March 2009 Archives by author

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

Starting: Sun Mar 1 00:08:50 CET 2009
Ending: Tue Mar 31 23:56:22 CEST 2009
Messages: 843

[gmx-users] atomtype OWT4 not found but OWT3 and OWT5 is ok in amber03 force field....how is that possible? Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 1 Mark Abraham
[gmx-users] Question Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] problem in creating .gro file Mark Abraham
[gmx-users] How to define protein surface residues Mark Abraham
[gmx-users] Can not open file: topol.tpr Mark Abraham
[gmx-users] gromacs on itanium2 Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] Problem configuring openMPI Mark Abraham
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons Mark Abraham
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons Mark Abraham
[gmx-users] combination rules -- the part aboutthecombinationrules Mark Abraham
[gmx-users] what is data type the string "rvec" stands for? Mark Abraham
[gmx-users] How g_energy program calculates the averages ? Mark Abraham
[gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory Mark Abraham
[gmx-users] How to break a disulfide bond ??? Mark Abraham
[gmx-users] pbc interference with g_dist Mark Abraham
[gmx-users] maintaining the overall conformation of a protein during simulation Mark Abraham
[gmx-users] Change only one atom pair VdW interaction Mark Abraham
[gmx-users] Polymer entanglement simulation Mark Abraham
[gmx-users] K+ ion missing from gromos96ff in ions.itp file Mark Abraham
[gmx-users] editconf and genbox using method Mark Abraham
[gmx-users] editconf and genbox using method Mark Abraham
[gmx-users] Re: Job Crash Mark Abraham
[gmx-users] question about parallel runing of gromacs Mark Abraham
[gmx-users] question about parallel runing of gromacs Mark Abraham
[gmx-users] pdb2gmx -vsite h hangs Mark Abraham
[gmx-users] Gromac4 grompp -v Err Mark Abraham
[gmx-users] Potential energy of a single amino acid residu Mark Abraham
[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials Mark Abraham
[gmx-users] Cuda support Mark Abraham
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Mark Abraham
[gmx-users] Re: Energy Drift in Gromacs 4.0 Mark Abraham
[gmx-users] g_analylse and g_energy give different average value Mark Abraham
[gmx-users] how could have integrated structure after sa. Mark Abraham
[gmx-users] is there a possibility to convert .gro files directly to PDB? Mark Abraham
[gmx-users] initial velocities Langevin dynamics Mark Abraham
[gmx-users] initial velocities Langevin dynamics Mark Abraham
[gmx-users] Broken trr-file Mark Abraham
[gmx-users] get a box of 100 molecules Mark Abraham
[gmx-users] redirect md.log to standard ourput Mark Abraham
[gmx-users] RE : big system Mark Abraham
[gmx-users] problem about compiling mdrun_mpi under cygwin Mark Abraham
[gmx-users] problems with gmxtest.pl Mark Abraham
[gmx-users] Broken trr-file Mark Abraham
[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION Mark Abraham
[gmx-users] Re: Energy Drift in Gromacs 4.0 Mark Abraham
[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION Mark Abraham
[gmx-users] Height of the box Mark Abraham
[gmx-users] Reducing Size of Data Mark Abraham
[gmx-users] removal of COM Mark Abraham
[gmx-users] about the restart of the mdrun Mark Abraham
[gmx-users] gtkmm Code Demos? Mark Abraham
[gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file Mark Abraham
[gmx-users] problem in energy minimization Mark Abraham
[gmx-users] gtkmm Code Demos? Mark Abraham
[gmx-users] GPU calculation of GROMACS in Windows System Mark Abraham
[gmx-users] two peptides in same water box Mark Abraham
[gmx-users] Questions About Gromacs Mark Abraham
[gmx-users] Continue run in Gromacs-4 with check point file Mark Abraham
[gmx-users] Re: About Gromacs Mark Abraham
[gmx-users] Trying to link C++ code with libgmx. Please help! Mark Abraham
[gmx-users] How to add another electrostatic summation method in Gromacs Mark Abraham
[gmx-users] How to avoid the error: "Shake block crossing node boundaries" Mark Abraham
[gmx-users] problem in simulation of DMPC lipid bilayer Mark Abraham
[gmx-users] k- means clustering Mark Abraham
[gmx-users] How to make pdb file of whole trajectory Mark Abraham
[gmx-users] Explicit \ implicit Mark Abraham
[gmx-users] what factors effetc the simulation during energy minimization Mark Abraham
[gmx-users] Using R.E.D. charges with OPLS AA Mark Abraham
[gmx-users] Applying an improper to S-S bond Mark Abraham
[gmx-users] Integrating with BOINC: failing at minimization Mark Abraham
[gmx-users] How to add another electrostatic summation method in Gromacs Mark Abraham
[gmx-users] question in pulling in gromacs 4.0 Mark Abraham
[gmx-users] How to add another electrostatic summation methodin Gromacs Mark Abraham
[gmx-users] How to add another electrostatic summation methodinGromacs Mark Abraham
[gmx-users] parallel install gromacs-4.0.4 Mark Abraham
[gmx-users] Elastic Network Model Joshua Adelman
[gmx-users] Re: Water models for amber03 (Justin A. Lemkul) Alan
[gmx-users] Announcing NMR validation web interface iCing Alan
[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1 Pietro Amodeo
[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1 Pietro Amodeo
[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1 Pietro Amodeo
[gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs Alexandre Suman de Araujo
[gmx-users] problem in pdb file after SA Homa Azizian
[gmx-users] do_dssp fatal error Homa Azizian
[gmx-users] how could have integrated structure after sa. Homa Azizian
[gmx-users] metal ion go out of protein after md Homa Azizian
[gmx-users] metal ion go out of protein after md Homa Azizian
[gmx-users] (no subject) Homa Azizian
[gmx-users] ion jump out of protein Homa Azizian
[gmx-users] how to save grace out put to jpeg or grafifal pic Homa Azizian
[gmx-users] how to save grace out put to jpeg or grafical pic Homa Azizian
[gmx-users] do_dssp fatal error Homa Azizian
[gmx-users] editconf and genbox using method Nuno Azoia
[gmx-users] editconf and genbox using method Nuno Azoia
[gmx-users] genion command with PDB files for amber03 force field Joshua Ballanco
[gmx-users] problems with gmxtest.pl Bernhard Bandow
[gmx-users] problems with gmxtest.pl Bernhard Bandow
[gmx-users] problems with gmxtest.pl Bernhard Bandow
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Zuzana Benkova
[gmx-users] virtual atoms: hydrogens on sugars Relly Brandman
[gmx-users] editconf and genbox using method Marian Butu
[gmx-users] editconf and genbox using method Marian Butu
[gmx-users] Venkat C has sent you a private message Venkat C
[gmx-users] what is data type the string "rvec" stands for? Cao, Yang
[gmx-users] localp Jose Javier Lopez Cascales
[gmx-users] relative constraint deviation after lincs Alessandro Casoni
[gmx-users] RE: Diffusion coefficients ( Exp X Simul ) Vitaly V. Chaban
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 44 Vitaly V. Chaban
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 48 Vitaly V. Chaban
[gmx-users] RE: g_vellac Vitaly V. Chaban
[gmx-users] Re: g_vellac Vitaly V. Chaban
[gmx-users] Non-equilibraium MD: simulating a moving plate. Vitaly V. Chaban
[gmx-users] Non-equilibraium MD: simulating a moving plate. Vitaly V. Chaban
[gmx-users] Re: Non-equilibraium MD: simulating a moving Vitaly V. Chaban
[gmx-users] Re: Non-equilibrium MD: simulating a moving plate Vitaly V. Chaban
[gmx-users] pbc interference with g_dist Suman Chakrabarty
[gmx-users] Calculate asphericity of a group of atoms Suman Chakrabarty
[gmx-users] Change only one atom pair VdW interaction Gaurav Chopra
[gmx-users] Re: Job Crash Ilya Chorny
[gmx-users] Re: Job Crash Ilya Chorny
[gmx-users] pdb2gmx -vsite h hangs Ilya Chorny
[gmx-users] pdb2gmx -vsite h hangs Ilya Chorny
[gmx-users] Infiniband Hardware Ilya Chorny
[gmx-users] Energy Drift in Gromacs 4.0 Ilya Chorny
[gmx-users] Re: Energy Drift in Gromacs 4.0 Ilya Chorny
[gmx-users] Re: Energy Drift in Gromacs 4.0 Ilya Chorny
[gmx-users] Re: Energy Drift in Gromacs 4.0 Ilya Chorny
[gmx-users] Height of the box Ilya Chorny
[gmx-users] pdb2gmx error Ilya Chorny
[gmx-users] pdb2gmx error Ilya Chorny
[gmx-users] pdb2gmx error Ilya Chorny
[gmx-users] Help parameterizing ddb to work with vsite -h option of pdb2gmx Ilya Chorny
[gmx-users] K+ ion missing from gromos96ff in ions.itp file Dean Cuebas
[gmx-users] combination rules -- the part aboutthecombinationrules Shuangxing Dai
[gmx-users] How to add another electrostatic summation method in Gromacs Shuangxing Dai
[gmx-users] How to add another electrostatic summation method in Gromacs Shuangxing Dai
[gmx-users] How to add another electrostatic summation methodin Gromacs Shuangxing Dai
[gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai
[gmx-users] get a box of 100 molecules Adrien Delmont
[gmx-users] get a box of 100 molecules Adrien Delmont
[gmx-users] get a box of 100 molecules Adrien Delmont
[gmx-users] get a box of 100 molecules Adrien Delmont
[gmx-users] get a box of 100 molecules Adrien Delmont
[gmx-users] get a box of 100 molecules Adrien Delmont
[gmx-users] Binding Copper to Protein DimitryASuplatov
[gmx-users] Applying an improper to S-S bond DimitryASuplatov
[gmx-users] Using R.E.D. charges with OPLS AA DimitryASuplatov
[gmx-users] g_vellac in the last versions Florian Dommert
[gmx-users] Re: g_vellac Florian Dommert
[gmx-users] Re: g_vellac Florian Dommert
[gmx-users] using more than one type of molecules Molecular Dynamics
[gmx-users] using more than one type of molecules Molecular Dynamics
[gmx-users] Error with equilibration of DPPC membrane with protein Edvin Erdtman
[gmx-users] Error with equilibration of DPPC membrane with protein Edvin Erdtman
[gmx-users] Trying to link C++ code with libgmx. Please help! Semen Esilevsky
[gmx-users] Trying to link C++ code with libgmx. Please help! Semen Esilevsky
[gmx-users] gromacs-4.0.2, parallel performance in two quadcore xeon machines Antoine FORTUNE
[gmx-users] problem extending simulation 64 proc Rebeca García Fandiño
[gmx-users] Diffusion coefficients ( Exp X Simul ) Eudes Fileti
[gmx-users] Diffusion coefficients ( Exp X Simul ) Eudes Fileti
[gmx-users] Softcores: sc-power = 1 ou 2 ? Eudes Fileti
[gmx-users] Softcores: sc-power = 1 or 2 ? again Eudes Fileti
[gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess) Eudes Fileti
[gmx-users] Re: Softcores: sc-power = 1 or 2 ? again (Berk and Justin) Eudes Fileti
[gmx-users] Wrong Shake Tolerance Andreas Boozo Frank
[gmx-users] Wrong Shake Tolerance Andreas Boozo Frank
[gmx-users] initial velocities Langevin dynamics Ran Friedman
[gmx-users] gromacs 4 mpi weirdness Ran Friedman
[gmx-users] Using R.E.D. charges with OPLS AA Ran Friedman
[gmx-users] Re: g_covar Ran Friedman
[gmx-users] (no subject) ANINDITA GAYEN
[gmx-users] gromacs in parallel version ANINDITA GAYEN
[gmx-users] Re: Energy Drift in Gromacs 4.0 Luca De Gaetani
[gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs Neha Gandhi
[gmx-users] Re: Drug-Enzyme tutorial- LIE energies in gromacs Neha Gandhi
[gmx-users] drug-enzyme simulation. Neha Gandhi
[gmx-users] drug-enzyme simulation. Neha Gandhi
[gmx-users] no ngmx? Dr. Barbara Gioffreda
[gmx-users] running GROMACS-MPI on Rocks cluster- strange results Diego Enry Gomes
[gmx-users] gromacs in parallel version Diego Enry Gomes
[gmx-users] question about parallel runing of gromacs Diego Enry Gomes
[gmx-users] Isn't dt=0.0001 very small? Diego Enry Gomes
[gmx-users] problem in pdb file after SA Diego Enry Gomes
[gmx-users] do_dssp fatal error Diego Enry Gomes
[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong) Gerrit Groenhof
[gmx-users] open positions Gerrit Groenhof
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system GuoGuangjun
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system GuoGuangjun
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system GuoGuangjun
[gmx-users] two peptides in same water box Bhawana Gupta
[gmx-users] how to make whole trajectory Pdb files Bhawana Gupta
[gmx-users] How to make pdb file of whole trajectory Bhawana Gupta
[gmx-users] Explicit \ implicit Bhawana Gupta
[gmx-users] Gromacs on SPARC Andrey Gurtovenko
[gmx-users] how to deal with the hydrogen bonding interactions between bases He, Yang
[gmx-users] how to define the dummy atoms in gromacs He, Yang
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system Berk Hess
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system Berk Hess
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system Berk Hess
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Berk Hess
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Berk Hess
WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Berk Hess
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Berk Hess
[gmx-users] eigenvec.trr and eigenval.xvg Berk Hess
[gmx-users] problem extending simulation 64 proc Berk Hess
[gmx-users] Re: Energy Drift in Gromacs 4.0 Berk Hess
[gmx-users] viscosity calculation using g_energy (3.3.3) Berk Hess
[gmx-users] viscosity calculation using g_energy (3.3.3) Berk Hess
[gmx-users] free energy coupling/decoupling equivalence Berk Hess
[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates." Berk Hess
[gmx-users] Wrong Shake Tolerance Berk Hess
[gmx-users] angular removal of COM and domain decomposition Berk Hess
[gmx-users] Wrong Shake Tolerance Berk Hess
[gmx-users] angular removal of COM and domain decomposition Berk Hess
[gmx-users] Softcores: sc-power = 1 ou 2 ? Berk Hess
[gmx-users] mdrun hangs with the pull option Berk Hess
[gmx-users] g_dipoles Berk Hess
[gmx-users] Softcores: sc-power = 1 or 2 ? again Berk Hess
[gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess) Berk Hess
[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Berk Hess
[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Berk Hess
[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Berk Hess
[gmx-users] How to add another electrostatic summation method in Gromacs Berk Hess
[gmx-users] [Fwd: Problems in pulling a molecule from the membrane] Berk Hess
[gmx-users] Positive energy for Coulumb term. Does this mean Coulumb interaction destabilizes protein? Seungpyo Hong
[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong) Seungpyo Hong
[gmx-users] g_wham 4..0.x input file: tpr-files.dat ? Y.C. Huang
[gmx-users] how to save grace out put to jpeg or grafifal pic Jochen Hub
[gmx-users] how to define the dummy atoms in gromacs Jochen Hub
GMX-4.0.4 failed test (Re: [gmx-users] gromacs on itanium2) Tru Huynh
[gmx-users] How to avoid the error: "Shake block crossing node boundaries" Leontyev Igor
[gmx-users] viscosity calculation using g_energy (3.3.3) JMandumpal
[gmx-users] viscosity calculation using g_energy (3.3.3) JMandumpal
[gmx-users] viscosity calculation using g_energy (3.3.3) JMandumpal
[gmx-users] viscosity calculation using g_energy (3.3.3) JMandumpal
[gmx-users] Broken trr-file Hansjoerg Jerabek
[gmx-users] Broken trr-file Hansjoerg Jerabek
[gmx-users] Broken trr-file Hansjoerg Jerabek
[gmx-users] Fatal error with g_hbond Grzegorz Jezierski
[gmx-users] g_analylse and g_energy give different average value Li Jianguo
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Chansoo Kim
[gmx-users] Fwd: Polyethylene (PE) simulations in Gromacs - please! Chansoo Kim
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Chansoo Kim
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Chansoo Kim
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Chansoo Kim
[gmx-users] Error in pdb2gmx Robert Kretschmer
[gmx-users] Lipid models for GROMOS96 53a6 Kukol, Andreas
[gmx-users] regarding dimethylated lysine topology file Anil Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 136 Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138 Pawan Kumar
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138 Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] grompp error in running simulation of lipid bilayer Pawan Kumar
[gmx-users] grompp error in running simulation of lipid bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] problem in simulation of lipid bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Doubt regarding membrane protein in POPC bilayer Pawan Kumar
[gmx-users] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig
[gmx-users] removal of COM Sun Joo Lee
[gmx-users] hydrophobicity Sunjoo Lee
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system Jussi Lehtola
[gmx-users] Timestep and force field Jussi Lehtola
[gmx-users] tool.top does not found Justin A. Lemkul
[gmx-users] help with FAD topology, please Justin A. Lemkul
[gmx-users] regarding dimethylated lysine topology file Justin A. Lemkul
[gmx-users] problem in creating .gro file Justin A. Lemkul
[gmx-users] settingparameters for energy minimization Justin A. Lemkul
SV: [gmx-users] g_order version 4.0.x Justin A. Lemkul
[gmx-users] settingparameters for energy minimization Justin A. Lemkul
[gmx-users] a question about analysis Justin A. Lemkul
[gmx-users] generalized order parameters S2 Justin A. Lemkul
[gmx-users] regarding dimethylated lysine topology file Justin A. Lemkul
[gmx-users] Can not open file: topol.tpr Justin A. Lemkul
[gmx-users] How to handle incomplete PDB file? Justin A. Lemkul
[gmx-users] How to handle incomplete PDB file? Justin A. Lemkul
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Justin A. Lemkul
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Justin A. Lemkul
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Justin A. Lemkul
[gmx-users] Polyethylene (PE) simulations in Gromacs - please! Justin A. Lemkul
[gmx-users] simulation box Justin A. Lemkul
[gmx-users] g_wham 4..0.x input file: tpr-files.dat ? Justin A. Lemkul
[gmx-users] Fatal error with g_hbond Justin A. Lemkul
[gmx-users] How to define "stretch" in ffoplsaabon.itp ? Justin A. Lemkul
[gmx-users] gromacs on itanium2 Justin A. Lemkul
[gmx-users] How to define "stretch" in ffoplsaabon.itp ? Justin A. Lemkul
Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ? Justin A. Lemkul
[gmx-users] Re: Ligand is moving far away after energy minimization Justin A. Lemkul
[gmx-users] How to add any new force field to GRMOACS for modelling the system of interest? Justin A. Lemkul
[gmx-users] genion command with PDB files for amber03 force field Justin A. Lemkul
[gmx-users] 1-4 interaction, infinite meanings for energies Justin A. Lemkul
[gmx-users] problem running grompp - error message here Justin A. Lemkul
[gmx-users] OXY not found Justin A. Lemkul
[gmx-users] How to build a coarse grained model and do the simulation with Gromacs Justin A. Lemkul
[gmx-users] How to build a coarse grained model and do the simulation with Gromacs Justin A. Lemkul
[gmx-users] Can make_ndx generate indices only for heavy atoms? Justin A. Lemkul
[gmx-users] How to break a disulfide bond ??? Justin A. Lemkul
[gmx-users] gromacs in parallel version Justin A. Lemkul
[gmx-users] Error in pdb2gmx Justin A. Lemkul
[gmx-users] using pdb2gmx Justin A. Lemkul
[gmx-users] .gro files problems Justin A. Lemkul
[gmx-users] pdb files Justin A. Lemkul
[gmx-users] Polymer entanglement simulation Justin A. Lemkul
[gmx-users] Polymer entanglement simulation Justin A. Lemkul
[gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory Justin A. Lemkul
[gmx-users] Simulated annealing Justin A. Lemkul
[gmx-users] Polymer entanglement simulation Justin A. Lemkul
[gmx-users] editconf and genbox using method Justin A. Lemkul
[gmx-users] solvent temperature Justin A. Lemkul
[gmx-users] The gromacs4 run err! Justin A. Lemkul
SV: SV: [gmx-users] g_order version 4.0.x Justin A. Lemkul
SV: SV: SV: [gmx-users] g_order version 4.0.x Justin A. Lemkul
SV: SV: SV: [gmx-users] g_order version 4.0.x Justin A. Lemkul
[gmx-users] pdb2gmx -vsite h hangs Justin A. Lemkul
[gmx-users] pdb2gmx -vsite h hangs Justin A. Lemkul
[gmx-users] Re: problems with editconf command Justin A. Lemkul
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system Justin A. Lemkul
[gmx-users] Re: problems with editconf command Justin A. Lemkul
[gmx-users] relative constraint deviation after lincs Justin A. Lemkul
[gmx-users] question about parallel runing of gromacs Justin A. Lemkul
[gmx-users] Potential energy of a single amino acid residu Justin A. Lemkul
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Justin A. Lemkul
[gmx-users] Simulated annealing Justin A. Lemkul
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Justin A. Lemkul
[gmx-users] Broken trr-file Justin A. Lemkul
[gmx-users] big system Justin A. Lemkul
[gmx-users] get a box of 100 molecules Justin A. Lemkul
[gmx-users] problems with gmxtest.pl Justin A. Lemkul
[gmx-users] get a box of 100 molecules Justin A. Lemkul
[gmx-users] get a box of 100 molecules Justin A. Lemkul
[gmx-users] get a box of 100 molecules Justin A. Lemkul
[gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION Justin A. Lemkul
[gmx-users] Re: Minimization not converging Justin A. Lemkul
[gmx-users] pdb files Justin A. Lemkul
[gmx-users] pdb files Justin A. Lemkul
[gmx-users] pdb files Justin A. Lemkul
[gmx-users] problem in energy minimization Justin A. Lemkul
[gmx-users] Reducing Size of Data Justin A. Lemkul
[gmx-users] Re: Fwd: Ligand is moving far away after energy minimization Justin A. Lemkul
[gmx-users] get a top file to run md simulation Justin A. Lemkul
[gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file Justin A. Lemkul
[gmx-users] get a box of 100 molecules Justin A. Lemkul
[gmx-users] using more than one type of molecules Justin A. Lemkul
[gmx-users] Triclinic water box for a protein MD Justin A. Lemkul
[gmx-users] Matching atom name and types in OPLS-aa FF Justin A. Lemkul
[gmx-users] ion jump out of protein Justin A. Lemkul
[gmx-users] how to parametrize Phos. Thr TPO Justin A. Lemkul
[gmx-users] using more than one type of molecules Justin A. Lemkul
[gmx-users] using more than one type of molecules Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] How can I record only molecule trajectory ? Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] no ngmx? Justin A. Lemkul
[gmx-users] Matching atom name and types in OPLS-aa FF Justin A. Lemkul
[gmx-users] do_dssp fatal error Justin A. Lemkul
[gmx-users] Equilibration Justin A. Lemkul
[gmx-users] Range checking error: only on double precision Justin A. Lemkul
[gmx-users] Range checking error: only on double precision Justin A. Lemkul
[gmx-users] make-hole Justin A. Lemkul
[gmx-users] Re: Free energy with Gromacs. Justin A. Lemkul
[gmx-users] Re: Free energy with Gromacs. Justin A. Lemkul
[gmx-users] Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 136 Justin A. Lemkul
[gmx-users] Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] inertia Justin A. Lemkul
[gmx-users] Simulated annealing Justin A. Lemkul
[gmx-users] problem in running simulation Justin A. Lemkul
[gmx-users] Binding Copper to Protein Justin A. Lemkul
[gmx-users] One more broken .trr file Justin A. Lemkul
[gmx-users] installation gromacs-3.2.1 in redhat-6 Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138 Justin A. Lemkul
[gmx-users] Questions about energy groups! Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138 (Doubt regarding membrane protein in POPC bilayer) Justin A. Lemkul
[gmx-users] how to merge the protein and lipid bilayer in a cell? Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
FW: [gmx-users] One more broken .trr file Justin A. Lemkul
[gmx-users] Simulated annealing Justin A. Lemkul
[gmx-users] grompp command: The solvent group SOL is not continuous Justin A. Lemkul
[gmx-users] problem in simulation of DMPC lipid bilayer Justin A. Lemkul
[gmx-users] what factors effetc the simulation during energy minimization Justin A. Lemkul
[gmx-users] Applying an improper to S-S bond Justin A. Lemkul
[gmx-users] Usually how do you decide the salt concentration? Justin A. Lemkul
[gmx-users] How to calculate PMF after AFM pulling Justin A. Lemkul
[gmx-users] How to calculate PMF after AFM pulling Justin A. Lemkul
[gmx-users] about parallel run Justin A. Lemkul
[gmx-users] question in pulling in gromacs 4.0 Justin A. Lemkul
[gmx-users] How to calculate PMF after AFM pulling Justin A. Lemkul
[gmx-users] drug-enzyme simulation. Justin A. Lemkul
[gmx-users] using Gaussian with Gromacs Justin A. Lemkul
[gmx-users] rmsd Justin A. Lemkul
[gmx-users] parallel install gromacs-4.0.4 Justin A. Lemkul
[gmx-users] Water models for amber03 Justin A. Lemkul
[gmx-users] Error with equilibration of DPPC membrane with protein Justin A. Lemkul
[gmx-users] water model and force field Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Prepping Docking Complexes Justin A. Lemkul
[gmx-users] new block lactitol Justin A. Lemkul
[gmx-users] Missing atom in residue Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Justin A. Lemkul
[gmx-users] new block lactitol Justin A. Lemkul
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Justin A. Lemkul
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Justin A. Lemkul
[gmx-users] POPE setup Marc F. Lensink
[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer Marc F. Lensink
[gmx-users] How to avoid the error: "Shake block crossing nodeboundaries" Igor Leontyev
[gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries" Igor Leontyev
[gmx-users] How to avoid the error:"Shake blockcrossing nodeboundaries" Igor Leontyev
[gmx-users] generalized order parameters S2 Dechang Li
[gmx-users] How VMD to display the velocity Dechang Li
[gmx-users] eigenvec.trr and eigenval.xvg Dechang Li
[gmx-users] where is the position of the partial charges? Chih-Ying Lin
[gmx-users] How can I record only molecule trajectory ? Chih-Ying Lin
[gmx-users] gromacs on itanium2 Erik Lindahl
[gmx-users] Rosetta Academic Training Webinar Nir London
[gmx-users] Nomenclature Inconsistency between *.rtp and *nb.itp in ffG53a5 and ffG53a6 (CH2r vs CH2R) Diana Lousa
[gmx-users] about parallel run Mahnam
[gmx-users] question about parallel runing of gromacs Xiang Mao
[gmx-users] question about parallel runing of gromacs Xiang Mao
[gmx-users] question about parallel runing of gromacs Xiang Mao
[gmx-users] problem about compiling mdrun_mpi under cygwin Xiang Mao
[gmx-users] Diffusion coefficients ( Exp X Simul ) Omer Markovitch
[gmx-users] initial velocities Langevin dynamics Omer Markovitch
[gmx-users] is there a possibility to convert .gro files directly to PDB? Omer Markovitch
[gmx-users] (no subject) Omer Markovitch
[gmx-users] How VMD to display the velocity Höfling Martin
[gmx-users] not referencing ffamber03.hdb Höfling Martin
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] Problem configuring openMPI Manik Mayur
[gmx-users] mdrun hangs with the pull option Manik Mayur
[gmx-users] mdrun hangs with the pull option Manik Mayur
[gmx-users] mdrun hangs with the pull option Manik Mayur
[gmx-users] Timestep and force field Manik Mayur
[gmx-users] Compiler and OS issue in gromacs Manik Mayur
[gmx-users] help with FAD topology, please Miguel Quiliano Meza
[gmx-users] gtkmm Code Demos? Stephen P. Molnar
[gmx-users] gtkmm Code Demos? Stephen P. Molnar
[gmx-users] gtkmm Code Demos? Stephen P. Molnar
[gmx-users] simulation box Lucio Montero
[gmx-users] Triclinic water box for a protein MD Lucio Montero
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Lucio Montero
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Lucio Montero
[gmx-users] FOMMS 2009 2nd Circular Jonathan Moore
[gmx-users] initial velocities Langevin dynamics Loris Moretti
[gmx-users] initial velocities Langevin dynamics Loris Moretti
[gmx-users] initial velocities Langevin dynamics Loris Moretti
[gmx-users] initial velocities Langevin dynamics Loris Moretti
[gmx-users] problem in energy minimization Abhik Mukhopadhyay
[gmx-users] problem in energy minimization Abhik Mukhopadhyay
[gmx-users] is there a possibility to convert .gro files directly to PDB? Andrea Muntean
[gmx-users] no ngmx? Abu Naser
[gmx-users] where is the position of the partial charges? Chris Neale
[gmx-users] OXY not found Chris Neale
[gmx-users] Pull code using two reaction coordinates?? Chris Neale
[gmx-users] Problem configuring openMPI Nicolas
[gmx-users] Problem configuring openMPI Nicolas
[gmx-users] Problem configuring openMPI Nicolas
[gmx-users] angle restraints in gromacs 4 Brian Novak
[gmx-users] Questions About Gromacs Xi Ouyang
[gmx-users] phi / psi values using g_chi XAvier Periole
[gmx-users] phi / psi values using g_chi XAvier Periole
[gmx-users] phi / psi values using g_chi XAvier Periole
[gmx-users] Karplus parameterization XAvier Periole
[gmx-users] How to carry out rigid body XAvier Periole
[gmx-users] Force Field - Gromos96 XAvier Periole
[gmx-users] about MARTINI forcefield XAvier Periole
[gmx-users] Matching atom name and types in OPLS-aa FF XAvier Periole
[gmx-users] angular removal of COM and domain decomposition XAvier Periole
[gmx-users] center of mass XAvier Periole
[gmx-users] angular removal of COM and domain decomposition XAvier Periole
[gmx-users] angular removal of COM and domain decomposition XAvier Periole
[gmx-users] Pull code using two reaction coordinates?? XAvier Periole
[gmx-users] Matching atom name and types in OPLS-aa FF XAvier Periole
[gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal XAvier Periole
[gmx-users] Doubt regarding membrane protein in POPC bilayer XAvier Periole
[gmx-users] problem in simulation of lipid bilayer XAvier Periole
[gmx-users] Equilibration Emanuel Peter
[gmx-users] Triclinic water box for a protein MD TJ Piggot
[gmx-users] Triclinic water box for a protein MD TJ Piggot
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Ran Friedman, Biochemisches Inst.
[gmx-users] Installing topolbuild Bruce D. Ray
[gmx-users] Installing topolbuild Bruce D. Ray
[gmx-users] How to break a disulfide bond ??? Venkat Reddy
[gmx-users] How to break a disulfide bond ??? Venkat Reddy
[gmx-users] How to break a disulfide bond ??? Venkat Reddy
[gmx-users] add zinc in gromacs/cpmd Marius Retegan
[gmx-users] gromacs on itanium2 Marius Retegan
[gmx-users] gromacs on itanium2 Marius Retegan
[gmx-users] gromacs on itanium2 Marius Retegan
[gmx-users] gromacs on itanium2 Marius Retegan
[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Josmar R. da Rocha
[gmx-users] Can not open file: topol.tpr J. Rui Rodrigues
[gmx-users] Problems with pulling code Marisa Roman
[gmx-users] grompp vel_gen = seg fault KS Rotondi
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Chitrita Dutta Roy
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Chitrita Dutta Roy
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Chitrita Dutta Roy
[gmx-users] No plot found running .xvg files using xmgrace produced by g_helix. Chitrita Dutta Roy
[gmx-users] Fwd: No plot found running .xvg files using xmgrace produced by g_helix. Chitrita Dutta Roy
[gmx-users] Re: Ligand is moving far away after energy minimization Ms. Aswathy S
[gmx-users] A Question About gmxtest Reza Salari
[gmx-users] problem with pull direction Thomas Schlesier
[gmx-users] how to get the the force plot after pulling, dynamic simulation using GMX-3.3 Thomas Schlesier
[gmx-users] RE: Question for pulling in GROMACS 4.0 Thomas Schlesier
[gmx-users] [Fwd: Problems in pulling a molecule from the membrane] Thomas Schlesier
[gmx-users] about LINCS WARNING Roland Schulz
[gmx-users] Problem configuring openMPI Roland Schulz
[gmx-users] Problem configuring openMPI Roland Schulz
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons Roland Schulz
[gmx-users] MPI-based errors on the power6 at large parallelization Roland Schulz
[gmx-users] grompp vel_gen = seg fault Roland Schulz
[gmx-users] add zinc in gromacs/cpmd Jacopo Sgrignani
[gmx-users] grompp command: The solvent group SOL is not continuous Halie Shah
[gmx-users] solvent box outside protein Halie Shah
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58 Jack Shultz
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58 Jack Shultz
[gmx-users] Cuda support Jack Shultz
[gmx-users] redirect md.log to standard ourput Jack Shultz
[gmx-users] redirect md.log to standard ourput Jack Shultz
[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION Jack Shultz
[gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION Jack Shultz
[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION Jack Shultz
[gmx-users] Minimization not converging Jack Shultz
[gmx-users] Re: Minimization not converging Jack Shultz
[gmx-users] Reducing Size of Data Jack Shultz
[gmx-users] Range checking error: only on double precision Jack Shultz
[gmx-users] Range checking error: only on double precision Jack Shultz
[gmx-users] Range checking error: only on double precision Jack Shultz
[gmx-users] not referencing ffamber03.hdb Jack Shultz
[gmx-users] Integrating with BOINC: failing at minimization Jack Shultz
[gmx-users] Water models for amber03 Jack Shultz
[gmx-users] Prepping Docking Complexes Jack Shultz
[gmx-users] Missing atom in residue Jack Shultz
[gmx-users] OS - Compiler - GROMACS compatibility Alexey Shvetsov
[gmx-users] g_sdf gives wrong refmol with multiple center molecules Atte Sillanpää
[gmx-users] box size Ricardo Soares
[gmx-users] simulation box Ricardo Soares
[gmx-users] How to define protein surface residues Lee Soin
[gmx-users] How to define protein surface residues Lee Soin
[gmx-users] How to handle incomplete PDB file? Lee Soin
[gmx-users] How to handle incomplete PDB file? Lee Soin
[gmx-users] Can make_ndx generate indices only for heavy atoms? Lee Soin
[gmx-users] maintaining the overall conformation of a protein during simulation Lee Soin
[gmx-users] About pull force in COM pulling Lee Soin
[gmx-users] Questions about urea.itp Lee Soin
[gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system David van der Spoel
[gmx-users] g_order version 4.0.x David van der Spoel
[gmx-users] How to define protein surface residues David van der Spoel
[gmx-users] Detail of Script.sh in Gromacs-4.0.3? David van der Spoel
[gmx-users] gromacs on itanium2 David van der Spoel
[gmx-users] Diffusion coefficients ( Exp X Simul ) David van der Spoel
[gmx-users] Diffusion coefficients ( Exp X Simul ) David van der Spoel
[gmx-users] gromacs on itanium2 David van der Spoel
[gmx-users] is there a possibility to convert .gro files directly to PDB? David van der Spoel
[gmx-users] problems with gmxtest.pl David van der Spoel
[gmx-users] Re: Energy Drift in Gromacs 4.0 David van der Spoel
[gmx-users] viscosity calculation using g_energy (3.3.3) David van der Spoel
[gmx-users] Questions about urea.itp David van der Spoel
[gmx-users] Karplus parameterization David van der Spoel
[gmx-users] Re: Hardware suggestion David van der Spoel
[gmx-users] problems with gmxtest.pl David van der Spoel
[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1 David van der Spoel
[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1 David van der Spoel
[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates." David van der Spoel
[gmx-users] How can I record only molecule trajectory ? David van der Spoel
[gmx-users] g_dipoles David van der Spoel
[gmx-users] how to save grace out put to jpeg or grafifal pic David van der Spoel
[gmx-users] Timestep and force field David van der Spoel
[gmx-users] (no subject) - fluctuations David van der Spoel
[gmx-users] Trying to link C++ code with libgmx. Please help! David van der Spoel
[gmx-users] (no subject) - fluctuations David van der Spoel
[gmx-users] (no subject) - fluctuations David van der Spoel
[gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs David van der Spoel
[gmx-users] how to make whole trajectory Pdb files David van der Spoel
[gmx-users] How to avoid the error: "Shake block crossing nodeboundaries" David van der Spoel
[gmx-users] How to make pdb file of whole trajectory David van der Spoel
[gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries" David van der Spoel
[gmx-users] Explicit \ implicit David van der Spoel
[gmx-users] metal ion go out of protein after md #NGUYEN CONG TRI#
[gmx-users] (no subject) Sunil Thapa
[gmx-users] POPE setup Peter Tieleman
[gmx-users] OXY not found Andy Torres
[gmx-users] Re: OXY not found Andy Torres
[gmx-users] How to define "stretch" in ffoplsaabon.itp ? Tree
[gmx-users] Fwd: How to define "stretch" in ffoplsaabon.itp ? Tree
[gmx-users] How to define "stretch" in ffoplsaabon.itp ? Tree
[gmx-users] How to define "stretch" in ffoplsaabon.itp ? Tree
Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ? Tree
[gmx-users] Polymer entanglement simulation Tree
[gmx-users] Polymer entanglement simulation Tree
[gmx-users] Polymer entanglement simulation Tree
[gmx-users] Fwd: Force Field - Gromos96 Tree
[gmx-users] Matching atom name and types in OPLS-aa FF Tree
[gmx-users] Fwd: Matching atom name and types in OPLS-aa FF Tree
[gmx-users] Matching atom name and types in OPLS-aa FF Tree
[gmx-users] Matching atom name and types in OPLS-aa FF Tree
[gmx-users] Cross-linking of polymers Tree
[gmx-users] Cross-linking of polymers Tree
[gmx-users] make-hole Urszula Uciechowska
[gmx-users] g_rdf program Pablo Umazano
[gmx-users] center of mass Antonia V.
[gmx-users] center of mass Antonia V.
[gmx-users] inertia Antonia V.
[gmx-users] Questions About Gromacs Antonia V.
[gmx-users] g_principal Antonia V.
[gmx-users] (no subject) Antonia V.
[gmx-users] (no subject) - fluctuations Antonia V.
[gmx-users] (no subject) - fluctuations Antonia V.
[gmx-users] (no subject) - fluctuations Antonia V.
[gmx-users] how to parametrize Phos. Thr TPO Lucio Ricardo Montero Valenzuela
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Claus Valka
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Claus Valka
WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Claus Valka
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Claus Valka
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Claus Valka
[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 Claus Valka
[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Claus Valka
[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Claus Valka
[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Claus Valka
[gmx-users] Calculation of fraction of native contacts Camilo Velez
[gmx-users] Does andersen thermostat work? Camilo Velez
[gmx-users] Potential energy of a single amino acid residu Tom Venken
[gmx-users] Potential energy of a single amino acid residu Tom Venken
[gmx-users] .gro files problems Andrew Voronkov
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58 Andrew Voronkov
[gmx-users] Isn't dt=0.0001 very small? Andrew Voronkov
[gmx-users] is there a possibility to convert .gro files directly to PDB? Andrew Voronkov
[gmx-users] (no subject) Antonia Vyrkou
[gmx-users] (no subject) Antonia Vyrkou
[gmx-users] regarding dimethylated lysine topology file Antonia Vyrkou
[gmx-users] regarding dimethylated lysine topology file Antonia Vyrkou
[gmx-users] exclude intramolecular coulombic Antonia Vyrkou
[gmx-users] exclude intramolecular coulombic Antonia Vyrkou
[gmx-users] exclude intramolecular coulombic Antonia Vyrkou
[gmx-users] exclude intramolecular coulombic Antonia Vyrkou
[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials David Waroquiers
[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials David Waroquiers
[gmx-users] g_rdf program Dallas B. Warren
[gmx-users] Cross-linking of polymers Dallas B. Warren
[gmx-users] (no subject) - fluctuations Dallas B. Warren
[gmx-users] grompp error in running simulation of lipid bilayer Dallas B. Warren
[gmx-users] How to handle incomplete PDB file? Tsjerk Wassenaar
[gmx-users] Can not open file: topol.tpr Tsjerk Wassenaar
[gmx-users] genion command with PDB files for amber03 force field Tsjerk Wassenaar
[gmx-users] Isn't dt=0.0001 very small? Tsjerk Wassenaar
[gmx-users] Gromac4 grompp -v Err Tsjerk Wassenaar
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Tsjerk Wassenaar
[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation. Tsjerk Wassenaar
[gmx-users] metal ion go out of protein after md Tsjerk Wassenaar
[gmx-users] Variance in ED Tsjerk Wassenaar
[gmx-users] Fwd: Force Field - Gromos96 Tsjerk Wassenaar
[gmx-users] Variance in ED Tsjerk Wassenaar
[gmx-users] Triclinic water box for a protein MD Tsjerk Wassenaar
[gmx-users] Triclinic water box for a protein MD Tsjerk Wassenaar
[gmx-users] Triclinic water box for a protein MD Tsjerk Wassenaar
[gmx-users] Fwd: using oplsaa in Gromacs Tsjerk Wassenaar
[gmx-users] pdb2gmx error Tsjerk Wassenaar
[gmx-users] gromacs 4 mpi weirdness Tsjerk Wassenaar
[gmx-users] gromacs 4 mpi weirdness Tsjerk Wassenaar
[gmx-users] Binding Copper to Protein Tsjerk Wassenaar
[gmx-users] PBC dodecahedron Tsjerk Wassenaar
[gmx-users] Re: About Gromacs Tsjerk Wassenaar
[gmx-users] Re: g_covar Tsjerk Wassenaar
[gmx-users] drug-enzyme simulation. Tsjerk Wassenaar
[gmx-users] grompp errors Tsjerk Wassenaar
[gmx-users] solvent box outside protein Tsjerk Wassenaar
[gmx-users] g_order version 4.0.x Sarah Witzke
SV: [gmx-users] g_order version 4.0.x Sarah Witzke
SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke
SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke
SV: SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke
SV: SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke
[gmx-users] One more broken .trr file Sarah Witzke
[gmx-users] One more broken .trr file Sarah Witzke
FW: [gmx-users] One more broken .trr file Sarah Witzke
[gmx-users] parallel install gromacs-4.0.4 Hongyan Xiao
[gmx-users] parallel install gromacs-4.0.4 Hongyan Xiao
[gmx-users] Usually how do you decide the salt concentration? Peggy Yao
[gmx-users] non-harmonic position restraints Makoto Yoneya
[gmx-users] Questions about energy groups! Zhong Zheng
[gmx-users] Re: Non-equilibraium MD: simulating a moving plate. Hu Zhongqiao
[gmx-users] Re: Non-equilibraium MD: simulating a moving Hu Zhongqiao
[gmx-users] The gromacs4 run err! li bai
[gmx-users] Gromac4 grompp -v Err li bai
[gmx-users] "Gromacs 4 grompp -v" err li bai
[gmx-users] Re: Fwd: gmx-users Digest, Vol 59, Issue 74 li bai
[gmx-users] problems with gmxtest.pl bandow
[gmx-users] installation gromacs-3.2.1 in redhat-6 akalabya bissoyi
[gmx-users] Variance in ED andrea carotti
[gmx-users] Variance in ED andrea carotti
[gmx-users] Pull code using two reaction coordinates?? rversace at ccny.cuny.edu
[gmx-users] what factors effetc the simulation during energy minimization bhargavi ch
[gmx-users] (no subject) bhargavi ch
[gmx-users] what factors effetc the simulation during energy minimization bhargavi ch
[gmx-users] factors effecting the simulation bhargavi ch
[gmx-users] k- means clustering sarbani chattopadhyay
[gmx-users] k means cluster sarbani chattopadhyay
[gmx-users] problem in running grompp victor doss
[gmx-users] problem running grompp - error message here victor doss
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 1 drugdesign
[gmx-users] tool.top does not found drugdesign
[gmx-users] Can not open file: topol.tpr drugdesign
[gmx-users] 1-4 interaction, infinite meanings for energies drugdesign
[gmx-users] genion command with PDB files for amber03 force field drugdesign
[gmx-users] Timestep and force field varsha gautham
[gmx-users] Timestep and force field varsha gautham
[gmx-users] water model and force field varsha gautham
[gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal maria goranovic
[gmx-users] rotate trajectory from self-assembly of lipid bilayer maria goranovic
[gmx-users] a question about analysis oguz gurbulak
[gmx-users] about force fields oguz gurbulak
[gmx-users] using pdb2gmx oguz gurbulak
[gmx-users] pdb files oguz gurbulak
[gmx-users] pdb files oguz gurbulak
[gmx-users] pdb files oguz gurbulak
[gmx-users] get a top file to run md simulation oguz gurbulak
[gmx-users] using Gaussian with Gromacs oguz gurbulak
[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates." xiaowu759 at hotmail.com
[gmx-users] Detail of Script.sh in Gromacs-4.0.3? mhviet at ifpan.edu.pl
[gmx-users] about LINCS WARNING mhviet at ifpan.edu.pl
[gmx-users] Thank Roland mhviet at ifpan.edu.pl
[gmx-users] OS - Compiler - GROMACS compatibility alkasrivastava at iitb.ac.in
[gmx-users] Compiler and OS issue in gromacs alkasrivastava at iitb.ac.in
[gmx-users] How g_energy program calculates the averages ? rashmi_chem at iitb.ac.in
[gmx-users] Simulated annealing jayant james
[gmx-users] Simulated annealing jayant james
[gmx-users] Simulated annealing jayant james
[gmx-users] Simulated annealing jayant james
[gmx-users] running GROMACS-MPI on Rocks cluster- strange results kala
[gmx-users] rmsd shahrbanoo karbalaee
[gmx-users] Invitation to connect on LinkedIn himanshu khandelia
[gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory nam kim
[gmx-users] wall modelling avinash kumar
[gmx-users] regarding dimethylated lysine topology file prasun kumar
[gmx-users] regarding dimethylated lysine topology file prasun kumar
[gmx-users] How to carry out rigid body lammps lammps
[gmx-users] about MARTINI forcefield lammps lammps
[gmx-users] about martini forcefield(MFF) lammps lammps
[gmx-users] Problems with SMD using gromacs huifang liu
[gmx-users] problems with pulling direction and the initial spring position huifang liu
[gmx-users] problem with pull direction huifang liu
[gmx-users] how to get the the force plot after pulling dynamic simulation using GMX-3.3 huifang liu
[gmx-users] Re:how to get the the force plot after pulling huifang liu
[gmx-users] Re:problem in DMPC lipid bilayer huifang liu
[gmx-users] How to calculate PMF after AFM pulling huifang liu
[gmx-users] How to calculate PMF after AFM pulling huifang liu
[gmx-users] How to calculate PMF after AFM pulling huifang liu
[gmx-users] how to parametrize Phos. Thr TPO nahren manuel
[gmx-users] PBC dodecahedron (corrected) nahren manuel
[gmx-users] gmx in GPU calculation li ming
[gmx-users] Re: gmx in GPU calculation li ming
[gmx-users] GPU calculation of GROMACS in Windows System li ming
[gmx-users] some peoblems about modeling... li ming
[gmx-users] three questions about GMX modeling... li ming
[gmx-users] incorporate multi proteins into a cell? li ming
[gmx-users] how to merge the protein and lipid bilayer in a cell? li ming
[gmx-users] supti mukherjee sent you a Friend Request on Yaari supti mukherjee
[gmx-users] Reminder: Please Respond to supti's Invitation supti mukherjee
[gmx-users] solvent temperature imparato at na.infn.it
[gmx-users] Interpretation of g_chi results naimah haron naimah
[gmx-users] Height of the box naimah haron naimah
[gmx-users] box size noob noob
[gmx-users] simulation box noob noob
[gmx-users] big system noob noob
[gmx-users] RE : big system noob noob
[gmx-users] distance restraints for alpha helix abhigna polavarapu
[gmx-users] pulling of molecule in GROMACS 4.03 anirban polley
[gmx-users] question in pulling in gromacs 4.0 anirban polley
[gmx-users] g_dipoles rams rams
[gmx-users] g_dipoles rams rams
[gmx-users] g_dipoles rams rams
[gmx-users] Question Elias santos
[gmx-users] How to break a disulfide bond ??? sharada
[gmx-users] How to break a disulfide bond ??? sharada
[gmx-users] How to break a disulfide bond ??? sharada
[gmx-users] problem in creating .gro file nitu sharma
[gmx-users] problem in running simulation nitu sharma
[gmx-users] nitu sharma has invited you to open a Google mail account nitu sharma
[gmx-users] problem in DMPC lipid bilayer nitu sharma
[gmx-users] problem in simulation of DMPC lipid bilayer nitu sharma
[gmx-users] grompp error in running simulation of lipid bilayer nitu sharma
[gmx-users] grompp error in running simulation of lipid bilayer nitu sharma
[gmx-users] problem in simulation of lipid bilayer nitu sharma
[gmx-users] settingparameters for energy minimization vivek sharma
[gmx-users] settingparameters for energy minimization vivek sharma
[gmx-users] Installing topolbuild vivek sharma
[gmx-users] Installing topolbuild vivek sharma
[gmx-users] about the restart of the mdrun sheerychen
[gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file sitiazma
[gmx-users] Force Field - Gromos96 tree
[gmx-users] Matching atom name and types in OPLS-aa FF tree
[gmx-users] Matching atom name and types in OPLS-aa FF tree
[gmx-users] grompp errors andrea.borgogno at unipd.it
[gmx-users] new block lactitol cesteban at unsl.edu.ar
[gmx-users] new block lactitol cesteban at unsl.edu.ar
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons chris.neale at utoronto.ca
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons chris.neale at utoronto.ca
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons chris.neale at utoronto.ca
[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons chris.neale at utoronto.ca
[gmx-users] MPI-based errors on the power6 at large parallelization chris.neale at utoronto.ca
[gmx-users] about force fields chris.neale at utoronto.ca
[gmx-users] phi / psi values using g_chi chris.neale at utoronto.ca
[gmx-users] phi / psi values using g_chi chris.neale at utoronto.ca
[gmx-users] free energy coupling/decoupling equivalence chris.neale at utoronto.ca
[gmx-users] gmx in GPU calculation chris.neale at utoronto.ca
[gmx-users] some peoblems about modeling... chris.neale at utoronto.ca
[gmx-users] Alert for Open MPI bug v1.3.0 and v1.3.1 chris.neale at utoronto.ca
[gmx-users] Calculate asphericity of a group of atoms loan.huynh at utoronto.ca
[gmx-users] How to add any new force field to GRMOACS for modelling the system of interest? wuxiao
[gmx-users] Continue run in Gromacs-4 with check point file xuji
[gmx-users] PBC dodecahedron meetnahren at yahoo.com
[gmx-users] How to build a coarse grained model and do the simulation with Gromacs 侃
[gmx-users] How to build a coarse grained model and do the simulation with Gromacs 侃

Last message date: Tue Mar 31 23:56:22 CEST 2009
Archived on: Thu Nov 14 12:06:31 CET 2013

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

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