re: gmx-users Digest, Vol 101, Issue 52 Justin Lemkul
[gmx-users] Issue with genbox Justin Lemkul
[gmx-users] PDB and XYZ Structure Files in GROMACS Justin Lemkul
[gmx-users] How to generate a .itp file for molecules? Justin Lemkul
[gmx-users] Residue 'UNK' not found in residue topology database Justin Lemkul
[gmx-users] Re: How to generate a .itp file for molecules Justin Lemkul
[gmx-users] use of PRODRG Justin Lemkul
[gmx-users] Is it possible adding new atomtype to force fields? Justin Lemkul
[gmx-users] Energy Minimization of Alanin Justin Lemkul
[gmx-users] Residue 'UNK' not found in residue topology database Justin Lemkul
[gmx-users] Equilibration Water around Alanin - Problem with Names Justin Lemkul
[gmx-users] use of PRODRG Justin Lemkul
[gmx-users] Ligand-Protein interaction with energy groups Justin Lemkul
[gmx-users] Theoretical questions about cut-offs and neighbor searching Justin Lemkul
[gmx-users] water dynamics Justin Lemkul
[gmx-users] distance calculation Justin Lemkul
[gmx-users] water dynamics Justin Lemkul
[gmx-users] Water molecules cannot be settled: V-rescale is the cause Justin Lemkul
[gmx-users] problem pdb2gmx and acetylation Justin Lemkul
[gmx-users] How to create a box of molecules with three layer? Justin Lemkul
[gmx-users] Analysis of enssemble of MD trajectories Justin Lemkul
[gmx-users] How to create a box of molecules with three layers? Justin Lemkul
[gmx-users] LINCS warning in md run Justin Lemkul
[gmx-users] How to create a box of molecules with three layers? Justin Lemkul
[gmx-users] tutorial for liquid-solid simulation Justin Lemkul
[gmx-users] Problems in mdrun - CHARMM27 Justin Lemkul
[gmx-users] Input/output error in GROMACS Justin Lemkul
[gmx-users] Photodissociation through MD Justin Lemkul
[gmx-users] Analysis of enssemble of MD trajectories Justin Lemkul
[gmx-users] why the output of g_saltbr is so large? Justin Lemkul
[gmx-users] Possible bug in the temperature calculation from rerun Justin Lemkul
[gmx-users] Water molecule can not be settled - mdrun error Justin Lemkul
[gmx-users] GridMAT Justin Lemkul
[gmx-users] monomer to dimer Justin Lemkul
[gmx-users] Water molecule can not be settled - mdrun error Justin Lemkul
[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins Justin Lemkul
[gmx-users] Water molecule can not be settled - mdrun error Justin Lemkul
[gmx-users] TIP4P water model Justin Lemkul
[gmx-users] Re: segentation fault -core dumped Justin Lemkul
[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins Justin Lemkul
[gmx-users] force field parameters Justin Lemkul
[gmx-users] force field parameters Justin Lemkul
[gmx-users] Domain decomposition error, is mdrun_mpi now obsolete? Justin Lemkul
[gmx-users] grompp warnings "Overriding atomtype ..." Justin Lemkul
[gmx-users] i have not atomtype K in my input files, Justin Lemkul
[gmx-users] About Warning in grompp Justin Lemkul
[gmx-users] force field parameters Justin Lemkul
[gmx-users] TIP4P water model Justin Lemkul
[gmx-users] content of secondary structure output file Justin Lemkul
[gmx-users] how to assign protonation sate at pH-8? Justin Lemkul
[gmx-users] exclude vdw interactions for pair of residues Justin Lemkul
[gmx-users] excess use of suplhate ions Justin Lemkul
[gmx-users] packing lipids Justin Lemkul
[gmx-users] Regarding RMSD analysis result Justin Lemkul
[gmx-users] Regarding RMSD analysis result Justin Lemkul
[gmx-users] packing lipids Justin Lemkul
[gmx-users] Water molecule can not be settled - mdrun error Justin Lemkul
[gmx-users] Water molecule can not be settled - mdrun error Justin Lemkul
[gmx-users] Error in domain decomposition Justin Lemkul
[gmx-users] i can not simulate box of water, Justin Lemkul
[gmx-users] error with x2top. Justin Lemkul
[gmx-users] error with x2top. Justin Lemkul
[gmx-users] Restrain specific lipid residues Justin Lemkul
[gmx-users] a quick question (forgot to ask). Justin Lemkul
[gmx-users] Deuterium and the meaning of the atomic number parameter Justin Lemkul
[gmx-users] Turning off charges of a particular atom type Justin Lemkul
[gmx-users] g_tcaf segmentation fault Justin Lemkul
[gmx-users] g_tcaf segmentation fault Justin Lemkul
[gmx-users] g_clustsize Justin Lemkul
[gmx-users] distance restraint Justin Lemkul
[gmx-users] doubt in minimization part Justin Lemkul
[gmx-users] tau_t and tc_grps for v-rescale (2) Justin Lemkul
[gmx-users] Re: distance restraint Justin Lemkul
[gmx-users] g_hbond Justin Lemkul
[gmx-users] Umbrella sampling-protein-ligand complex Justin Lemkul
[gmx-users] provide opt way to perform simulation for protein and peptide -reg Justin Lemkul
[gmx-users] Re: distance restraint Justin Lemkul
[gmx-users] Re: distance restraint Justin Lemkul
[gmx-users] Re: distance restraint Justin Lemkul
[gmx-users] Re:provide opt way to perform simulation for protein and peptide -reg Justin Lemkul
[gmx-users] Umbrella sampling-protein-ligand complex Justin Lemkul
[gmx-users] mails of other users in this mailing list Justin Lemkul
[gmx-users] Re: distance restraint Justin Lemkul
[gmx-users] Notes and warnings using grompp Justin Lemkul
[gmx-users] Re: Notes and warnings using grompp Justin Lemkul
[gmx-users] Energy minimization Justin Lemkul
[gmx-users] Assignment of new velocities for multi-runs Justin Lemkul
[gmx-users] Calculate Density with respect to time... Justin Lemkul
[gmx-users] Assignment of new velocities for multi-runs Justin Lemkul
[gmx-users] grompp errors.. Justin Lemkul
[gmx-users] make_ndx Justin Lemkul
[gmx-users] .itp and .rtp file modifications? Justin Lemkul
[gmx-users] Restrain specific lipid residues Katrina Lexa
[gmx-users] Restrain specific lipid residues Katrina Lexa
[gmx-users] umbrella sampling (PMF) position discrepancy Jianguo Li
[gmx-users] Orientation of protein Jianguo Li
[gmx-users] Possible bug in the temperature calculation from rerun Bastien Loubet
[gmx-users] Re: Possible bug in the temperature calculation from rerun Bastien Loubet
[gmx-users] error in producing top file for a structure Elie M
[gmx-users] error in producing top file for a structure Elie M
[gmx-users] error in producing top file for a structure Elie M
[gmx-users] Segmentation fault (core dumped error) Elie M
[gmx-users] Segmentation fault (core dumped error) Elie M
[gmx-users] energy minimisation of carbon nanotubes. Elie M
[gmx-users] energy minimisation of carbon nanotubes. Elie M
[gmx-users] use of PRODRG Elie M
[gmx-users] use of PRODRG Elie M
[gmx-users] use of PRODRG Elie M
[gmx-users] Input/output error in GROMACS Elie M
[gmx-users] Missing charges in a .gro file Elie M
[gmx-users] Missing charges in a .gro file Elie M
[gmx-users] error with x2top. Elie M
[gmx-users] error with x2top. Elie M
[gmx-users] error with x2top. Elie M
[gmx-users] a quick question (forgot to ask). Elie M
[gmx-users] .itp and .rtp file modifications? Elie M
[gmx-users] Re: Turning off electrostatics between groups using custom tables? Erik Marklund
[gmx-users] Effect of refcoord_scaling Erik Marklund
[gmx-users] Rotated protein Erik Marklund
[gmx-users] charge calculation........ Erik Marklund
[gmx-users] Extracting bond information from topol.tpr file using template.c Erik Marklund
[gmx-users] select randomly some of my moleculesand replace them, Erik Marklund
[gmx-users] energy minimization output Erik Marklund
[gmx-users] energy minimization output Erik Marklund
[gmx-users] How to create two parallel wall? Alex Marshall
[gmx-users] g_hbond Gavin Melaugh
[gmx-users] Effect of refcoord_scaling Christopher Neale
[gmx-users] Effect of refcoord_scaling Christopher Neale
[gmx-users] Effect of refcoord_scaling Christopher Neale
[gmx-users] Effect of refcoord_scaling Christopher Neale
[gmx-users] The .pdb file compatible with structure of .itp file, Christopher Neale
[gmx-users] gold nanoparticle simulation,use pbc or not? Christopher Neale
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer Christopher Neale
[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine Christopher Neale
[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine Christopher Neale
[gmx-users] Intercalation DNA-Ethidium bromide Paulo Netz
[gmx-users] from GMX to NAMD/Amber Steven Neumann
[gmx-users] Charmm for Proteins Steven Neumann
[gmx-users] Installation in a SGI Cluster Diego Nolasco
[gmx-users] Specifics on tabulated pair potentials MURAT OZTURK
[gmx-users] Instantaneous dipole moment of water molecule Deepak Ojha
[gmx-users] water dynamics Eduardo Oliveira
[gmx-users] Re: segentation fault -core dumped Keerthana S.P Periasamy
[gmx-users] using martinize.py to martinize two chains complex XAvier Periole
[gmx-users] using martinize.py to martinize two chains complex XAvier Periole
[gmx-users] .xtc support in UCSF Chimera Eric Pettersen
[gmx-users] ParmBSC0 Force Field Contribution Thomas Piggot
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer Thomas Piggot
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer Thomas Piggot
[gmx-users] Smaller Area Per Lipid for DPPC Bilayer Thomas Piggot
[gmx-users] Reference for CHARMM36 Force Field Conversion Thomas Piggot
[gmx-users] distance restraint Paula Andrea Delgado Pinzon
[gmx-users] gromac-4.5.5 installation error Pawan Raghav
[gmx-users] g_mindist - reg Raj
[gmx-users] Re: g_mindist - reg Raj
[gmx-users] Calculating tertiary structure rotation Rajiv
[gmx-users] DelG of LJ Transformation Negative Glu--->Ala Mutation Sai Kumar Ramadugu
[gmx-users] Glutamate to Alanine Mutation Sai Kumar Ramadugu
[gmx-users] Published articles which have used Gromcas for their work Mohsen Ramezanpour
[gmx-users] On creating pdb file using dynamic indices from g_select Mr Bernard Ramos
AW: [gmx-users] Adding phosphate to protein Rausch, Felix
[gmx-users] g_nmtraj -temp Joaquim Rui de Castro Rodrigues
[gmx-users] Error in domain decomposition Dipankar Roy
[gmx-users] Hbond-ETH-WATER Praveen Kumar Sappidi
[gmx-users] Re: gmx-users Digest, Vol 101, Issue 52 Praveen Kumar Sappidi
[gmx-users] Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR Sonia Milena Aguilera Segura
[gmx-users] Notes and warnings using grompp Sonia Milena Aguilera Segura
[gmx-users] Notes and warnings using grompp Sonia Milena Aguilera Segura
[gmx-users] DNA MD PROBLEM Anik Sen
[gmx-users] Extracting bond information from topol.tpr file using template.c Amit Shavit
[gmx-users] Re: umbrella sampling (PMF) position discrepancy Sheeba
[gmx-users] How to delete atoms during MD runs? Yun Shi
[gmx-users] How to delete atoms during MD runs? Yun Shi
[gmx-users] Re: v-rescale Michael Shirts
[gmx-users] Experiences with Gromacs scaling on US supercomputer centers? Michael Shirts
[gmx-users] Re: Fast exchanges for REMD Michael Shirts
[gmx-users] Re: Turning off electrostatics between groups using custom tables? Smitty
[gmx-users] Re: Turning off electrostatics between groups using custom tables? Smitty
[gmx-users] Problem in atom typing for Nitro group using CHARMM27 Archana Sonawani
[gmx-users] Regarding RMSD analysis result Archana Sonawani
[gmx-users] energy minimization output Archana Sonawani
[gmx-users] Umbrella sampling-protein-ligand complex Archana Sonawani
[gmx-users] Umbrella sampling-protein-ligand complex Archana Sonawani
[gmx-users] Automatic calculations of forces in tabulated potentials? David van der Spoel
[gmx-users] Experiences with Gromacs scaling on US supercomputer centers? David van der Spoel
[gmx-users] Error regarding topology and coordinate files Bharath K. Srikanth
[gmx-users] Fatal error during lipid bilayer minimization Bharath K. Srikanth
[gmx-users] Issue with genbox Bharath K. Srikanth
[gmx-users] Different initial conditions for the membrane protein simulation James Starlight
[gmx-users] On the usage of the Noose-Hover chains James Starlight
[gmx-users] Different initial conditions for the membrane protein simulation James Starlight
[gmx-users] Resuming of calculation from last *.cpt James Starlight
[gmx-users] Resuming of calculation from last *.cpt James Starlight
[gmx-users] Resuming of calculation from last *.cpt James Starlight
[gmx-users] Resuming of calculation from last *.cpt James Starlight
[gmx-users] Resuming of calculation from last *.cpt James Starlight
[gmx-users] Resuming of calculation from last *.cpt James Starlight
[gmx-users] Analysis of enssemble of MD trajectories James Starlight
[gmx-users] Analysis of enssemble of MD trajectories James Starlight
[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins James Starlight
[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins James Starlight
[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] Analysis of enssemble of MD trajectories James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] Assignment of new velocities for multi-runs James Starlight
[gmx-users] Assignment of new velocities for multi-runs James Starlight
[gmx-users] Re: Umbrella Sampling Pull code Problem - Follow-Up Steinbrecher, Thomas (IPC)
[gmx-users] exclude vdw interactions for pair of residues Shreyas Supekar
[gmx-users] Re:Re: exclude vdw interactions for pair of residues Shreyas Supekar
[gmx-users] Missing charges in a .gro file Terry
[gmx-users] using martinize.py to martinize two chains complex Lingyun Wang
[gmx-users] using martinize.py to martinize two chains complex Lingyun Wang
[gmx-users] using martinize.py to martinize two chains complex Lingyun Wang
[gmx-users] v-rescale Tsjerk Wassenaar
[gmx-users] Extracting bond information from topol.tpr file using template.c Tsjerk Wassenaar
[gmx-users] Regarding RMSD analysis result Tsjerk Wassenaar
[gmx-users] g_tcaf segmentation fault Tsjerk Wassenaar
[gmx-users] Regarding RMSD analysis result Tsjerk Wassenaar
[gmx-users] rapid change in the angle of simulation cell - regd Tsjerk Wassenaar
[gmx-users] g_tcaf segmentation fault Tsjerk Wassenaar
[gmx-users] g_tcaf segmentation fault Tsjerk Wassenaar
[gmx-users] something wrong with BlueGene/P Tsjerk Wassenaar
[gmx-users] Output of rotation Tsjerk Wassenaar
[gmx-users] Fast exchanges for REMD Andreas Zink
[gmx-users] Re: Fast exchanges for REMD Andreas Zink
[gmx-users] something wrong with BlueGene/P Matthew Zwier
[gmx-users] v-rescale mohammad agha
[gmx-users] diffusion mohammad agha
[gmx-users] g_clustsize mohammad agha
[gmx-users] Variation of angles of simulation cell - regd ramesh cheerla
[gmx-users] Variation of angles of simulation cell - regd ramesh cheerla
[gmx-users] Variation of angles of simulation cell - regd ramesh cheerla
[gmx-users] Rotational time correlation function - regd ramesh cheerla
[gmx-users] Rotational correlation function - regd ramesh cheerla
[gmx-users] Decoupling non-bonded energies - regd ramesh cheerla
[gmx-users] rapid change in angles of simulation cell - regd ramesh cheerla
[gmx-users] rapid change in the angle of simulation cell - regd ramesh cheerla
[gmx-users] Calculate Density with respect to time... rama david
[gmx-users] on tpbconv rama david
[gmx-users] Calculate Density with respect to time... rama david
[gmx-users] hi marzieh dehghan
[gmx-users] problem pdb2gmx and acetylation menica dibenedetto
[gmx-users] problem pdb2gmx and acetylation menica dibenedetto
[gmx-users] Re: genion problem with divalent ions ran friedman
[gmx-users] Reminder: vermaprakash38 at gmail.com wants to follow you vermaprakash38 at gmail.com
[gmx-users] How to determin the simulation time xiaojing gong
[gmx-users] time constant in V-rescale algorithm xiaojing gong
[gmx-users] Re: How to determin the simulation time xiaojing gong
[gmx-users] Re: time constant in V-rescale algorithm xiaojing gong
[gmx-users] Calculate Density with respect to time... bharat gupta
[gmx-users] No molecules were defined in the system/ No such molecule type Dio sarah k
[gmx-users] Re: No molecules were defined in the system/ No such molecule type sarah k
[gmx-users] -ee option in the g_analyze leila karami
[gmx-users] charge calculation........ tarak karmakar
[gmx-users] charge calculation........ tarak karmakar
[gmx-users] distance calculation tarak karmakar
[gmx-users] distance calculation tarak karmakar
[gmx-users] distance calculation tarak karmakar
[gmx-users] distance calculation tarak karmakar
[gmx-users] specific dihedral plotting tarak karmakar
[gmx-users] specific dihedral plotting tarak karmakar
[gmx-users] g_tcaf segmentation fault lina
[gmx-users] g_tcaf segmentation fault lina
[gmx-users] g_tcaf segmentation fault lina
[gmx-users] Re: v-rescale ms
[gmx-users] g_confrms Ankita naithani
[gmx-users] g_confrms Ankita naithani
[gmx-users] TIP4P water model Ankita naithani
[gmx-users] TIP4P water model Ankita naithani
[gmx-users] tutorial for liquid-solid simulation cuong nguyen
[gmx-users] GROMOS angle type ga_13 or ga_15? nikpap
[gmx-users] why the output of g_saltbr is so large? francesco oteri
[gmx-users] Analysis of enssemble of MD trajectories francesco oteri
[gmx-users] Photodissociation through MD francesco oteri
[gmx-users] why the output of g_saltbr is so large? francesco oteri
[gmx-users] PCA comparison between two simulations francesco oteri
[gmx-users] Re: distance restraint pauladelgado
[gmx-users] Re: distance restraint pauladelgado
[gmx-users] Re: distance restraint pauladelgado
[gmx-users] Re: distance restraint pauladelgado
[gmx-users] Re: distance restraint pauladelgado
[gmx-users] (no subject) niaz poorgholami
[gmx-users] au virtual site fatemeh ramezani
[gmx-users] au virtual atom fatemeh ramezani
[gmx-users] gold nanoparticle simulation,use pbc or not? fatemeh ramezani
[gmx-users] Calculating number of water molecules involves between dimer protein. lloyd riggs
[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine lloyd riggs
[gmx-users] Analysis of enssemble of MD trajectories lloyd riggs
[gmx-users] Regarding RMSD analysis result lloyd riggs
[gmx-users] Adding phosphate to protein reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Adding phosphate to protein reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Adding phosphate to protein reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] question about aminoacids.rtp file when adding a new residue reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] question about aminoacids.rtp file when adding a new residue reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] adding hydrogens to protein with pdb2gmx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] adding hydrogens to protein with pdb2gmx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] adding hydrogens to protein with pdb2gmx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] adding hydrogens to protein with pdb2gmx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] adding hydrogens to protein with pdb2gmx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] minimisation with protonated residues reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] minimisation with protonated residues reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] dihedraltypes amber forcefield reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] make index groups with make_ndx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] make index groups with make_ndx reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] LINCS warning in md run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] g_sas doubt -reg venkatesh s
[gmx-users] g_covar -reg venkatesh s
[gmx-users] provide opt way to perform simulation for protein and peptide -reg venkatesh s
[gmx-users] Re:provide opt way to perform simulation for protein and peptide -reg venkatesh s
[gmx-users] number of coordinates in coordinate file does not match topology -reg venkatesh s
[gmx-users] About Bond breaking and usage of constraints vidhya sankar
[gmx-users] Reg pdb2gmx for Cyclic peptide vidhya sankar
[gmx-users] Pdb2gmx for cyclic Peptide vidhya sankar
[gmx-users] About pdb2gmx for cyclic pepetide vidhya sankar
[gmx-users] About EM for Cyclic Peptide vidhya sankar
[gmx-users] About topology construction for yclic pepetide vidhya sankar
[gmx-users] About topology construction for Cyclic peptide vidhya sankar
[gmx-users] About Energy Minimisation vidhya sankar
[gmx-users] About Presence of Bond In Topology vidhya sankar
[gmx-users] About Bond in Topology vidhya sankar
[gmx-users] About Warning in grompp vidhya sankar
[gmx-users] Elastic Network Model -harmonic pot mohan maruthi sena
[gmx-users] Elastic network model mohan maruthi sena
[gmx-users] elastic network model - normal mode analysis mohan maruthi sena
[gmx-users] elastic network model - atoms movement mohan maruthi sena
[gmx-users] Do not want to add hydrogens to intial pdb structure mohan maruthi sena
[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine bipin singh
[gmx-users] periodicity in msd calculation Bala subramanian
[gmx-users] permittivity value Bala subramanian
[gmx-users] Regarding RMSD graph nalysis naga sundar
[gmx-users] Residue 'UNK' not found in residue topology database naga sundar
[gmx-users] Regarding RMSD analysis result naga sundar
[gmx-users] Regarding RMSD analysis result naga sundar
[gmx-users] Regarding RMSD analysis result naga sundar
[gmx-users] Regarding RMSD analysis result naga sundar
[gmx-users] content of secondary structure output file ahmet yıldırım
[gmx-users] Regarding RMSD analysis result ahmet yıldırım
[gmx-users] Regarding RMSD analysis result ahmet yıldırım
[gmx-users] MD problem with nwall=2 김현식
[gmx-users] Ligand-Protein interaction with energy groups 이종화

Last message date: Sun Sep 30 19:06:29 CEST 2012
Archived on: Thu Nov 14 12:13:23 CET 2013

Messages sorted by: [ thread ] [ subject ] [ date ]
More info on this list...

This archive was generated by Pipermail 0.09 (Mailman edition).