May 2011 Archives by author

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Starting: Sun May 1 07:51:19 CEST 2011
Ending: Tue May 31 21:49:33 CEST 2011
Messages: 939

[gmx-users] CG database for POPC Du Jiangfeng (BIOCH)
[gmx-users] How to make a membrane system with 512 DPPCs Du Jiangfeng (BIOCH)
[gmx-users] problem during energy minimization before MD Itamar Kass (Med)
[gmx-users] Using the XTC library Ryan S Davis (rsdavis1)
[gmx-users] RE: gmx-users Digest, Vol 85, Issue 53 Ryan S Davis (rsdavis1)
[gmx-users] Indexing problem when using genconf Ryan S Davis (rsdavis1)
[gmx-users] itp file for trehalose ABEL Stephane 175950
[gmx-users] itp file for trehalose ABEL Stephane 175950
[gmx-users] lyzosyme tutorial Mark Abraham
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 Mark Abraham
[gmx-users] Source Code for Lennard jones truncation schemes Mark Abraham
[gmx-users] Re: Simluations in vacuum - energy increase Mark Abraham
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 Mark Abraham
[gmx-users] Adding OPLS-UA forcefield Mark Abraham
[gmx-users] Invalid order for directive atomtypes Mark Abraham
[gmx-users] running job parallel Mark Abraham
[gmx-users] running job parallel Mark Abraham
[gmx-users] invalid order for directive Mark Abraham
[gmx-users] excluding electrostatic interactions Mark Abraham
[gmx-users] running job parallel Mark Abraham
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Mark Abraham
[gmx-users] nrexcl=3 Mark Abraham
[gmx-users] trjconv problem Mark Abraham
[gmx-users] serial gromacs on windows Mark Abraham
[gmx-users] RMSD with Vsite vs No Vsites Mark Abraham
[gmx-users] RMSD with Vsite vs No Vsites Mark Abraham
[gmx-users] DO_DSSP Mark Abraham
[gmx-users] virtual sites set up for topology file Mark Abraham
[gmx-users] virtual sites set up for topology file Mark Abraham
[gmx-users] ambar to opls force field Mark Abraham
[gmx-users] Using the XTC library Mark Abraham
[gmx-users] g_sas query Mark Abraham
[gmx-users] liquid/liquid Mark Abraham
[gmx-users] g_sas query Mark Abraham
[gmx-users] On posre.itp Mark Abraham
[gmx-users] On posre.itp Mark Abraham
[gmx-users] How to recenter solvent around solute Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 61 Mark Abraham
[gmx-users] RE: gmx-users Digest, Vol 85, Issue 53 Mark Abraham
[gmx-users] regarding nacl simulation in water using tabulated potentials Mark Abraham
[gmx-users] regarding nacl simulation in water using tabulated potentials Mark Abraham
[gmx-users] freeze the carbonyl carbon atoms Mark Abraham
[gmx-users] frozen CNT with carbonyls Mark Abraham
[gmx-users] Re: freeze the carbonyl carbon atoms Mark Abraham
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 Mark Abraham
[gmx-users] Fatal error: Atomtype CB not found Mark Abraham
[gmx-users] writing trajectory with water molecules within a distance from protein Mark Abraham
[gmx-users] total force acting on group Mark Abraham
[gmx-users] How to recenter solvent around solute Mark Abraham
[gmx-users] regarding nacl simulation in water using tabulated potentials Mark Abraham
[gmx-users] gromacs make error Mark Abraham
[gmx-users] reg pdb2gmx Mark Abraham
[gmx-users] REMD multi core for each replica Mark Abraham
[gmx-users] REMD multi core for each replica Mark Abraham
[gmx-users] regarding nacl simulation in water using tabulated potentials Mark Abraham
[gmx-users] principal moments of ellipsoid Mark Abraham
[gmx-users] qmmm temp definition Mark Abraham
[gmx-users] qmmm linking atom Mark Abraham
[gmx-users] re: simulation-rigid Mark Abraham
[gmx-users] REMD: after replica exchange breakdown Mark Abraham
[gmx-users] energy group error Mark Abraham
[gmx-users] Continuing job in another machine Mark Abraham
[gmx-users] REMD: after replica exchange breakdown Mark Abraham
[gmx-users] index file Mark Abraham
[gmx-users] exclusions Mark Abraham
[gmx-users] Getting nonbonded interactions from gmxdump Mark Abraham
[gmx-users] problem in multichain protein solvation Mark Abraham
[gmx-users] numbering of .gro file Mark Abraham
[gmx-users] Reference pressure and pressure fluctuations in an NPT simulation Mark Abraham
[gmx-users] decomposing the energy Mark Abraham
[gmx-users] decomposing the energy Mark Abraham
[gmx-users] decomposing the energy Mark Abraham
[gmx-users] problem regarding npt equilibration Mark Abraham
[gmx-users] compilation of g_hbond after bugfix Mark Abraham
[gmx-users] recovering topology Mark Abraham
[gmx-users] P-LINCS and nstlist Mark Abraham
[gmx-users] problem in gmx-users list archive? Mark Abraham
[gmx-users] simulation of a peptide anchored to a support Mark Abraham
[gmx-users] Fwd: energy groups in tabulated potentials Mark Abraham
R: Re: [gmx-users] simulation of a peptide anchored to a support Mark Abraham
[gmx-users] Manually aborting a simulation Mark Abraham
[gmx-users] X-ray Structures Mark Abraham
[gmx-users] Specify run time Mark Abraham
[gmx-users] Atomtype not found Mark Abraham
[gmx-users] NPT for compressing Mark Abraham
[gmx-users] Water molecule starting at atom X can not be settled. Mark Abraham
[gmx-users] Water molecule starting at atom X can not be settled. Mark Abraham
[gmx-users] Water molecule starting at atom X can not be settled. Mark Abraham
[gmx-users] need help Mark Abraham
[gmx-users] memory problem of g_hbond? Mark Abraham
[gmx-users] Velocity and temperature profiles Mark Abraham
[gmx-users] Re: Replica Exchange MD using Gromacs Mark Abraham
[gmx-users] regarding table for water water interactions Mark Abraham
[gmx-users] Potential of mean force Mark Abraham
[gmx-users] Charmm36 in Gromacs: missing dihedrals Mark Abraham
[gmx-users] query regarding replica exchange Mark Abraham
[gmx-users] problem with replica exchange Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] problem using trjconv command Mark Abraham
[gmx-users] oplsaa vs. charmm Mark Abraham
[gmx-users] Fwd: request Mark Abraham
[gmx-users] Minimum periodic distance Mark Abraham
[gmx-users] My problem is How to define 5-methyl cytosine by amberff port in gromacs? Mark Abraham
[gmx-users] hi Mark Abraham
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Mark Abraham
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Mark Abraham
[gmx-users] Minimum periodic distance Mark Abraham
[gmx-users] implicit solvent LINCS errors Mark Abraham
[gmx-users] implicit solvent LINCS errors Mark Abraham
[gmx-users] simulation of a non complete structure Sajad Ahrari
[gmx-users] gromacs make error Sajad Ahrari
[gmx-users] New parameter for boron Hernan Ahumada
[gmx-users] Cumulative number Juliana Angeiras
[gmx-users] git server maintenance downtime Rossen Apostolov
[gmx-users] git server maintenance finished Rossen Apostolov
[gmx-users] Re: git server maintenance finished Rossen Apostolov
[gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM Rossen Apostolov
[gmx-users] call for papers: IEEE eScience2011 Workshop on "Computing Advances in Life Sciences" Rossen Apostolov
[gmx-users] Fw: ionic liquids Prema Awati
[gmx-users] Fw: Fw: ionic liquids Prema Awati
[gmx-users] Fw: Re: Re: ionic liquids Prema Awati
[gmx-users] viscosity Prema Awati
[gmx-users] running job parallel Saikat Banerjee
[gmx-users] Problem with pdb2gmx in gromacs 4.5.3 Tomy van Batis
[gmx-users] How to use Inflategro with different lipid types Ioannis Beis
[gmx-users] RE: How to use Inflategro with different lipid types Ioannis Beis
[gmx-users] selecting groups for full trajectory Ravi Bhadauria
[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8 Matthew Bick
[gmx-users] Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8 Matthew Bick
[gmx-users] Re: Re: Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8 Matthew Bick
[gmx-users] adding new lipid into /charmm27.ff/lipids.rtp Bing Bing
[gmx-users] qmmm linking atom Pradip Biswas
[gmx-users] Unsteady Density Fabian Casteblanco
[gmx-users] Re: Unsteady Density Fabian Casteblanco
[gmx-users] Re: Unsteady Density Fabian Casteblanco
[gmx-users] Genbox question Fabian Casteblanco
[gmx-users] reg speed of MD Javier Cerezo
[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side Vitaly Chaban
[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side Vitaly Chaban
[gmx-users] Re: mixtures. I want to build my simulation box as tutorial Vitaly Chaban
[gmx-users] Re: Unsteady Density Vitaly Chaban
[gmx-users] Re: ionic liquids Vitaly Chaban
[gmx-users] Re: Unsteady Density Vitaly Chaban
[gmx-users] Re: Re: ionic liquids Vitaly Chaban
[gmx-users] serial gromacs on windows Vitaly Chaban
[gmx-users] serial gromacs on windows Vitaly Chaban
[gmx-users] Re: "No molecules were defined in the system" Vitaly Chaban
[gmx-users] tip4p.itp Vitaly Chaban
[gmx-users] Re: Re: tip4p.itp Vitaly Chaban
[gmx-users] g_current and output redirection Vitaly Chaban
[gmx-users] g_current and output redirection Vitaly Chaban
[gmx-users] g_current and output redirection Vitaly Chaban
[gmx-users] Re: water dimer is gas phase Vitaly Chaban
[gmx-users] Re: water dimer is gas phase Vitaly Chaban
[gmx-users] Re: water dimer is gas phase Vitaly Chaban
[gmx-users] Re: water dimer is gas phase Vitaly Chaban
[gmx-users] Re: NPT for compressing Vitaly Chaban
[gmx-users] Re: NPT for compressing Vitaly Chaban
[gmx-users] Re: compressing with NPT Vitaly Chaban
[gmx-users] Re: Velocity autocorrelation function of water using g_velacc Vitaly Chaban
[gmx-users] Re: Velocity autocorrelation function of water using g_velacc Vitaly Chaban
[gmx-users] Re: g_velacc Vitaly Chaban
[gmx-users] Re: g_velacc Vitaly Chaban
[gmx-users] Re: g_velacc Vitaly Chaban
[gmx-users] Error of installing gromacs v4.5.4 Hsin-Lin Chiang
[gmx-users] Re: Error of installing gromacs v4.5.4 Hsin-Lin Chiang
[gmx-users] Re: Error of installing gromacs v4.5.4 Hsin-Lin Chiang
[gmx-users] Re: gmx-users Re: Error of installing gromacs v4.5.4 Hsin-Lin Chiang
[gmx-users] (no subject) Michael D. Daily
[gmx-users] implicit solvent LINCS errors Michael D. Daily
[gmx-users] implicit solvent LINCS errors Michael D. Daily
[gmx-users] implicit solvent LINCS errors Michael D. Daily
[gmx-users] hi Sarath Chandra Dantu
[gmx-users] Reference pressure and pressure fluctuations in an NPT simulation Andrew DeYoung
[gmx-users] Re: Reference pressure and pressure fluctuations in an NPT simulation Andrew DeYoung
[gmx-users] Manually aborting a simulation Andrew DeYoung
[gmx-users] Velocity autocorrelation function of water using g_velacc Andrew DeYoung
[gmx-users] Re: Velocity autocorrelation function of water using g_velacc Andrew DeYoung
[gmx-users] Plan for energy minimization, NPT equilibration, and NPT dynamics Andrew DeYoung
[gmx-users] Box size error during attempted NPT equilibration Andrew DeYoung
[gmx-users] Recommended way to run production using the same conditions as equilibration Andrew DeYoung
[gmx-users] My problem is How to define 5-methyl cytosine by amberff port in gromacs? Masomeh Dehghani
[gmx-users] constraints Nilesh Dhumal
[gmx-users] ambar to opls force field Nilesh Dhumal
[gmx-users] ambar to opls force field Nilesh Dhumal
[gmx-users] ambar to opls force field Nilesh Dhumal
[gmx-users] ambar to opls force field Nilesh Dhumal
[gmx-users] ambar to opls force field Nilesh Dhumal
[gmx-users] Re: [gmx-developers] flexible water model Nilesh Dhumal
[gmx-users] Re: [gmx-developers] flexible water model Nilesh Dhumal
[gmx-users] pressure in NPT and NVT Nilesh Dhumal
[gmx-users] Re: [gmx-developers] flexible water model Nilesh Dhumal
[gmx-users] water dimer is gas phase Nilesh Dhumal
[gmx-users] Re: water dimer is gas phase Nilesh Dhumal
[gmx-users] Re: water dimer is gas phase Nilesh Dhumal
[gmx-users] Re: water dimer is gas phase Nilesh Dhumal
[gmx-users] g_sdf Nilesh Dhumal
[gmx-users] dipole moment Nilesh Dhumal
[gmx-users] dipole moment Nilesh Dhumal
[gmx-users] dipole moment Nilesh Dhumal
[gmx-users] dipole moment Nilesh Dhumal
[gmx-users] g_velacc Nilesh Dhumal
[gmx-users] g_velacc Nilesh Dhumal
[gmx-users] Re: g_velacc Nilesh Dhumal
[gmx-users] g_velacc Nilesh Dhumal
[gmx-users] Re: g_velacc Nilesh Dhumal
[gmx-users] g_velacc Nilesh Dhumal
[gmx-users] How to freeze groups Elisabeth
[gmx-users] NPT for compressing Elisabeth
[gmx-users] NPT for compressing Elisabeth
[gmx-users] NPT for compressing Elisabeth
[gmx-users] compressing with NPT Elisabeth
[gmx-users] problem in multichain protein solvation Asmaa Elsheshiny
[gmx-users] writing trajectory with water molecules within a distance from protein Thomas Evangelidis
[gmx-users] about side chain and structure rifinement Thomas Evangelidis
[gmx-users] about side chain and structure rifinement Thomas Evangelidis
[gmx-users] Fw: Re: Re: ionic liquids Dommert Florian
[gmx-users] g_current and output redirection Dommert Florian
[gmx-users] Plan for energy minimization, NPT equilibration, and NPT dynamics Dommert Florian
[gmx-users] unit of ekrot and ektrans Dommert Florian
[gmx-users] Changing the pH Tanos Celmar Costa Franca
[gmx-users] Charmm36 in Gromacs: missing dihedrals Jon Fuller
[gmx-users] Charmm36 in Gromacs: missing dihedrals Jon Fuller
[gmx-users] decomposing the energy Ramachandran G
[gmx-users] recovering topology Ramachandran G
[gmx-users] Rigid structure and flexible structure present in sing system Ignacio Fernández Galván
[gmx-users] Getting nonbonded interactions from gmxdump Ignacio Fernández Galván
[gmx-users] average trajectory Yulian Gavrilov
[gmx-users] trjcat error of different spacing Anirban Ghosh
[gmx-users] trjcat error of different spacing Anirban Ghosh
[gmx-users] trjcat error of different spacing Anirban Ghosh
[gmx-users] g_sas query Anirban Ghosh
[gmx-users] g_sas query Anirban Ghosh
[gmx-users] g_sas query Anirban Ghosh
[gmx-users] g_msd query Anirban Ghosh
[gmx-users] About -pbc option of trjconv Anirban Ghosh
[gmx-users] GridMatMD and CGMD Anirban Ghosh
[gmx-users] GridMatMD and CGMD Anirban Ghosh
[gmx-users] (no subject) Jayeeta Ghosh
[gmx-users] (no subject) Jayeeta Ghosh
[gmx-users] Fw: IEEE e-Science 2011 workshop on Interoperability in Scientific Computing Daniele Gianni
[gmx-users] Re: polarizable water models Ivan Gladich
[gmx-users] g_order for water Ivan Gladich
[gmx-users] g_order for water Ivan Gladich
[gmx-users] g_select and make_ndx Ivan Gladich
[gmx-users] Rigid structure and flexible structure present in sing system Luke Goodsell
[gmx-users] Rigid structure and flexible structure present in sing system Luke Goodsell
[gmx-users] Rigid structure and flexible structure present in sing system Luke Goodsell
[gmx-users] How to get angle distribution between two tyrosine stacking residues Oliver Grant
[gmx-users] Re:qmmm temp definition + linking atom Gerrit Groenhof
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 114 Gerrit Groenhof
[gmx-users] error in kalp15 in water tutorial Preeti Gupta
[gmx-users] Re: Simluations in vacuum - energy increase Zoe Hall
[gmx-users] Adding OPLS-UA forcefield Zoe Hall
[gmx-users] amber force field Maria Hamilton
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 2 Maria Hamilton
[gmx-users] adding an identified number of water molecules Maria Hamilton
[gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side Maria Hamilton
[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side Maria Hamilton
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 9 Maria Hamilton
[gmx-users] Nitrate ion Maria Hamilton
[gmx-users] "No molecules were defined in the system" Maria Hamilton
[gmx-users] liquid/liquid Maria Hamilton
[gmx-users] Fwd: liquid/liquid Maria Hamilton
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 61 Maria Hamilton
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 65 Maria Hamilton
[gmx-users] Atomtype not found Maria Hamilton
[gmx-users] Changing the pH João Henriques
[gmx-users] g_traj -ox -com slight inconsistency Jochen Hub
[gmx-users] Fatal error: Atomtype CB not found ITHAYARAJA
[gmx-users] Re: Fatal error: Atomtype CB not found ITHAYARAJA
[gmx-users] Request to solve this fatal error-reg ITHAYARAJA
[gmx-users] Invalid order for directive atomtypes Geethu Issac
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 19 Geethu Issac
[gmx-users] Invalid order for directive atomtypes Geethu Issac
[gmx-users] gmembed Sweta Iyer
[gmx-users] Source Code for Lennard jones truncation schemes Apoorv Kalyankar
[gmx-users] -ci option Jon Kapla
[gmx-users] recovering topology Taylor Kaplan
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 Faezeh Kargar
[gmx-users] number of molecules generated during pdb2gmx Hyunjin Kim
[gmx-users] forgetten password Hyunjin Kim
[gmx-users] g_energy Thomas Koller
[gmx-users] Fw: g_energy Thomas Koller
[gmx-users] g_energy Thomas Koller
[gmx-users] Viscosity and surface tension Thomas Koller
[gmx-users] surface tension of monolayer Sriprajak Krongsuk
[gmx-users] How to calculate lateral pressure for monolayer compression or expansion Sriprajak Krongsuk
[gmx-users] serial gromacs on windows Peter C. Lai
[gmx-users] RMSD with Vsite vs No Vsites Peter C. Lai
[gmx-users] RHEL OS, g_mdrun Peter C. Lai
[gmx-users] lipids per area charmm36 popc Peter C. Lai
[gmx-users] Specify run time Peter C. Lai
[gmx-users] -ci option Peter C. Lai
[gmx-users] Error in energy group exclusion Peter C. Lai
[gmx-users] compressing with NPT Peter C. Lai
[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8 Peter C. Lai
[gmx-users] Re: Unsteady Density Peter C. Lai
[gmx-users] Improper dihedrals in Charmm FF Peter C. Lai
[gmx-users] How to make a membrane system with 512 DPPCs Peter C. Lai
[gmx-users] How to make a membrane system with 512 DPPCs Peter C. Lai
[gmx-users] g_energy unable to -skip Peter C. Lai
[gmx-users] oplsaa vs. charmm Peter C. Lai
[gmx-users] Tesla S2050 issues Matthew Lardy
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Per Larsson
[gmx-users] Surface area calculation Laura Leay
[gmx-users] amber force field Justin A. Lemkul
[gmx-users] reg error in coordinate file Justin A. Lemkul
[gmx-users] How to use Inflategro with different lipid types Justin A. Lemkul
[gmx-users] amber force field Justin A. Lemkul
[gmx-users] reg lincs error and exploding problem during mdrun Justin A. Lemkul
[gmx-users] Continuation=yes From? Justin A. Lemkul
[gmx-users] Adding OPLS-UA forcefield Justin A. Lemkul
[gmx-users] Continuation=yes From? Justin A. Lemkul
[gmx-users] adding an identified number of water molecules Justin A. Lemkul
[gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side Justin A. Lemkul
[gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1 Justin A. Lemkul
[gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side Justin A. Lemkul
[gmx-users] Unsteady Density Justin A. Lemkul
[gmx-users] Re: Unsteady Density Justin A. Lemkul
[gmx-users] Re: Unsteady Density Justin A. Lemkul
[gmx-users] question of smd Justin A. Lemkul
[gmx-users] Invalid order for directive atomtypes Justin A. Lemkul
[gmx-users] itp file for trehalose Justin A. Lemkul
[gmx-users] REG grompp error Justin A. Lemkul
[gmx-users] excluding electrostatic interactions Justin A. Lemkul
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Justin A. Lemkul
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Justin A. Lemkul
[gmx-users] mdrun Fatal error: Domain decomposition does not support simple neighbor searching Justin A. Lemkul
[gmx-users] using command g_traj to output the trajectory of an ion in the z direction Justin A. Lemkul
[gmx-users] RTP file formats Justin A. Lemkul
[gmx-users] trjcat error of different spacing Justin A. Lemkul
[gmx-users] trjcat error of different spacing Justin A. Lemkul
[gmx-users] trjcat error of different spacing Justin A. Lemkul
[gmx-users] trjconv problem Justin A. Lemkul
[gmx-users] virtual sites Justin A. Lemkul
[gmx-users] virtual sites Justin A. Lemkul
[gmx-users] constraints Justin A. Lemkul
[gmx-users] trjorder not working Justin A. Lemkul
[gmx-users] trjconv center on protein Justin A. Lemkul
[gmx-users] virtual sites set up for topology file Justin A. Lemkul
[gmx-users] virtual sites set up for topology file Justin A. Lemkul
[gmx-users] virtual sites set up for topology file Justin A. Lemkul
[gmx-users] virtual sites set up for topology file Justin A. Lemkul
[gmx-users] virtual sites set up for topology file Justin A. Lemkul
[gmx-users] trjorder not working Justin A. Lemkul
[gmx-users] trjconv center on protein Justin A. Lemkul
[gmx-users] ambar to opls force field Justin A. Lemkul
[gmx-users] different number of waters (grompp) Justin A. Lemkul
[gmx-users] different number of waters (grompp) Justin A. Lemkul
[gmx-users] How to recenter solvent around solute Justin A. Lemkul
[gmx-users] How to recenter solvent around solute Justin A. Lemkul
[gmx-users] Umberella sampling Justin A. Lemkul
[gmx-users] reg pulling Justin A. Lemkul
[gmx-users] Umberella sampling Justin A. Lemkul
[gmx-users] ambar to opls force field Justin A. Lemkul
[gmx-users] Umberella sampling Justin A. Lemkul
[gmx-users] about pullinng in steered MD Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] ambar to opls force field Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] problem while running grompp command Justin A. Lemkul
[gmx-users] freeze the carbonyl carbon atoms Justin A. Lemkul
[gmx-users] liquid/liquid Justin A. Lemkul
[gmx-users] ambar to opls force field Justin A. Lemkul
[gmx-users] simulation of a non complete structure Justin A. Lemkul
[gmx-users] ambar to opls force field Justin A. Lemkul
[gmx-users] Fatal error: Atomtype CB not found Justin A. Lemkul
[gmx-users] tip4p.itp Justin A. Lemkul
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 Justin A. Lemkul
[gmx-users] DFLEXIBLE option Justin A. Lemkul
[gmx-users] principal moments of ellipsoid Justin A. Lemkul
[gmx-users] principal moments of ellipsoid Justin A. Lemkul
[gmx-users] Re: Fatal error: Atomtype CB not found Justin A. Lemkul
[gmx-users] Changing the pH Justin A. Lemkul
[gmx-users] energy group error Justin A. Lemkul
[gmx-users] charge groups Justin A. Lemkul
[gmx-users] g_current and output redirection Justin A. Lemkul
[gmx-users] charge groups Justin A. Lemkul
[gmx-users] charge groups Justin A. Lemkul
[gmx-users] charge groups Justin A. Lemkul
[gmx-users] re: simulation-rigid Justin A. Lemkul
[gmx-users] Re: [gmx-developers] flexible water model Justin A. Lemkul
[gmx-users] reg pushing rate Justin A. Lemkul
[gmx-users] about g_hbond Justin A. Lemkul
[gmx-users] Rigid structure and flexible structure present in sing system Justin A. Lemkul
[gmx-users] selecting groups for full trajectory Justin A. Lemkul
[gmx-users] CG database for POPC Justin A. Lemkul
[gmx-users] Genbox question Justin A. Lemkul
[gmx-users] Genbox question Justin A. Lemkul
[gmx-users] How to freeze groups Justin A. Lemkul
[gmx-users] Re: [gmx-developers] flexible water model Justin A. Lemkul
[gmx-users] Re: [gmx-developers] flexible water model Justin A. Lemkul
[gmx-users] Rigid structure and flexible structure present in sing system Justin A. Lemkul
[gmx-users] Re: CG database for POPC Justin A. Lemkul
[gmx-users] use AMBER ff03 force field in gromacs 4 Justin A. Lemkul
[gmx-users] index file Justin A. Lemkul
[gmx-users] index file Justin A. Lemkul
[gmx-users] Bond constraints during the equilibration for membrane-protein system Justin A. Lemkul
[gmx-users] reg puuling error Justin A. Lemkul
[gmx-users] numbering of .gro file Justin A. Lemkul
R: Re: [gmx-users] numbering of .gro file Justin A. Lemkul
[gmx-users] pressure in NPT and NVT Justin A. Lemkul
[gmx-users] numbering of .gro file Justin A. Lemkul
[gmx-users] Bond constraints during the equilibration for membrane-protein system Justin A. Lemkul
[gmx-users] Re: [gmx-developers] flexible water model Justin A. Lemkul
[gmx-users] g_energy statistical information Justin A. Lemkul
[gmx-users] Reference pressure and pressure fluctuations in an NPT simulation Justin A. Lemkul
[gmx-users] decomposing the energy Justin A. Lemkul
[gmx-users] reg push pull Justin A. Lemkul
[gmx-users] use g_mindist to generate restraints Justin A. Lemkul
[gmx-users] thermodynamic integration with implicit solvent Justin A. Lemkul
[gmx-users] calculating electrostatic potential Justin A. Lemkul
[gmx-users] reg bonds missing in the final pdb Justin A. Lemkul
[gmx-users] reg pull code for protein ligand interaction Justin A. Lemkul
[gmx-users] error in kalp15 in water tutorial Justin A. Lemkul
[gmx-users] adding new lipid into /charmm27.ff/lipids.rtp Justin A. Lemkul
[gmx-users] "Command Not Found" Justin A. Lemkul
R: Re: [gmx-users] numbering of .gro file Justin A. Lemkul
[gmx-users] "Command Not Found" Justin A. Lemkul
[gmx-users] how to obtain binding energy? Justin A. Lemkul
[gmx-users] how to obtain binding energy? Justin A. Lemkul
[gmx-users] how to obtain binding energy? Justin A. Lemkul
[gmx-users] mirroring a trajectorie Justin A. Lemkul
[gmx-users] Request to solve this fatal error-reg Justin A. Lemkul
[gmx-users] g_order output is mirrored Justin A. Lemkul
[gmx-users] g_order output is mirrored Justin A. Lemkul
[gmx-users] how to obtain binding energy? Justin A. Lemkul
[gmx-users] surface tension of monolayer Justin A. Lemkul
[gmx-users] g_order output is mirrored Justin A. Lemkul
[gmx-users] P-LINCS and nstlist Justin A. Lemkul
[gmx-users] RHEL OS, g_mdrun Justin A. Lemkul
[gmx-users] lipids per area charmm36 popc Justin A. Lemkul
[gmx-users] reg centre of mass in SMD Justin A. Lemkul
[gmx-users] About -pbc option of trjconv Justin A. Lemkul
[gmx-users] average trajectory Justin A. Lemkul
[gmx-users] Manually aborting a simulation Justin A. Lemkul
[gmx-users] Re: water dimer is gas phase Justin A. Lemkul
[gmx-users] Re: water dimer is gas phase Justin A. Lemkul
[gmx-users] issue with newest version of martini model Justin A. Lemkul
[gmx-users] problem during energy minimization Justin A. Lemkul
[gmx-users] NPT and NVT ensembles Justin A. Lemkul
[gmx-users] segmentation fault. Justin A. Lemkul
[gmx-users] Re: water dimer is gas phase Justin A. Lemkul
[gmx-users] extract histograms of phi and psi Justin A. Lemkul
[gmx-users] Fluorescence Anisotropy Justin A. Lemkul
[gmx-users] re: ciis peptide linkage Justin A. Lemkul
[gmx-users] problem during Energy minimization Justin A. Lemkul
[gmx-users] g_sdf Justin A. Lemkul
[gmx-users] NPT for compressing Justin A. Lemkul
[gmx-users] NPT for compressing Justin A. Lemkul
[gmx-users] -ci option Justin A. Lemkul
[gmx-users] Error in energy group exclusion Justin A. Lemkul
[gmx-users] Error in energy group exclusion Justin A. Lemkul
[gmx-users] Velocity autocorrelation function of water using g_velacc Justin A. Lemkul
[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8 Justin A. Lemkul
[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8 Justin A. Lemkul
[gmx-users] Rg Justin A. Lemkul
[gmx-users] Error in energy group exclusion Justin A. Lemkul
[gmx-users] Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8 Justin A. Lemkul
[gmx-users] Helix to coil Justin A. Lemkul
[gmx-users] what's the philosophy of -ci option in "genbox"? Justin A. Lemkul
[gmx-users] Potential of mean force Justin A. Lemkul
[gmx-users] Charmm36 in Gromacs: missing dihedrals Justin A. Lemkul
[gmx-users] How to make a membrane system with 512 DPPCs Justin A. Lemkul
[gmx-users] How to make a membrane system with 512 DPPCs Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] sphere around a protein Justin A. Lemkul
[gmx-users] To get PMF using pull geometry of cylinder Justin A. Lemkul
[gmx-users] Charge group problem from pdb2gmx Justin A. Lemkul
[gmx-users] query regarding replica exchange Justin A. Lemkul
[gmx-users] To get PMF using pull geometry of cylinder Justin A. Lemkul
[gmx-users] To get PMF using pull geometry of cylinder Justin A. Lemkul
[gmx-users] electron density Justin A. Lemkul
[gmx-users] Re: Error of installing gromacs v4.5.4 Justin A. Lemkul
[gmx-users] solvent implicit error Justin A. Lemkul
[gmx-users] Error while trying REMD on cluster Justin A. Lemkul
[gmx-users] g_velacc Justin A. Lemkul
[gmx-users] oplsaa vs. charmm Justin A. Lemkul
[gmx-users] protein-ligand interaction Justin A. Lemkul
[gmx-users] about POPC in Gromacs Justin A. Lemkul
[gmx-users] How to simulate spc216.pdb in different water potentials Justin A. Lemkul
[gmx-users] gmembed Justin A. Lemkul
[gmx-users] GridMatMD and CGMD Justin A. Lemkul
[gmx-users] GridMatMD and CGMD Justin A. Lemkul
[gmx-users] Problem with pdb2gmx in gromacs 4.5.3 Justin A. Lemkul
[gmx-users] PMF curve Justin A. Lemkul
[gmx-users] PMF curve Justin A. Lemkul
[gmx-users] PMF curve Justin A. Lemkul
[gmx-users] PMF curve Justin A. Lemkul
[gmx-users] Box size error during attempted NPT equilibration Justin A. Lemkul
[gmx-users] implicit solvent LINCS errors Justin A. Lemkul
[gmx-users] Fwd: Simulation of protein with phosphate ion... Justin A. Lemkul
[gmx-users] Fwd: Simulation of protein with phosphate ion... Justin A. Lemkul
[gmx-users] Fwd: Simulation of protein with phosphate ion... Justin A. Lemkul
[gmx-users] Fwd: Simulation of protein with phosphate ion... Justin A. Lemkul
[gmx-users] implicit solvent LINCS errors Justin A. Lemkul
[gmx-users] Grompp error on index file Justin A. Lemkul
[gmx-users] Grompp error on index file Justin A. Lemkul
[gmx-users] Indexing problem when using genconf Justin A. Lemkul
[gmx-users] Indexing problem when using genconf Justin A. Lemkul
[gmx-users] flexiblity Justin A. Lemkul
[gmx-users] Re: need help Justin A. Lemkul
[gmx-users] how to cite gromacs? Justin A. Lemkul
[gmx-users] Thermal_Unfolding Justin A. Lemkul
[gmx-users] Pulling a ligand out of protein cavity Justin A. Lemkul
[gmx-users] forgetten password Justin A. Lemkul
[gmx-users] number of molecules generated during pdb2gmx Justin A. Lemkul
[gmx-users] Recommended way to run production using the same conditions as equilibration Justin A. Lemkul
[gmx-users] difference of protein dynamics between NPT and NVE ensemble? Da-Wei Li
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Jianguo Li
[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ? Chih-Ying Lin
[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ? Chih-Ying Lin
[gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun
[gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun
[gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun
[gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun
[gmx-users] Invitation to connect on LinkedIn Raymond Friendli via LinkedIn
[gmx-users] Bromide ions in gromos forcefield Diana Lousa
[gmx-users] DFLEXIBLE option Kavyashree M
[gmx-users] DFLEXIBLE option Kavyashree M
[gmx-users] Running md in different systems Kavyashree M
[gmx-users] Continuing job in another machine Kavyashree M
[gmx-users] Continuing job in another machine Kavyashree M
[gmx-users] Minimum periodic distance Kavyashree M
[gmx-users] Minimum periodic distance Kavyashree M
[gmx-users] Minimum periodic distance Kavyashree M
[gmx-users] Minimum periodic distance Kavyashree M
[gmx-users] Minimum periodic distance Kavyashree M
[gmx-users] trjconv problem Sanku M
[gmx-users] trjconv problem Sanku M
[gmx-users] trjconv problem Sanku M
[gmx-users] query regarding replica exchange Sanku M
[gmx-users] query regarding replica exchange Sanku M
[gmx-users] Restarting replica exchange simulation Sanku M
[gmx-users] where can I download POPC membrane file? Sergio Manzetti
[gmx-users] numbering of .gro file Anna Marabotti
R: Re: [gmx-users] numbering of .gro file Anna Marabotti
[gmx-users] R: gmx-users Digest, Vol 85, Issue 101 Anna Marabotti
[gmx-users] numbering of .gro file Anna Marabotti
R: Re: [gmx-users] numbering of .gro file Anna Marabotti
[gmx-users] problem in gmx-users list archive? Anna Marabotti
[gmx-users] simulation of a peptide anchored to a support Anna Marabotti
R: Re: [gmx-users] simulation of a peptide anchored to a support Anna Marabotti
[gmx-users] Re: Simluations in vacuum - energy increase Erik Marklund
[gmx-users] Adding OPLS-UA forcefield Erik Marklund
[gmx-users] writing trajectory with water molecules within a distance from protein Erik Marklund
[gmx-users] principal moments of ellipsoid Erik Marklund
[gmx-users] Important bugfix for g_hbond Erik Marklund
[gmx-users] Surface area calculation Erik Marklund
[gmx-users] Important bugfix for g_hbond Erik Marklund
[gmx-users] g_msd query Erik Marklund
[gmx-users] average trajectory Erik Marklund
[gmx-users] Re: water dimer is gas phase Erik Marklund
[gmx-users] Re: water dimer is gas phase Erik Marklund
[gmx-users] memory problem of g_hbond? Erik Marklund
[gmx-users] memory problem of g_hbond? Erik Marklund
[gmx-users] g_order output is mirrored Igor Marques
[gmx-users] g_order output is mirrored Igor Marques
[gmx-users] g_order output is mirrored Igor Marques
[gmx-users] g_order output is mirrored Igor Marques
[gmx-users] electron density Igor Marques
[gmx-users] electron density Igor Marques
[gmx-users] g_msd capabilities Luis Martins
[gmx-users] g_msd mutual diffusion coefficient Luis Martins
[gmx-users] tabulated potentials for non-bonded interactions Sikandar Mashayak
[gmx-users] excluding electrostatic interactions Sikandar Mashayak
[gmx-users] excluding electrostatic interactions Sikandar Mashayak
[gmx-users] Virtual site at COM of more than 4 atoms Sikandar Mashayak
[gmx-users] tabulated potentials Sikandar Mashayak
[gmx-users] virtual sites Sikandar Mashayak
[gmx-users] virtual sites Sikandar Mashayak
[gmx-users] RMSD with Vsite vs No Vsites Sikandar Mashayak
[gmx-users] virtual sites Sikandar Mashayak
[gmx-users] virtual sites Sikandar Mashayak
[gmx-users] RMSD with Vsite vs No Vsites Sikandar Mashayak
[gmx-users] virtual sites set up for topology file Sikandar Mashayak
[gmx-users] virtual sites set up for topology file Sikandar Mashayak
[gmx-users] decomposing the energy Sikandar Mashayak
[gmx-users] free energy Gavin Melaugh
[gmx-users] free energy Gavin Melaugh
[gmx-users] free energy Gavin Melaugh
[gmx-users] nrexcl=3 Gavin Melaugh
[gmx-users] virtual sites Gavin Melaugh
[gmx-users] virtual sites Gavin Melaugh
[gmx-users] virtual sites Gavin Melaugh
[gmx-users] virtual sites Gavin Melaugh
[gmx-users] virtual sites Gavin Melaugh
[gmx-users] virtual sites Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] virtual sites set up for topology file Gavin Melaugh
[gmx-users] energy group error Gavin Melaugh
[gmx-users] energy group error Gavin Melaugh
[gmx-users] charge groups Gavin Melaugh
[gmx-users] charge groups Gavin Melaugh
[gmx-users] charge groups Gavin Melaugh
[gmx-users] charge groups Gavin Melaugh
[gmx-users] charge groups Gavin Melaugh
[gmx-users] exclusions Gavin Melaugh
[gmx-users] exclusions Gavin Melaugh
[gmx-users] Energy groups Gavin Melaugh
[gmx-users] where can I download POPC membrane file? Krzysztof Mlynarczyk
[gmx-users] g_energy statistical information Juliette N.
[gmx-users] Arrest Naba
[gmx-users] g_traj -ox -com slight inconsistency Chris Neale
[gmx-users] Count mismatch for state entry SDx, code count is 754728, file count is 0 Chris Neale
[gmx-users] Re: Count mismatch for state entry SDx, code count is 754728, file count is 0 Chris Neale
[gmx-users] constraints Chris Neale
[gmx-users] re: simulation-rigid Frank Neuhaus
[gmx-users] re: ciis peptide linkage Frank Neuhaus
[gmx-users] what's the philosophy of -ci option in "genbox"? Jinan Niu
[gmx-users] g_rmsf Efrat Noy
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Francesco Oteri
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Francesco Oteri
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Francesco Oteri
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Francesco Oteri
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Francesco Oteri
[gmx-users] Fwd: Simulation of protein with phosphate ion... Francesco Oteri
[gmx-users] How to recenter solvent around solute Dimitar Pachov
[gmx-users] How to recenter solvent around solute Dimitar Pachov
[gmx-users] How to recenter solvent around solute Dimitar Pachov
[gmx-users] How to recenter solvent around solute Dimitar Pachov
[gmx-users] thermodynamic integration with implicit solvent Samrat Pal
[gmx-users] Surface area calculation XAvier Periole
[gmx-users] decomposing the energy XAvier Periole
[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ? XAvier Periole
[gmx-users] Using the XTC library Joshua L. Phillips
[gmx-users] Using the XTC library Joshua L. Phillips
[gmx-users] query regarding replica exchange Joshua L. Phillips
[gmx-users] query regarding replica exchange Joshua L. Phillips
[gmx-users] implicit solvent LINCS errors Joshua L. Phillips
[gmx-users] How to use Inflategro with different lipid types Thomas Piggot
[gmx-users] lipids per area charmm36 popc Thomas Piggot
[gmx-users] Modified Gromacs and OPENMM Szilárd Páll
[gmx-users] openmm 3.0, opencl support Szilárd Páll
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 Szilárd Páll
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 SOLVED ! Szilárd Páll
[gmx-users] gromacs make error Szilárd Páll
[gmx-users] P-LINCS and nstlist Szilárd Páll
[gmx-users] RHEL OS, g_mdrun Szilárd Páll
[gmx-users] Re: Re: Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8 Szilárd Páll
[gmx-users] Error of installing gromacs v4.5.4 Szilárd Páll
[gmx-users] Re: Error of installing gromacs v4.5.4 Szilárd Páll
[gmx-users] Important bugfix for g_hbond Baofu Qiao
[gmx-users] memory problem of g_hbond? Baofu Qiao
[gmx-users] memory problem of g_hbond? Baofu Qiao
[gmx-users] residue number starting from not 1 Baofu Qiao
[gmx-users] RTP file formats Mr Bernard Ramos
[gmx-users] RTP file formats Mr Bernard Ramos
[gmx-users] On posre.itp Mr Bernard Ramos
[gmx-users] On posre.itp Mr Bernard Ramos
[gmx-users] On posre.itp Mr Bernard Ramos
[gmx-users] Grompp error on index file Mr Bernard Ramos
[gmx-users] Grompp error on index file Mr Bernard Ramos
[gmx-users] NMA problem Rashmi
AW: Re: [gmx-users] where can I download POPC membrane file? Rausch, Felix
[gmx-users] where can I download POPC membrane file? Rausch, Felix
[gmx-users] use AMBER ff03 force field in gromacs 4 Bruce D. Ray
[gmx-users] (no subject) X Rules
[gmx-users] (no subject) X Rules
[gmx-users] Bromide ions in gromos forcefield sulatha M. S
[gmx-users] Re: question of smd Thomas Schlesier
[gmx-users] mirroring a trajectorie Thomas Schlesier
[gmx-users] pdb2gmx, disulfide bonds and PDB CONECT lines Ehud Schreiber
[gmx-users] writing trajectory with water molecules within a distance from protein Roland Schulz
[gmx-users] writing trajectory with water molecules within a distance from protein Roland Schulz
[gmx-users] Trouble loading User data with a Tcl script (only half the data seems to load) J. Nathan Scott
[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load) J. Nathan Scott
[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load) J. Nathan Scott
[gmx-users] REMD multi core for each replica SebastianWaltz
[gmx-users] REMD multi core for each replica SebastianWaltz
[gmx-users] REMD: after replica exchange breakdown SebastianWaltz
[gmx-users] REMD: after replica exchange breakdown SebastianWaltz
[gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1 Alexey Shvetsov
[gmx-users] running job parallel Bharati Singh
[gmx-users] running job parallel Bharati Singh
[gmx-users] running job parallel Bharati Singh
[gmx-users] running job parallel Bharati Singh
[gmx-users] running job parallel Bharati Singh
[gmx-users] running job parallel Bharati Singh
[gmx-users] different number of waters (grompp) Ricardo O. S. Soares
Res: [gmx-users] different number of waters (grompp) Ricardo O. S. Soares
[gmx-users] Re: Simluations in vacuum - energy increase David van der Spoel
[gmx-users] tip4p.itp David van der Spoel
[gmx-users] lipids per area charmm36 popc David van der Spoel
[gmx-users] energy minimization error David van der Spoel
[gmx-users] Velocity autocorrelation function of water using g_velacc David van der Spoel
[gmx-users] dipole moment David van der Spoel
[gmx-users] dipole moment David van der Spoel
[gmx-users] dipole moment David van der Spoel
[gmx-users] dipole moment David van der Spoel
[gmx-users] g_velacc David van der Spoel
[gmx-users] g_velacc David van der Spoel
[gmx-users] g_velacc David van der Spoel
[gmx-users] oplsaa vs. charmm David van der Spoel
[gmx-users] Schlitters entropy calculation David van der Spoel
[gmx-users] Bromide ions in gromos forcefield David van der Spoel
[gmx-users] question regarding g_energy -aver output in gromacs 4.5.4 Jacob Alan Spooner
[gmx-users] P-LINCS and nstlist Sławomir Stachura
[gmx-users] P-LINCS and nstlist Sławomir Stachura
[gmx-users] "Command Not Found" Natalie Stephenson
[gmx-users] "Command Not Found" Natalie Stephenson
[gmx-users] "Command Not Found" Natalie Stephenson
[gmx-users] Specify run time Natalie Stephenson
[gmx-users] Specify run time Natalie Stephenson
[gmx-users] RE: How to use Inflategro with different lipid types Oliver Stueker
[gmx-users] Velocity and temperature profiles Mikhail Stukan
[gmx-users] Pulling a ligand out of protein cavity Shay Teaching
[gmx-users] Pulling a ligand out of protein cavity Shay Teaching
[gmx-users] gen-pairs Emine Deniz Tekin
[gmx-users] unit of ekrot and ektrans Swarnendu Tripathi
[gmx-users] unit of ekrot and ektrans Swarnendu Tripathi
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Ozlem Ulucan
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Ozlem Ulucan
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Ozlem Ulucan
[gmx-users] Is it possible to run implicit solvent simulations in parallel? Ozlem Ulucan
[gmx-users] about POPC in Gromacs Unknown
[gmx-users] (no subject) Ravi Kumar Venkatraman
[gmx-users] How to simulate spc216.pdb in different water potentials Ravi Kumar Venkatraman
[gmx-users] Charge group problem from pdb2gmx Felipe Villanelo
[gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM Zhi Wang
[gmx-users] liquid/liquid Dallas Warren
[gmx-users] g_rmsf Tsjerk Wassenaar
[gmx-users] trjconv center on protein Tsjerk Wassenaar
[gmx-users] g_sas query Tsjerk Wassenaar
[gmx-users] How to recenter solvent around solute Tsjerk Wassenaar
[gmx-users] problem in multichain protein solvation Tsjerk Wassenaar
[gmx-users] pressure in NPT and NVT Tsjerk Wassenaar
[gmx-users] R: gmx-users Digest, Vol 85, Issue 101 Tsjerk Wassenaar
[gmx-users] Fwd: Question => g_anaeig -first -last Tsjerk Wassenaar
[gmx-users] "Command Not Found" Tsjerk Wassenaar
[gmx-users] mirroring a trajectorie Tsjerk Wassenaar
[gmx-users] average trajectory Tsjerk Wassenaar
[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ? Tsjerk Wassenaar
[gmx-users] Minimum periodic distance Tsjerk Wassenaar
[gmx-users] is it possible to convert NAMD psf file to gromacas format? Tsjerk Wassenaar
[gmx-users] GTG to GAG with amber FF99SB force field Tsjerk Wassenaar
[gmx-users] Minimum periodic distance Tsjerk Wassenaar
[gmx-users] use g_mindist to generate restraints Weingarth, M.H.
[gmx-users] trjconv center on protein Tomek Wlodarski
[gmx-users] trjconv center on protein Tomek Wlodarski
[gmx-users] trjconv center on protein Tomek Wlodarski
[gmx-users] qmmm temp definition Yao Yao
[gmx-users] qmmm linking atom Yao Yao
[gmx-users] QMMM+NMA Yao Yao
[gmx-users] The problem of .trr file size limit? Matthew Zwier
[gmx-users] question about g_sgangle jeremy adler
[gmx-users] Re: question about g_sgangle jeremy adler
[gmx-users] using tcl to scipt gromacs jeremy adler
[gmx-users] issue with newest version of martini model jeremy adler
[gmx-users] electrostatic potential delara aghaie
[gmx-users] calculating electrostatic potential delara aghaie
[gmx-users] where can I download POPC membrane file? albert
[gmx-users] where can I download POPC membrane file? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
[gmx-users] is it possible to convert NAMD psf file to gromacas format? albert
AW: Re: [gmx-users] where can I download POPC membrane file? albert
[gmx-users] DO_DSSP anna
[gmx-users] RHEL OS, g_mdrun ram bio
[gmx-users] RHEL OS, g_mdrun ram bio
[gmx-users] flexiblity shiva birgani
[gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM zw258 at cam.ac.uk
[gmx-users] question of smd fancy2012
[gmx-users] Re:gmx-users Digest, Vol 85, Issue 20 fancy2012
[gmx-users] Arrest geethumelody at gmail.com
[gmx-users] hi rashi.parihar at gmail.com
[gmx-users] hi rashi.parihar at gmail.com
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 Kalavera at gmx.net
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 Kalavera at gmx.net
[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 SOLVED ! Kalavera at gmx.net
[gmx-users] writing trajectory with water molecules within a distance from protein maria goranovic
[gmx-users] writing trajectory with water molecules within a distance from protein maria goranovic
[gmx-users] The problem of .trr file size limit? gromacs564
[gmx-users] Simulation of protein with phosphate ion... bharat gupta
[gmx-users] Fwd: Simulation of protein with phosphate ion... bharat gupta
[gmx-users] Fwd: Simulation of protein with phosphate ion... bharat gupta
[gmx-users] Fwd: Simulation of protein with phosphate ion... bharat gupta
[gmx-users] Fwd: Simulation of protein with phosphate ion... bharat gupta
[gmx-users] Fwd: Simulation of protein with phosphate ion... bharat gupta
[gmx-users] Fwd: Simulation of protein with phosphate ion... bharat gupta
[gmx-users] modified PRODRG2 itp file ana johari
[gmx-users] extract histograms of phi and psi ana johari
[gmx-users] Fluorescence Anisotropy ana johari
[gmx-users] how to cite gromacs? leila karami
[gmx-users] principal moments of ellipsoid lammps lammps
[gmx-users] principal moments of ellipsoid lammps lammps
[gmx-users] principal moments of ellipsoid lammps lammps
[gmx-users] reflecting boundary conditions wall liaoxyi
[gmx-users] DO_DSSP battistia at libero.it
[gmx-users] amber force field lina
[gmx-users] running job parallel lina
[gmx-users] about g_hbond lina
[gmx-users] about g_hbond lina
[gmx-users] about g_hbond lina
[gmx-users] about g_hbond lina
[gmx-users] index file lina
[gmx-users] index file lina
[gmx-users] hi lina
[gmx-users] Bond constraints during the equilibration for membrane-protein system li lv
[gmx-users] Bond constraints during the equilibration for membrane-protein system li lv
[gmx-users] Bond constraints during the equilibration for membrane-protein system li lv
[gmx-users] Re: Replica Exchange MD using Gromacs jen.johnston at lycos.com
[gmx-users] about side chain and structure rifinement marco miele
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 114 marco miele
[gmx-users] problem with replica exchange jagannath mondal
[gmx-users] GTG to GAG with amber FF99SB force field yaolisha at msu.edu
[gmx-users] GTG to GAG with amber FF99SB force field yaolisha at msu.edu
[gmx-users] mdrun Fatal error: Domain decomposition does not support simple neighbor searching shivangi nangia
[gmx-users] trjorder not working shivangi nangia
[gmx-users] trjorder not working shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] -ci option shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] sphere around a protein shivangi nangia
[gmx-users] Thermal_Unfolding shahid nayeem
[gmx-users] problem while running grompp command rashi parihar
[gmx-users] problem regarding npt equilibration rashi parihar
[gmx-users] need help rashi parihar
[gmx-users] problem using trjconv command rashi parihar
[gmx-users] regarding creating tabulated potentials sreelakshmi ramesh
[gmx-users] regarding nacl simulation in water using tabulated potentials sreelakshmi ramesh
[gmx-users] regarding nacl simulation in water using tabulated potentials sreelakshmi ramesh
[gmx-users] regarding nacl simulation in water using tabulated potentials sreelakshmi ramesh
[gmx-users] regarding nacl simulation in water using tabulated potentials sreelakshmi ramesh
[gmx-users] problem during energy minimization sreelakshmi ramesh
[gmx-users] problem during energy minimization sreelakshmi ramesh
[gmx-users] segmentation fault. sreelakshmi ramesh
[gmx-users] energy minimization error sreelakshmi ramesh
[gmx-users] Water molecule starting at atom X can not be settled. sreelakshmi ramesh
[gmx-users] Water molecule starting at atom X can not be settled. sreelakshmi ramesh
[gmx-users] Water molecule starting at atom X can not be settled. sreelakshmi ramesh
[gmx-users] regarding table for water water interactions sreelakshmi ramesh
[gmx-users] regarding table for water water interactions sreelakshmi ramesh
[gmx-users] Continuation=yes From? mohsen ramezanpour
[gmx-users] Continuation=yes From? mohsen ramezanpour
[gmx-users] Continuation=yes From? mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] how to obtain binding energy mohsen ramezanpour
[gmx-users] how to obtain binding energy? mohsen ramezanpour
[gmx-users] PMF curve mohsen ramezanpour
[gmx-users] PMF curve mohsen ramezanpour
[gmx-users] PMF curve mohsen ramezanpour
[gmx-users] PMF curve mohsen ramezanpour
[gmx-users] PMF curve mohsen ramezanpour
[gmx-users] PMF curve mohsen ramezanpour
[gmx-users] reg error in coordinate file vidhya sankar
[gmx-users] reg lincs error and exploding problem during mdrun vidhya sankar
[gmx-users] REG grompp error vidhya sankar
[gmx-users] reg speed of MD vidhya sankar
[gmx-users] reg pulling vidhya sankar
[gmx-users] about pullinng in steered MD vidhya sankar
[gmx-users] reg pdb2gmx vidhya sankar
[gmx-users] reg pushing rate vidhya sankar
[gmx-users] reg puuling error vidhya sankar
[gmx-users] reg push pull vidhya sankar
[gmx-users] reg bonds missing in the final pdb vidhya sankar
[gmx-users] reg pull code for protein ligand interaction vidhya sankar
[gmx-users] reg centre of mass in SMD vidhya sankar
[gmx-users] X-ray Structures simon sham
[gmx-users] Rg simon sham
[gmx-users] Helix to coil simon sham
[gmx-users] oplsaa vs. charmm simon sham
[gmx-users] oplsaa vs. charmm simon sham
[gmx-users] g_helix and g_rotacf simon sham
[gmx-users] how to obtain binding energy shahab shariati
[gmx-users] how to obtain binding energy? shahab shariati
[gmx-users] how to obtain binding energy? shahab shariati
[gmx-users] how to obtain binding energy? shahab shariati
[gmx-users] how to obtain binding energy? shahab shariati
[gmx-users] Simulated annealing with implicit water model vivek sharma
[gmx-users] Error while trying REMD on cluster vivek sharma
[gmx-users] Error while trying REMD on cluster vivek sharma
[gmx-users] using command g_traj to output the trajectory of an ion in the z direction toby10222224 at sina.com
[gmx-users] How to get angle distribution between two tyrosine stacking residues bipin singh
[gmx-users] compilation of g_hbond after bugfix bipin singh
[gmx-users] Error in energy group exclusion bipin singh
[gmx-users] Error in energy group exclusion bipin singh
[gmx-users] Error in energy group exclusion bipin singh
[gmx-users] use AMBER ff03 force field in gromacs 4 mircial at sjtu.edu.cn
[gmx-users] use AMBER ff03 force field in gromacs 4 mircial at sjtu.edu.cn
[gmx-users] Schlitters entropy calculation Bala subramanian
[gmx-users] problem during energy minimization before MD Parul tew
[gmx-users] problem during Energy minimization Parul tew
[gmx-users] freeze the carbonyl carbon atoms toby10222224
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 67 toby10222224
[gmx-users] Re: freeze the carbonyl carbon atoms toby10222224
[gmx-users] solvent implicit error cesteban at unsl.edu.ar
[gmx-users] total force acting on group rasool.fakhimi at ut.ac.ir
[gmx-users] lipid ff decisions chris.neale at utoronto.ca
[gmx-users] g_select is pretty fantastic chris.neale at utoronto.ca
[gmx-users] free energy chris.neale at utoronto.ca
[gmx-users] free energy chris.neale at utoronto.ca
[gmx-users] free energy chris.neale at utoronto.ca
[gmx-users] difference of protein dynamics between NPT and NVE ensemble? chris.neale at utoronto.ca
[gmx-users] tabulated potential energy=nan for r=0 nm and charged atoms chris.neale at utoronto.ca
[gmx-users] beware gen-vel=no chris.neale at utoronto.ca
[gmx-users] tabulated potential energy=nan for r=0 nm and charged atoms chris.neale at utoronto.ca
[gmx-users] Rigid structure and flexible structure present in sing system chris.neale at utoronto.ca
[gmx-users] How to get angle distribution between two tyrosine stacking residues chris.neale at utoronto.ca
[gmx-users] problem during energy minimization chris.neale at utoronto.ca
[gmx-users] itp file for trehalose nishap.patel at utoronto.ca
[gmx-users] oplsaa vs. charmm jalemkul at vt.edu
[gmx-users] protein-ligand interaction jalemkul at vt.edu
[gmx-users] protein-ligand interaction jalemkul at vt.edu
[gmx-users] principal moments of ellipsoid ahmet yıldırım
[gmx-users] index file ahmet yıldırım
[gmx-users] index file ahmet yıldırım
[gmx-users] NPT and NVT ensembles ahmet yıldırım
[gmx-users] protein-ligand interaction ahmet yıldırım
[gmx-users] protein-ligand interaction ahmet yıldırım
[gmx-users] protein-ligand interaction ahmet yıldırım
[gmx-users] protein-ligand interaction ahmet yıldırım
[gmx-users] what's the philosophy of -ci option in "genbox"? 牛继南
[gmx-users] Potential of mean force 郭漫

Last message date: Tue May 31 21:49:33 CEST 2011
Archived on: Thu Nov 14 12:10:56 CET 2013

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