April 2011 Archives by author

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Starting: Fri Apr 1 00:19:43 CEST 2011
Ending: Sat Apr 30 22:56:40 CEST 2011
Messages: 983

[gmx-users] Still model Mu Yuguang (Dr)
[gmx-users] dhfr-impl-1nm.bench run keeps failing Miah Wadud Dr (ITCS)
[gmx-users] dhfr-impl-1nm.bench run keeps failing Miah Wadud Dr (ITCS)
[gmx-users] GROMOS45ACARBO force fields in the GROMACS format. ABEL Stephane 175950
[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field Stephane Abel
[gmx-users] VDW parameters: Martini Forcefield + Implicit Solvation Mark Abraham
[gmx-users] Installtion of gromacs-4.5.3 Mark Abraham
[gmx-users] Groups in mdp file Mark Abraham
[gmx-users] RE: VDW parameters: Martini Forcefield + Implicit Solvation Mark Abraham
[gmx-users] Groups in mdp file Mark Abraham
[gmx-users] Replica Exchange MD using Gromacs Mark Abraham
[gmx-users] Replica Exchange MD using Gromacs Mark Abraham
[gmx-users] The solvent group Water is not continuous Mark Abraham
[gmx-users] The solvent group Water is not continuous Mark Abraham
[gmx-users] Precision mismatch Mark Abraham
[gmx-users] domain decomposition Mark Abraham
[gmx-users] implicit water and a layer of explicit water molecule Mark Abraham
[gmx-users] Setting the C6 LJ term for OPLSA FF Mark Abraham
R: [gmx-users] implicit water and a layer of explicit water molecule Mark Abraham
[gmx-users] autocorrelation functions Mark Abraham
[gmx-users] the total charge of system is not an integer Mark Abraham
[gmx-users] Invalid order for directive atomtypes Mark Abraham
[gmx-users] domain decomposition Mark Abraham
[gmx-users] domain decomposition Mark Abraham
[gmx-users] the total charge of system is not an integer Mark Abraham
[gmx-users] OPLS-AA atom types Mark Abraham
[gmx-users] How to remove charge of 5e-2 ?? Mark Abraham
[gmx-users] OPLS-AA atom types Mark Abraham
[gmx-users] OPLS-AA atom types Mark Abraham
[gmx-users] invalid line Mark Abraham
[gmx-users] help on converting charmm/cgenff parameters to gromacs Mark Abraham
[gmx-users] How to remove charge of 5e-2 ?? Mark Abraham
[gmx-users] How to remove charge of 5e-2 ?? Mark Abraham
[gmx-users] How to remove charge of 5e-2 ?? Mark Abraham
[gmx-users] Methodology Check Mark Abraham
[gmx-users] How to remove charge of 5e-2 ?? Mark Abraham
[gmx-users] not enough space Mark Abraham
[gmx-users] PME Mark Abraham
[gmx-users] how to simulate crystals in Gromacs Mark Abraham
[gmx-users] help on converting charmm/cgenff parameters to gromacs Mark Abraham
[gmx-users] help on converting charmm/cgenff parameters to gromacs Mark Abraham
[gmx-users] how to simulate crystals in Gromacs Mark Abraham
[gmx-users] help on converting charmm/cgenff parameters to gromacs Mark Abraham
[gmx-users] help on converting charmm/cgenff parameters to gromacs Mark Abraham
[gmx-users] membedded.gro from g_membed has broken molecules (fix periodicity?) Mark Abraham
[gmx-users] Still model Mark Abraham
[gmx-users] aminoacids.n.tdb Mark Abraham
[gmx-users] multicomponent system- units Mark Abraham
[gmx-users] Error while performing a REMD simulation Mark Abraham
[gmx-users] Error while performing a REMD simulation Mark Abraham
[gmx-users] On dihedral type for CHARMM Mark Abraham
[gmx-users] Extending Simulation Mark Abraham
[gmx-users] Extending Simulation Mark Abraham
[gmx-users] converging value Mark Abraham
[gmx-users] converging value Mark Abraham
[gmx-users] the gmx-4.5.4 can not be compiled but the gmx-4.5.3 can Mark Abraham
[gmx-users] mdrun segmentation fault Mark Abraham
[gmx-users] 1,5 and 1,6 LJ interactions for OPLS AA SEI Mark Abraham
[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL Mark Abraham
[gmx-users] problem with mpiexec, mdrun in gromacs/4.0.7 Mark Abraham
[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL Mark Abraham
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein Mark Abraham
[gmx-users] multicomponent system- units Mark Abraham
[gmx-users] orientational relaxation Mark Abraham
[gmx-users] orientational relaxation Mark Abraham
[gmx-users] aminoacids.n.tdb Mark Abraham
[gmx-users] Regarding creating interface between two solvent at particular site Mark Abraham
[gmx-users] Differences in default values for nstpcouple and cmap atomtypes between versions 4.0 and 4.5.4 Mark Abraham
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR Mark Abraham
[gmx-users] load imbalance!!! Mark Abraham
[gmx-users] Re: Problems about the simulation involving cytochrome C Mark Abraham
[gmx-users] load imbalance!!! Mark Abraham
[gmx-users] compression- NPT Mark Abraham
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Mark Abraham
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Mark Abraham
[gmx-users] compression- NPT Mark Abraham
[gmx-users] Residue 'HEM' not found in residue topology database Mark Abraham
[gmx-users] How to solve GBSA problem ? Mark Abraham
[gmx-users] Re: EDO and TRS ligand Mark Abraham
[gmx-users] tip5p.gro Mark Abraham
[gmx-users] micelles and trjconv -pbc cluster Mark Abraham
[gmx-users] Installation error Mark Abraham
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Mark Abraham
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Mark Abraham
[gmx-users] Re: Trajectory visualization Mark Abraham
[gmx-users] Re: Trajectory visualization Mark Abraham
[gmx-users] Fwd: genbox Mark Abraham
[gmx-users] error in running jobs in parallel !!! Mark Abraham
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology Mark Abraham
[gmx-users] suitable forcefield Mark Abraham
[gmx-users] error in running jobs in parallel !!! Mark Abraham
[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup Mark Abraham
[gmx-users] Adding Virtual Site to the Molecule Mark Abraham
[gmx-users] the ligand have more than one molecules Mark Abraham
[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup Mark Abraham
[gmx-users] aminoacids.n.tdb Mark Abraham
[gmx-users] coordination file Mark Abraham
[gmx-users] parallel run breaks !! Mark Abraham
[gmx-users] Re: energy group exclusions Mark Abraham
[gmx-users] Re: energy group exclusions Mark Abraham
[gmx-users] how to deal with xleap to simulate a protein-ligand complex? Mark Abraham
[gmx-users] pdb2gmx segmentation fault Mark Abraham
[gmx-users] Re: energy group exclusions Mark Abraham
[gmx-users] any software which could convert a polypeptide sequence to a pdb file? Mark Abraham
答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? Mark Abraham
[gmx-users] dhfr-impl-1nm.bench run keeps failing Mark Abraham
[gmx-users] restarting from cpt and binary identical Mark Abraham
[gmx-users] dhfr-impl-1nm.bench run keeps failing Mark Abraham
[gmx-users] PYP chromophore force field Mark Abraham
[gmx-users] problem with g_dipoles and index file Mark Abraham
[gmx-users] problem with g_dipoles and index file Mark Abraham
[gmx-users] cholesterol Mark Abraham
[gmx-users] Tcoupl default setting Mark Abraham
[gmx-users] temperature effect on potential energy Mark Abraham
[gmx-users] Improper dihedrals in Charmm FF Mark Abraham
[gmx-users] Help: Gromacs Installation Mark Abraham
[gmx-users] DNA not wrapping around CNT in MD simulation Mark Abraham
[gmx-users] DNA not wrapping around CNT in MD simulation Mark Abraham
[gmx-users] DNA not wrapping around CNT in MD simulation Mark Abraham
[gmx-users] DNA not wrapping around CNT in MD simulation Mark Abraham
[gmx-users] Query Mark Abraham
[gmx-users] Virtual site at COM of more than 4 atoms Mark Abraham
[gmx-users] introducing ADP and ATP to Gromacs Mark Abraham
[gmx-users] dealing with ATP Mark Abraham
[gmx-users] trjcat eneconv time continuation Mark Abraham
[gmx-users] flexiable water - model Mark Abraham
[gmx-users] error when running grompp Mark Abraham
[gmx-users] Placing anion/cation at a particular distance from peptide Mark Abraham
[gmx-users] Re:gmx-users Digest, Vol 84, Issue 207 Mark Abraham
[gmx-users] Re: Probable error in trjcat; skipping frames Mark Abraham
[gmx-users] Urey-Bradley constant in CHARMM to GMX Mark Abraham
[gmx-users] Fw: trjconv -pbc and broken reside Mark Abraham
[gmx-users] Re: [gmx-developers] positive Coulomb LR potential for 100 A molecules system, A is positive molecules! Mark Abraham
[gmx-users] MG-ATP Mark Abraham
[gmx-users] Docking Mark Abraham
[gmx-users] Docking Mark Abraham
[gmx-users] gromacs Mark Abraham
[gmx-users] Using Gromacs on Condor Mark Abraham
[gmx-users] Re: Re: Probable error in trjcat; skipping frames Mark Abraham
[gmx-users] polarizable water models Mark Abraham
[gmx-users] Help: Gromacs Installation Mark Abraham
[gmx-users] rigid tetrahedral molecule Mark Abraham
[gmx-users] multicomponent system- units Mark Abraham
[gmx-users] rigid tetrahedral molecule Mark Abraham
[gmx-users] Error while compiling gromacs-4.5.4 Mark Abraham
[gmx-users] rigid tetrahedral molecule Mark Abraham
[gmx-users] simulation with ligand at the active site Mark Abraham
[gmx-users] rigid tetrahedral molecule Mark Abraham
[gmx-users] Fwd: Fwd: Need some assistence Mark Abraham
[gmx-users] R: Md continuation with cpt Mark Abraham
[gmx-users] pdb2gmx with input topology Mark Abraham
[gmx-users] Turning OFF/ON distance restraints during a simulation Mark Abraham
[gmx-users] vdw cutoff options for opls forcefield Mark Abraham
[gmx-users] how to get higher precision values for g_velacc Mark Abraham
[gmx-users] trjorder not working Mark Abraham
[gmx-users] how to get higher precision values for g_velacc Mark Abraham
[gmx-users] trjorder not working Mark Abraham
[gmx-users] R: Md continuation with cpt Mark Abraham
[gmx-users] rigid tetrahedral molecule Mark Abraham
[gmx-users] rigid tetrahedral molecule Mark Abraham
[gmx-users] Fw: ionic liquids Mark Abraham
[gmx-users] sulfate ion Mark Abraham
[gmx-users] Gromacs 4.5.4 MPI Mark Abraham
[gmx-users] LINCS error- 4.5.4 installation? Mark Abraham
[gmx-users] Re: Tcoupl default setting Mark Abraham
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 Mark Abraham
[gmx-users] drawing the plots Sajad Ahrari
[gmx-users] suitable forcefield Sajad Ahrari
[gmx-users] erorr while using grep command Sajad Ahrari
[gmx-users] erorr while using grep command Sajad Ahrari
[gmx-users] fetal erorr while running" pdb2gmx" command Sajad Ahrari
[gmx-users] how to deal with xleap to simulate a protein-ligand complex? Sajad Ahrari
[gmx-users] dealing with ATP Sajad Ahrari
[gmx-users] dealing with ATP Sajad Ahrari
[gmx-users] introducing ADP and ATP to Gromacs Sajad Ahrari
[gmx-users] dealing with ATP Sajad Ahrari
[gmx-users] MG-ATP Sajad Ahrari
[gmx-users] MG-ATP Sajad Ahrari
[gmx-users] Problem g_x2top Hernan Ahumada
[gmx-users] Microporous simulation Hernan Ahumada
[gmx-users] Check out my photos on Facebook Gokul Algates
[gmx-users] Check out my photos on Facebook Gokul Algates
[gmx-users] Help: Gromacs Installation Hrachya Astsatryan
[gmx-users] Help: Gromacs Installation Hrachya Astsatryan
[gmx-users] Help: Gromacs Installation Hrachya Astsatryan
[gmx-users] gromacs Prema Awati
[gmx-users] ionic liquids Prema Awati
[gmx-users] Fw: ionic liquids Prema Awati
[gmx-users] time of dynamic Víctor Bahamonde
[gmx-users] Setting the C6 LJ term for OPLSA FF Luca Bellucci
[gmx-users] Setting the C6 LJ term for OPLSA FF Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] FEP and loss of performance Luca Bellucci
[gmx-users] Is there still interest in rigid-body simulation? Luca Bellucci
[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC" Luca Bellucci
[gmx-users] g_hbond in 4.5.4 gives wrong output Bert
[gmx-users] salt bridge Caterina Bianchi
[gmx-users] salt bridge Caterina Bianchi
[gmx-users] speed issue, gmx runtime estimate = f(t) Michael Brunsteiner
[gmx-users] PME Michael Brunsteiner
[gmx-users] PME Michael Brunsteiner
[gmx-users] sugar force fields Michael Brunsteiner
[gmx-users] unexpected results with stochastic dynamics Michael Brunsteiner
[gmx-users] Postdoc position available Marcelo A. Carignano
[gmx-users] coordination number and g_analysis Marcelo A. Carignano
[gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000) Andrea Carotti
[gmx-users] Re: error when running grompp Daniel Casimir
[gmx-users] Pressure coupling problem Fabian Casteblanco
[gmx-users] Pressure coupling problem Fabian Casteblanco
[gmx-users] Pressure coupling problem Fabian Casteblanco
[gmx-users] Genbox command question Fabian Casteblanco
[gmx-users] Re: Genbox command question Fabian Casteblanco
[gmx-users] Potential energy methanol in a box Fabian Casteblanco
[gmx-users] Re: Potential energy methanol in a box Fabian Casteblanco
[gmx-users] Re: NPT equilibration Vitaly Chaban
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 62 Vitaly Chaban
[gmx-users] Re: 1/viscosity from g_energy Vitaly Chaban
[gmx-users] Re: ionic liquids Vitaly Chaban
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 Yan Chai
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 Yan Chai
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 Yan Chai
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 Yan Chai
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 Yan Chai
[gmx-users] Still model Chi-cheng Chiu
[gmx-users] Still model Chi-cheng Chiu
[gmx-users] Modified Gromacs and OPENMM Chi-cheng Chiu
[gmx-users] Modified Gromacs and OPENMM Chi-cheng Chiu
[gmx-users] g_hbond error Chandan Choudhury
[gmx-users] Re: g_hbond error Chandan Choudhury
[gmx-users] any software which could convert a polypeptide sequence to a pdb file? Liao Chuan
答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? Liao Chuan
[gmx-users] Fwd: Fwd: Need some assistence Ruben Cloete
[gmx-users] coordination number and g_analysis Nilesh Dhumal
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] make a patch Nilesh Dhumal
[gmx-users] saving coordinates Nilesh Dhumal
[gmx-users] saving coordinates Nilesh Dhumal
[gmx-users] grompp error Nilesh Dhumal
[gmx-users] grompp error Nilesh Dhumal
[gmx-users] flexiable water - model Nilesh Dhumal
[gmx-users] flexiable water - model Nilesh Dhumal
[gmx-users] Differences in default values for nstpcouple and cmap atomtypes between versions 4.0 and 4.5.4 Anna Duncan
[gmx-users] Methodology Check Tom Dupree
[gmx-users] gromacs 4.5.4 analysis tools Molecular Dynamics
[gmx-users] Heat of vap Elisabeth
[gmx-users] Heat of vap Elisabeth
[gmx-users] PME Elisabeth
[gmx-users] PME Elisabeth
[gmx-users] PME Elisabeth
[gmx-users] multicomponent system- units Elisabeth
[gmx-users] multicomponent system- units Elisabeth
[gmx-users] multicomponent system- units Elisabeth
[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC" Pablo Englebienne
[gmx-users] Help needed with hacking mdrun Semen Esilevsky
[gmx-users] Is there still interest in rigid-body simulation? Semen Esilevsky
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein Thomas Evangelidis
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein Thomas Evangelidis
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein Thomas Evangelidis
[gmx-users] Adding water to protein to start the simulation process Thomas Evangelidis
[gmx-users] Studying protein folding: An approach Rodrigo Faccioli
[gmx-users] dipole moment of a charged peptide Dommert Florian
[gmx-users] dipole moment of a charged peptide Dommert Florian
[gmx-users] Unexpected results arising from T- and P-coupling methods Dommert Florian
[gmx-users] Re: Trajectory visualization Dommert Florian
[gmx-users] diverging temperature with pressure coupling Dommert Florian
[gmx-users] diverging temperature with pressure coupling Dommert Florian
[gmx-users] Tcoupl default setting Charlie Forde
[gmx-users] Tcoupl default setting‏ Charlie Forde
[gmx-users] Re: Tcoupl default setting Charlie Forde
[gmx-users] CPMD continue running although the job is finished Elena Formoso
[gmx-users] Re: CPMD continue running although the job is finished Elena Formoso
[gmx-users] RE: micelles and trjconv -pbc cluster Ran Friedman
[gmx-users] RE: micelles and trjconv -pbc cluste Ran Friedman
[gmx-users] RE: Metal surfaces (Sergio Manzetti) Ran Friedman
[gmx-users] PYP chromophore force field Ramachandran G
[gmx-users] PYP chromophore force field Ramachandran G
[gmx-users] Input files for g_bar Warren Gallin
[gmx-users] Help with using g_bar Warren Gallin
[gmx-users] Help with using g_bar Warren Gallin
[gmx-users] Splitted DMPC bilayer "Dr. Ramón Garduño-Juárez"
[gmx-users] Splitted DMPC bilayer "Dr. Ramón Garduño-Juárez"
[gmx-users] g_mdmat distance matrices Yulian Gavrilov
[gmx-users] POL3 water model Ivan Gladich
[gmx-users] polarizable water models Ivan Gladich
[gmx-users] sugar force fields Oliver Grant
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 177 Gerrit Groenhof
[gmx-users] cholesterol Preeti Gupta
[gmx-users] Replica Exchange MD using Gromacs Ruchi Gupta
[gmx-users] Adding water to protein to start the simulation process Monisha Hajra
[gmx-users] Simulations in vacuo - energy increase Zoe Hall
[gmx-users] Alkanes, Alkens in Amber forcefield Maria Hamilton
[gmx-users] Adding water to protein to start the simulation process João Henriques
[gmx-users] create a sphere of water molecules Esteban Gabriel Vega Hissi
[gmx-users] Cylinder Pulling output file pullx.xvg wrong? Kun Huang
[gmx-users] Re: Cylinder Pulling output file pullx.xvg wrong Kun Huang
[gmx-users] How to remove charge of 5e-2 ?? Hyunsik
[gmx-users] How to remove charge of 5e-2 ?? Hyunsik
[gmx-users] How to remove charge of 5e-2 ?? Hyunsik
[gmx-users] How to remove charge of 5e-2 ?? Hyunsik
[gmx-users] How to solve GBSA problem ? Hyunsik
[gmx-users] Invalid order for directive atomtypes Geethu Issac
[gmx-users] create a sphere of water molecules Olga Ivchenko
[gmx-users] orientational relaxation Daniel P. Luis J.
[gmx-users] orientational relaxation Daniel P. Luis J.
[gmx-users] orientational relaxation Daniel P. Luis J.
[gmx-users] RMSF: Different results for same residue Alok Jain
[gmx-users] How to control the temperature when using an electric field? Apoorv Kalyankar
[gmx-users] PYP Connection Taylor Kaplan
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 Faezeh Kargar
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 Faezeh Kargar
[gmx-users] any software which could convert a polypeptide sequence to a pdb file? Itamar Kass
[gmx-users] dealing with ATP Itamar Kass
[gmx-users] grompp error with new format of angletypes Hyunjin Kim
[gmx-users] Simulation Crash...Reg Kishore
[gmx-users] Re:Simulation Crash Kishore
[gmx-users] Regarding missing files in gromos53a6.ff Hirdesh Kumar
[gmx-users] Re: Regarding missing files in gromos53a6.ff Hirdesh Kumar
[gmx-users] 2nd question related to load imbalance Peter Lai
[gmx-users] How to merge 2 top-files Peter C. Lai
[gmx-users] are TPR files compatible across minor version changes? Peter C. Lai
[gmx-users] help on converting charmm/cgenff parameters to gromacs Peter C. Lai
[gmx-users] help on converting charmm/cgenff parameters to gromacs Peter C. Lai
[gmx-users] help on converting charmm/cgenff parameters to gromacs Peter C. Lai
[gmx-users] help on converting charmm/cgenff parameters to gromacs Peter C. Lai
[gmx-users] help on converting charmm/cgenff parameters to gromacs Peter C. Lai
[gmx-users] help on converting charmm/cgenff parameters to gromacs Peter C. Lai
[gmx-users] membedded.gro from g_membed has broken molecules (fix periodicity?) Peter C. Lai
[gmx-users] unable to equilibrate protein in membrane with NPT Peter C. Lai
[gmx-users] unable to equilibrate protein in membrane with NPT Peter C. Lai
[gmx-users] unable to equilibrate protein in membrane with NPT Peter C. Lai
[gmx-users] NPT.mdp parameters NOTE Peter C. Lai
[gmx-users] comm-grps for a membrane-protein-ligand system Peter C. Lai
[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL Peter C. Lai
[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL Peter C. Lai
[gmx-users] comm-grps for a membrane-protein-ligand system Peter C. Lai
[gmx-users] Pressure coupling problem Peter C. Lai
[gmx-users] restarting from cpt and binary identical Peter C. Lai
[gmx-users] pdb2gmx segmentation fault Peter C. Lai
[gmx-users] PYP chromophore force field Peter C. Lai
[gmx-users] Using Gromacs on Condor Peter C. Lai
[gmx-users] Benchmarking gromacs over large number of cores Peter C. Lai
[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup Larcombe, Lee
[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup Larcombe, Lee
[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup Larcombe, Lee
[gmx-users] question about adding two functions for one torsional angle Ming-Tsung Lee
[gmx-users] Taking difference of forces in two trajectories Justin A. Lemkul
[gmx-users] FW: protein split over boundary Justin A. Lemkul
[gmx-users] FW: protein split over boundary Justin A. Lemkul
[gmx-users] The solvent group Water is not continuous Justin A. Lemkul
[gmx-users] The solvent group Water is not continuous Justin A. Lemkul
[gmx-users] The solvent group Water is not continuous Justin A. Lemkul
[gmx-users] The solvent group Water is not continuous Justin A. Lemkul
[gmx-users] R: Re: adding a new residue in the ff Justin A. Lemkul
[gmx-users] tpr file for trjconv command Justin A. Lemkul
[gmx-users] Re: distance restraints for atoms on 2 chains Justin A. Lemkul
[gmx-users] OPLS parametrizaton Justin A. Lemkul
[gmx-users] Re: distance restraints for atoms on 2 chains Justin A. Lemkul
[gmx-users] Precision mismatch Justin A. Lemkul
[gmx-users] g_sasa Justin A. Lemkul
[gmx-users] smooth trajectory Justin A. Lemkul
[gmx-users] grompp error with new format of angletypes Justin A. Lemkul
[gmx-users] Heat of vap Justin A. Lemkul
[gmx-users] Re: distance restraints for atoms on 2 chains Justin A. Lemkul
[gmx-users] Input files for g_bar Justin A. Lemkul
[gmx-users] Simulation Crash...Reg Justin A. Lemkul
[gmx-users] Heat of vap Justin A. Lemkul
[gmx-users] Re:Simulation Crash Justin A. Lemkul
[gmx-users] Umbrella Sampling Justin A. Lemkul
[gmx-users] Umbrella Sampling Justin A. Lemkul
[gmx-users] FEP and loss of performance Justin A. Lemkul
[gmx-users] FEP and loss of performance Justin A. Lemkul
[gmx-users] FEP and loss of performance Justin A. Lemkul
[gmx-users] g_chi Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 28 Justin A. Lemkul
[gmx-users] Splitted DMPC bilayer Justin A. Lemkul
[gmx-users] Splitted DMPC bilayer Justin A. Lemkul
[gmx-users] g_chi Justin A. Lemkul
[gmx-users] OPLS-AA atom types Justin A. Lemkul
[gmx-users] OPLS-AA atom types Justin A. Lemkul
[gmx-users] How to remove charge of 5e-2 ?? Justin A. Lemkul
[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC" Justin A. Lemkul
[gmx-users] OPLS-AA atom types Justin A. Lemkul
[gmx-users] OPLS-AA atom types Justin A. Lemkul
[gmx-users] ffbonded.itp file Justin A. Lemkul
[gmx-users] invalid line Justin A. Lemkul
[gmx-users] OPLS parametrizaton Justin A. Lemkul
[gmx-users] How to merge 2 top-files Justin A. Lemkul
[gmx-users] How to remove charge of 5e-2 ?? Justin A. Lemkul
[gmx-users] are TPR files compatible across minor version changes? Justin A. Lemkul
[gmx-users] what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy Justin A. Lemkul
[gmx-users] How to remove charge of 5e-2 ?? Justin A. Lemkul
[gmx-users] How to remove charge of 5e-2 ?? Justin A. Lemkul
[gmx-users] speed issue, gmx runtime estimate = f(t) Justin A. Lemkul
[gmx-users] FEP and loss of performance Justin A. Lemkul
[gmx-users] Umberella sampling Justin A. Lemkul
[gmx-users] NPT equilibration Justin A. Lemkul
[gmx-users] Help with using g_bar Justin A. Lemkul
[gmx-users] Help with using g_bar Justin A. Lemkul
[gmx-users] PME Justin A. Lemkul
[gmx-users] Re: invalid line Justin A. Lemkul
[gmx-users] PME Justin A. Lemkul
[gmx-users] PME Justin A. Lemkul
[gmx-users] Regarding missing files in gromos53a6.ff Justin A. Lemkul
[gmx-users] Carbohydrate simulation: problem with the terminal atoms Justin A. Lemkul
[gmx-users] FEP and loss of performance Justin A. Lemkul
[gmx-users] Is there still interest in rigid-body simulation? Justin A. Lemkul
[gmx-users] Re: invalid line (coordinates) Justin A. Lemkul
[gmx-users] unable to equilibrate protein in membrane with NPT Justin A. Lemkul
[gmx-users] unable to equilibrate protein in membrane with NPT Justin A. Lemkul
[gmx-users] unable to equilibrate protein in membrane with NPT Justin A. Lemkul
[gmx-users] .n2t file for ssDNA Justin A. Lemkul
[gmx-users] .n2t file for ssDNA Justin A. Lemkul
[gmx-users] .n2t file for ssDNA Justin A. Lemkul
[gmx-users] .n2t file for ssDNA Justin A. Lemkul
[gmx-users] Position restraints Justin A. Lemkul
[gmx-users] molecule type Justin A. Lemkul
[gmx-users] molecule type Justin A. Lemkul
[gmx-users] Naming of DNA residues, and structure of .pdb file Justin A. Lemkul
[gmx-users] Error while performing a REMD simulation Justin A. Lemkul
[gmx-users] Error while performing a REMD simulation Justin A. Lemkul
[gmx-users] Dangling bond error for dna Justin A. Lemkul
[gmx-users] Dangling bond error for dna Justin A. Lemkul
[gmx-users] probelm of using amber force field Justin A. Lemkul
[gmx-users] Dangling bond error for dna Justin A. Lemkul
[gmx-users] comm-grps for a membrane-protein-ligand system Justin A. Lemkul
[gmx-users] mdrun segmentation fault Justin A. Lemkul
[gmx-users] g_hbond Justin A. Lemkul
[gmx-users] g_hbond Justin A. Lemkul
[gmx-users] comm-grps for a membrane-protein-ligand system Justin A. Lemkul
[gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR Justin A. Lemkul
[gmx-users] Pressure coupling problem Justin A. Lemkul
[gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR Justin A. Lemkul
[gmx-users] g_saltbr Justin A. Lemkul
[gmx-users] Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR Justin A. Lemkul
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR Justin A. Lemkul
[gmx-users] Regarding creating interface between two solvent at particular site Justin A. Lemkul
[gmx-users] Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR Justin A. Lemkul
[gmx-users] mdrun_mpi!! Justin A. Lemkul
[gmx-users] Density Differences Justin A. Lemkul
[gmx-users] Density Differences Justin A. Lemkul
[gmx-users] Density Differences Justin A. Lemkul
[gmx-users] amide partial charges in G56A3 Justin A. Lemkul
[gmx-users] make a patch Justin A. Lemkul
[gmx-users] pulling of a metal Justin A. Lemkul
[gmx-users] Regarding g_enemat Justin A. Lemkul
[gmx-users] Regarding g_enemat Justin A. Lemkul
[gmx-users] OPLS with Water models Justin A. Lemkul
[gmx-users] saving coordinates Justin A. Lemkul
[gmx-users] binding_affinity Justin A. Lemkul
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology Justin A. Lemkul
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology Justin A. Lemkul
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology Justin A. Lemkul
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Justin A. Lemkul
[gmx-users] genbox Justin A. Lemkul
[gmx-users] Adding water to protein to start the simulation process Justin A. Lemkul
[gmx-users] Energy minimization error Justin A. Lemkul
[gmx-users] RMSF: Different results for same residue Justin A. Lemkul
[gmx-users] Genbox command question Justin A. Lemkul
[gmx-users] Adding water to protein to start the simulation process Justin A. Lemkul
[gmx-users] the ligand have more than one molecules Justin A. Lemkul
[gmx-users] ions problem Justin A. Lemkul
[gmx-users] ions problem Justin A. Lemkul
[gmx-users] 1/viscosity from g_energy Justin A. Lemkul
[gmx-users] 1/viscosity from g_energy Justin A. Lemkul
[gmx-users] Issues of NEMD + 1/viscosity from g_energy Justin A. Lemkul
[gmx-users] Issues with NEMD simulations Justin A. Lemkul
[gmx-users] genbox output taking forever to complete Justin A. Lemkul
[gmx-users] genbox output taking forever to complete Justin A. Lemkul
[gmx-users] genbox output taking forever to complete Justin A. Lemkul
[gmx-users] genbox output taking forever to complete Justin A. Lemkul
[gmx-users] genbox output taking forever to complete Justin A. Lemkul
[gmx-users] .top file for DNA-CNT Justin A. Lemkul
[gmx-users] .top file for DNA-CNT Justin A. Lemkul
[gmx-users] Re: energy group exclusions Justin A. Lemkul
[gmx-users] Simulation of CNT with Amber forcefield Justin A. Lemkul
[gmx-users] protein-ligand complex tutorial Justin A. Lemkul
[gmx-users] coordination file Justin A. Lemkul
[gmx-users] protein-ligand complex tutorial Justin A. Lemkul
[gmx-users] Simulation of CNT with Amber forcefield Justin A. Lemkul
[gmx-users] protein-ligand complex tutorial Justin A. Lemkul
[gmx-users] protein-ligand complex tutorial Justin A. Lemkul
[gmx-users] protein-ligand complex tutorial Justin A. Lemkul
[gmx-users] protein-ligand complex tutorial Justin A. Lemkul
[gmx-users] binding_affinity Justin A. Lemkul
[gmx-users] binding_affinity Justin A. Lemkul
[gmx-users] binding_affinity Justin A. Lemkul
[gmx-users] how to prepare implicit solvent system?? Justin A. Lemkul
[gmx-users] how to prepare implicit solvent system?? Justin A. Lemkul
[gmx-users] saving coordinates Justin A. Lemkul
[gmx-users] atomname2type.n2t file for CNT in amber99 Justin A. Lemkul
[gmx-users] DNA molecule builder compatible with gromacs amber ff Justin A. Lemkul
[gmx-users] atomname2type.n2t file for CNT in amber99 Justin A. Lemkul
[gmx-users] atomname2type.n2t file for CNT in amber99 Justin A. Lemkul
[gmx-users] pdb2gmx segmentation fault Justin A. Lemkul
[gmx-users] pdb2gmx segmentation fault Justin A. Lemkul
[gmx-users] Microporous simulation Justin A. Lemkul
[gmx-users] pdb2gmx segmentation fault Justin A. Lemkul
[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt Justin A. Lemkul
[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt Justin A. Lemkul
[gmx-users] pdb2gmx segmentation fault Justin A. Lemkul
[gmx-users] time of dynamic Justin A. Lemkul
[gmx-users] dna and cnt get distorted in md simulation Justin A. Lemkul
[gmx-users] binding_affinity Justin A. Lemkul
[gmx-users] dna and cnt get distorted in md simulation Justin A. Lemkul
[gmx-users] dna and cnt get distorted in md simulation Justin A. Lemkul
[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC" Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] GROMACS 4.5.3 simulation stop without mesages in Ubuntu 10.10 Justin A. Lemkul
[gmx-users] DNA not wrapping around CNT in MD simulation Justin A. Lemkul
[gmx-users] DNA not wrapping around CNT in MD simulation Justin A. Lemkul
[gmx-users] pdb2gmx segmentation fault Justin A. Lemkul
[gmx-users] DNA not wrapping around CNT in MD simulation Justin A. Lemkul
[gmx-users] dealing with ATP Justin A. Lemkul
[gmx-users] dealing with ATP Justin A. Lemkul
[gmx-users] Potential energy methanol in a box Justin A. Lemkul
[gmx-users] g_hbond in 4.5.4 gives wrong output Justin A. Lemkul
[gmx-users] Simulation of protein at specific pH Justin A. Lemkul
[gmx-users] Re: error in g_x2top Justin A. Lemkul
[gmx-users] tutorials of REMD Justin A. Lemkul
[gmx-users] flexiable water - model Justin A. Lemkul
[gmx-users] flexiable water - model Justin A. Lemkul
[gmx-users] Re: error when running grompp Justin A. Lemkul
[gmx-users] Probable error in trjcat; skipping frames Justin A. Lemkul
[gmx-users] how to define charge group? Justin A. Lemkul
[gmx-users] Is it flexible water or all the bond, angle fixed? what is the potential energy in Gromacs 4.5 using OPLSAA Justin A. Lemkul
[gmx-users] Re: Re: Probable error in trjcat; skipping frames Justin A. Lemkul
[gmx-users] Md continuation with cpt Justin A. Lemkul
[gmx-users] Md continuation with cpt Justin A. Lemkul
[gmx-users] sulfate ion Justin A. Lemkul
[gmx-users] rigid tetrahedral molecule Justin A. Lemkul
[gmx-users] Error while compiling gromacs-4.5.4 Justin A. Lemkul
[gmx-users] simulation with ligand at the active site Justin A. Lemkul
[gmx-users] rigid tetrahedral molecule Justin A. Lemkul
[gmx-users] pdb2gmx with input topology Justin A. Lemkul
[gmx-users] MG-ATP Justin A. Lemkul
[gmx-users] Modified Gromacs and OPENMM Justin A. Lemkul
[gmx-users] Modified Gromacs and OPENMM Justin A. Lemkul
[gmx-users] Alkanes, Alkens in Amber forcefield Justin A. Lemkul
[gmx-users] Improper dihedrals in Charmm FF Jianguo Li
[gmx-users] BUG in angular removal part?? Xiaohu Li
[gmx-users] BUG in angular removal part?? Xiaohu Li
[gmx-users] Installation error ZHAO Lina
[gmx-users] drawing the plots ZHAO Lina
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? ZHAO Lina
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? ZHAO Lina
[gmx-users] Saikat Banerjee wants to stay in touch on LinkedIn Saikat Banerjee via LinkedIn
[gmx-users] how to simulate crystals in Gromacs ZHANG Lu
[gmx-users] how to simulate crystals in Gromacs ZHANG Lu
[gmx-users] comparison of covariance analysis and normal mode analysis for entropy calculations Hari Shankar M
[gmx-users] Density Differences Kavyashree M
[gmx-users] Density Differences Kavyashree M
[gmx-users] Density Differences Kavyashree M
[gmx-users] Density Differences Kavyashree M
[gmx-users] Energy minimization error Kavyashree M
[gmx-users] Energy minimization error Kavyashree M
[gmx-users] dipole moment of a charged peptide Sanku M
[gmx-users] integral equation theory in gromacs? Sanku M
[gmx-users] g_dipoles and index file Sanku M
[gmx-users] problem with g_dipoles and index file Sanku M
[gmx-users] how to define charge group? Sanku M
[gmx-users] rigid tetrahedral molecule Sanku M
[gmx-users] rigid tetrahedral molecule Sanku M
[gmx-users] rigid tetrahedral molecule Sanku M
[gmx-users] rigid tetrahedral molecule Sanku M
[gmx-users] rigid tetrahedral molecule Sanku M
[gmx-users] vdw cutoff options for opls forcefield Sanku M
[gmx-users] rigid tetrahedral molecule Sanku M
[gmx-users] Query NAGA MANI
[gmx-users] Is it flexible water or all the bond, angle fixed? what is the potential energy in Gromacs 4.5 using OPLSAA MD
[gmx-users] Re:gmx-users Digest, Vol 84, Issue 207 MD
[gmx-users] error while loading shared libraries: libgmx.so.6 Lutz Maibaum
[gmx-users] Metal surfaces Sergio Manzetti
[gmx-users] RE: Metal surfaces (Sergio Manzetti) Sergio Manzetti
[gmx-users] R: Re: adding a new residue in the ff Anna Marabotti
[gmx-users] Md continuation with cpt Anna Marabotti
[gmx-users] R: Md continuation with cpt Anna Marabotti
[gmx-users] R: Md continuation with cpt Anna Marabotti
[gmx-users] R: Md continuation with cpt Anna Marabotti
[gmx-users] dipole moment of a charged peptide Erik Marklund
[gmx-users] The solvent group Water is not continuous Erik Marklund
[gmx-users] How to remove charge of 5e-2 ?? Erik Marklund
[gmx-users] How to remove charge of 5e-2 ?? Erik Marklund
[gmx-users] g_hbond Erik Marklund
[gmx-users] g_hbond Erik Marklund
[gmx-users] g_hbond Erik Marklund
[gmx-users] 2nd question related to load imbalance Erik Marklund
[gmx-users] Re: g_hbond error Erik Marklund
[gmx-users] create a sphere of water molecules Erik Marklund
[gmx-users] micelles and trjconv -pbc cluster Erik Marklund
[gmx-users] Re: Trajectory visualization Erik Marklund
[gmx-users] Placing anion/cation at a particular distance from peptide Erik Marklund
[gmx-users] g_velacc -mol Luis Martins
[gmx-users] Adding Virtual Site to the Molecule Sikandar Mashayak
[gmx-users] forces on water spce due to settle Sikandar Mashayak
[gmx-users] energy group exclusions Sikandar Mashayak
[gmx-users] Re: energy group exclusions Sikandar Mashayak
[gmx-users] Re: energy group exclusions Sikandar Mashayak
[gmx-users] Re: energy group exclusions Sikandar Mashayak
[gmx-users] Re: energy group exclusions Sikandar Mashayak
[gmx-users] Re: energy group exclusions Sikandar Mashayak
[gmx-users] Virtual site at COM of more than 4 atoms Sikandar Mashayak
[gmx-users] Load imbalance vs accuracy Sikandar Mashayak
[gmx-users] Umbrella Sampling Gavin Melaugh
[gmx-users] Umbrella Sampling Gavin Melaugh
[gmx-users] Umbrella Sampling Gavin Melaugh
[gmx-users] how to Installing GROMACS in rocks cluster Miguel Quiliano Meza
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 28 Miguel Quiliano Meza
[gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR Miguel Quiliano Meza
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 90 Miguel Quiliano Meza
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR Miguel Quiliano Meza
[gmx-users] Studying protein folding: An approach Miguel Quiliano Meza
[gmx-users] FEP and loss of performance David Mobley
[gmx-users] compression- NPT Moeed
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Moeed
[gmx-users] compression- NPT Moeed
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Moeed
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Moeed
[gmx-users] NPT issue in 4.0.7 and 4.5.3 Moeed
[gmx-users] Benchmarking gromacs over large number of cores Bruno Monnet
[gmx-users] Re: micelles and trjconv -pbc cluster André Farias de Moura
[gmx-users] pulling of a metal Jon Mujika
[gmx-users] density off Juliette N.
[gmx-users] density off Juliette N.
[gmx-users] temperature effect on potential energy Juliette N.
[gmx-users] temperature effect on potential energy Juliette N.
[gmx-users] Gromacs 4.5.4 MPI Juliette N.
[gmx-users] LINCS error- 4.5.4 installation? Juliette N.
[gmx-users] FEP and loss of performance Chris Neale
[gmx-users] minimization and simulation problems Chris Neale
[gmx-users] FEP and loss of performance Chris Neale
[gmx-users] GROMACS 4.5.3 simulation stop without mesages in Ubuntu 10.10 Alcides Nicastro
[gmx-users] g_chi Francesco Oteri
[gmx-users] g_cluster: optimal cutoff Francesco Oteri
[gmx-users] RMSF: Different results for same residue Francesco Oteri
[gmx-users] free energy perturbation Jignesh Patel
[gmx-users] help on converting charmm/cgenff parameters to gromacs Thomas Piggot
[gmx-users] Groups in mdp file Sai Pooja
[gmx-users] Groups in mdp file Sai Pooja
[gmx-users] distance restraints for atoms on 2 chains Sai Pooja
[gmx-users] Re: distance restraints for atoms on 2 chains Sai Pooja
[gmx-users] Re: distance restraints for atoms on 2 chains Sai Pooja
[gmx-users] Precision mismatch Sai Pooja
[gmx-users] Re: distance restraints for atoms on 2 chains Sai Pooja
[gmx-users] Essential Dynamics lincs warning Sai Pooja
[gmx-users] speed issue, gmx runtime estimate = f(t) Szilárd Páll
[gmx-users] no CUDA-capable device detected Szilárd Páll
[gmx-users] Re: ionic liquids Baofu Qiao
[gmx-users] error while loading shared libraries: libgmx.so.6 Qin Qiao
[gmx-users] On dihedral type for CHARMM Mr Bernard Ramos
[gmx-users] 1,5 and 1,6 LJ interactions for OPLS AA SEI Mr Bernard Ramos
[gmx-users] Urey-Bradley constant in CHARMM to GMX Mr Bernard Ramos
[gmx-users] Fw: trjconv -pbc and broken reside Rausch, Felix
[gmx-users] MG-ATP Rausch, Felix
[gmx-users] trjcat eneconv time continuation David Rodríguez
[gmx-users] trjcat eneconv time continuation David Rodríguez
[gmx-users] trjcat eneconv time continuation David Rodríguez
[gmx-users] pdb2gmx with input topology Ehud Schreiber
[gmx-users] Installtion of gromacs-4.5.3 Roland Schulz
[gmx-users] gromacs 4.5.4 analysis tools Roland Schulz
[gmx-users] diverging temperature with pressure coupling Roland Schulz
[gmx-users] Load imbalance vs accuracy Roland Schulz
[gmx-users] Help: Gromacs Installation Roland Schulz
[gmx-users] Benchmarking gromacs over large number of cores Roland Schulz
[gmx-users] no CUDA-capable device detected SebastianWaltz
[gmx-users] Acpype error Aldo Segura
[gmx-users] re: Acpype error Aldo Segura
[gmx-users] Docking Aldo Segura
[gmx-users] simulation with ligand at the active site Aldo Segura
[gmx-users] Acpype error Alan Wilter Sousa da Silva
[gmx-users] OPLS parametrizaton Marcelo Silva
[gmx-users] OPLS parametrizaton Marcelo Silva
[gmx-users] Error while performing a REMD simulation Luis Miguel Medina Solano
[gmx-users] Error while performing a REMD simulation Luis Miguel Medina Solano
[gmx-users] Error while performing a REMD simulation Luis Miguel Medina Solano
[gmx-users] Heat of vap David van der Spoel
[gmx-users] Heat of vap David van der Spoel
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC David van der Spoel
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC David van der Spoel
[gmx-users] 2nd question related to load imbalance David van der Spoel
[gmx-users] diverging temperature with pressure coupling David van der Spoel
[gmx-users] question about adding two functions for one torsional angle David van der Spoel
[gmx-users] g_velacc -mol David van der Spoel
[gmx-users] density off David van der Spoel
[gmx-users] density off David van der Spoel
[gmx-users] temperature effect on potential energy David van der Spoel
[gmx-users] How to control the temperature when using an electric field? David van der Spoel
[gmx-users] Simulation of protein at specific pH David van der Spoel
[gmx-users] BUG in angular removal part?? David van der Spoel
[gmx-users] Re: Probable error in trjcat; skipping frames David van der Spoel
[gmx-users] Articles using Gromacs to do simulation, calculation, evaluation David van der Spoel
[gmx-users] BUG in angular removal part?? David van der Spoel
[gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000) David van der Spoel
[gmx-users] rigid tetrahedral molecule David van der Spoel
[gmx-users] rigid tetrahedral molecule David van der Spoel
[gmx-users] rigid tetrahedral molecule David van der Spoel
[gmx-users] Simulations in vacuo - energy increase David van der Spoel
[gmx-users] DNA molecule builder compatible with gromacs amber ff william Stebbeds
[gmx-users] Using Gromacs on Condor Natalie Stephenson
[gmx-users] Position restraints Mikhail Stukan
[gmx-users] Velocity distribution Mikhail Stukan
[gmx-users] Velocity distribution (a bug?) Mikhail Stukan
[gmx-users] amide partial charges in G56A3 XUEMING TANG
[gmx-users] aminoacids.n.tdb Emine Deniz Tekin
[gmx-users] aminoacids.n.tdb Emine Deniz Tekin
[gmx-users] aminoacids.n.tdb Emine Deniz Tekin
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? Terry
[gmx-users] integral equation theory in gromacs? Jared Thompson
[gmx-users] Probable error in trjcat; skipping frames Lipi Thukral
[gmx-users] Re: Probable error in trjcat; skipping frames Lipi Thukral
[gmx-users] Re: Re: Probable error in trjcat; skipping frames Lipi Thukral
[gmx-users] OPLS with Water models Jianhui Tian
[gmx-users] OPLS with Water models Jianhui Tian
[gmx-users] Regarding creating interface between two solvent at particular site YUVRAJ UBOVEJA
[gmx-users] re: Acpype error Lucio Ricardo Montero Valenzuela
[gmx-users] openmm 3.0, opencl support Claus Valka
[gmx-users] openmm 3.0, opencl support Claus Valka
[gmx-users] Errors when running SMD, in three direction pulling Yukun Wang
[gmx-users] FW: protein split over boundary Tsjerk Wassenaar
[gmx-users] how to simulate crystals in Gromacs Tsjerk Wassenaar
[gmx-users] membedded.gro from g_membed has broken molecules (fix periodicity?) Tsjerk Wassenaar
[gmx-users] orientational relaxation Tsjerk Wassenaar
[gmx-users] Re: EDO and TRS ligand Tsjerk Wassenaar
[gmx-users] micelles and trjconv -pbc cluster Tsjerk Wassenaar
[gmx-users] micelles and trjconv -pbc cluster Tsjerk Wassenaar
[gmx-users] Adding water to protein to start the simulation process Tsjerk Wassenaar
[gmx-users] erorr while using grep command Tsjerk Wassenaar
[gmx-users] ask for help on connection to vpn from two computers Tsjerk Wassenaar
[gmx-users] fetal erorr while running" pdb2gmx" command Tsjerk Wassenaar
[gmx-users] saving coordinates Tsjerk Wassenaar
[gmx-users] Coarse-grained force field Tsjerk Wassenaar
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file? Tsjerk Wassenaar
[gmx-users] trjcat eneconv time continuation Tsjerk Wassenaar
[gmx-users] trjcat eneconv time continuation Tsjerk Wassenaar
[gmx-users] Amanda Watkins Amanda Watkins
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] pdb2gmx segmentation fault Ragothaman Yennamalli
[gmx-users] OPLS-AA atom types Austin B. Yongye
[gmx-users] OPLS-AA atom types Austin B. Yongye
[gmx-users] OPLS-AA atom types Austin B. Yongye
[gmx-users] OPLS-AA atom types Austin B. Yongye
[gmx-users] pdb2gmx segmentation fault Matthew Zwier
[gmx-users] pdb2gmx segmentation fault Matthew Zwier
[gmx-users] pdb2gmx segmentation fault Matthew Zwier
[gmx-users] problem with mpiexec, mdrun in gromacs/4.0.7 delara aghaie
[gmx-users] load imbalance!!! delara aghaie
[gmx-users] 2nd question related to load imbalance delara aghaie
[gmx-users] 2nd question related to load imbalance delara aghaie
[gmx-users] 2nd question related to load imbalance delara aghaie
[gmx-users] mdrun_mpi!! delara aghaie
[gmx-users] error in running jobs in parallel !!! delara aghaie
[gmx-users] error in running jobs in parallel !!! delara aghaie
[gmx-users] parallel run breaks !! delara aghaie
[gmx-users] ask for help on connection to vpn from two computers delara aghaie
[gmx-users] error when running grompp delara aghaie
[gmx-users] lyzosyme tutorial delara aghaie
[gmx-users] FW: protein split over boundary anahita
[gmx-users] FW: protein split over boundaries anahita
[gmx-users] Simulation of protein at specific pH prerna bhardwaj
[gmx-users] Simulation of protein at specific pH prerna bhardwaj
[gmx-users] Replica Exchange MD using Gromacs bsmith
[gmx-users] Error while performing a REMD simulation devicerandom
[gmx-users] g_cluster: optimal cutoff devicerandom
[gmx-users] Error while performing a REMD simulation devicerandom
[gmx-users] probelm of using amber force field fancy2012
[gmx-users] Re:gmx-users Digest, Vol 84, Issue 81 fancy2012
[gmx-users] Acpype error fancy2012
[gmx-users] re: Acpype error fancy2012
[gmx-users] tutorials of REMD fancy2012
[gmx-users] Is there still interest in rigid-body simulation? gyorgy.hantal at fc.up.pt
[gmx-users] rigid tetrahedral molecule gyorgy.hantal at fc.up.pt
[gmx-users] rigid tetrahedral molecule gyorgy.hantal at fc.up.pt
[gmx-users] minimization and simulation problems politr at fh.huji.ac.il
[gmx-users] minimization and simulation problems politr at fh.huji.ac.il
[gmx-users] minimization and simulation problems politr at fh.huji.ac.il
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein bharat gupta
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein bharat gupta
[gmx-users] Re: Trajectory visualization bharat gupta
[gmx-users] Re: Trajectory visualization bharat gupta
[gmx-users] .n2t file for ssDNA majid hasan
[gmx-users] .n2t file for ssDNA majid hasan
[gmx-users] .n2t file for ssDNA majid hasan
[gmx-users] .n2t file for ssDNA majid hasan
[gmx-users] .n2t file for ssDNA majid hasan
[gmx-users] Naming of DNA residues, and structure of .pdb file majid hasan
[gmx-users] Naming of DNA residues, and structure of .pdb file majid hasan
[gmx-users] Dangling bond error for dna majid hasan
[gmx-users] Dangling bond error for dna majid hasan
[gmx-users] Dangling bond error for dna majid hasan
[gmx-users] Dangling bond error for dna majid hasan
[gmx-users] Dangling bond error for dna majid hasan
[gmx-users] genbox output taking forever to complete majid hasan
[gmx-users] genbox output taking forever to complete majid hasan
[gmx-users] genbox output taking forever to complete majid hasan
[gmx-users] genbox output taking forever to complete majid hasan
[gmx-users] genbox output taking forever to complete majid hasan
[gmx-users] genbox output taking forever to complete majid hasan
[gmx-users] .top file for DNA-CNT majid hasan
[gmx-users] .top file for DNA-CNT majid hasan
[gmx-users] .top file for DNA-CNT majid hasan
[gmx-users] Simulation of CNT with Amber forcefield majid hasan
[gmx-users] Simulation of CNT with Amber forcefield majid hasan
[gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan
[gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan
[gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan
[gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan
[gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan
[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan
[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan
[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan
[gmx-users] dna and cnt get distorted in md simulation majid hasan
[gmx-users] dna and cnt get distorted in md simulation majid hasan
[gmx-users] dna and cnt get distorted in md simulation majid hasan
[gmx-users] dna and cnt get distorted in md simulation majid hasan
[gmx-users] DNA not wrapping around CNT in MD simulation majid hasan
[gmx-users] DNA not wrapping around CNT in MD simulation majid hasan
[gmx-users] DNA not wrapping around CNT in MD simulation majid hasan
[gmx-users] DNA not wrapping around CNT in MD simulation majid hasan
[gmx-users] DNA not wrapping around CNT in MD simulation majid hasan
[gmx-users] DNA not wrapping around CNT in MD simulation majid hasan
[gmx-users] GB/SA terms per-residue/domain decomposition boaz inbal
[gmx-users] I added you as a friend on Quepasa.com boaz inbal
[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field intra\sa175950
[gmx-users] ffbonded.itp file anna.marabotti at isa.cnr.it
[gmx-users] micelles and trjconv -pbc cluster jim jack
[gmx-users] Re: micelles and trjconv -pbc cluster jim jack
[gmx-users] Re: micelles and trjconv -pbc cluster jim jack
[gmx-users] POL3 water model saly jackson
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 213 saly jackson
[gmx-users] sulfate ion saly jackson
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 217 saly jackson
[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 217 saly jackson
[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 213 saly jackson
[gmx-users] sulfate ion saly jackson
[gmx-users] Turning OFF/ON distance restraints during a simulation jayant james
[gmx-users] molecule split over bounderies ana johari
[gmx-users] FW: protein split over boundary ana johari
[gmx-users] FW: protein split over boundary ana johari
[gmx-users] tpr file for trjconv command ana johari
[gmx-users] (no subject) ana johari
[gmx-users] smooth trajectory ana johari
[gmx-users] trjconv ana johari
[gmx-users] Fw: trjconv -pbc and broken reside ana johari
[gmx-users] invalid line sarah k
[gmx-users] Re: invalid line sarah k
[gmx-users] Re: invalid line (coordinates) sarah k
[gmx-users] molecule type sarah k
[gmx-users] tip5p.gro sarah k
[gmx-users] coordination file sarah k
[gmx-users] Coarse-grained force field ksenia248
[gmx-users] How to control the temperature when using an electric field? lammps lammps
[gmx-users] How to control the temperature when using an electric field? lammps lammps
[gmx-users] Defined number of molecule of water into box battistia at libero.it
[gmx-users] Defined number of molecule of water into box battistia at libero.it
[gmx-users] implicit water and a layer of explicit water molecule battistia at libero.it
R: [gmx-users] implicit water and a layer of explicit water molecule battistia at libero.it
R: [gmx-users] implicit water and a layer of explicit water molecule battistia at libero.it
[gmx-users] openmm 3.0, opencl support lina
[gmx-users] protein-ligand complex tutorial lucioric
[gmx-users] stress autocorrelation function shikha nangia
[gmx-users] 1/viscosity from g_energy shikha nangia
[gmx-users] 1/viscosity from g_energy shikha nangia
[gmx-users] Issues of NEMD + 1/viscosity from g_energy shikha nangia
[gmx-users] Issues with NEMD simulations shikha nangia
[gmx-users] how to get higher precision values for g_velacc shikha nangia
[gmx-users] autocorrelation functions shivangi nangia
[gmx-users] autocorrelation functions shivangi nangia
[gmx-users] NPT equilibration shivangi nangia
[gmx-users] mdrun segmentation fault shivangi nangia
[gmx-users] mdrun segmentation fault shivangi nangia
[gmx-users] Placing anion/cation at a particular distance from peptide shivangi nangia
[gmx-users] ordering components of system using trjorder shivangi nangia
[gmx-users] trjorder not working shivangi nangia
[gmx-users] how to get higher precision values for g_velacc shivangi nangia
[gmx-users] trjorder not working shivangi nangia
[gmx-users] binding_affinity shahid nayeem
[gmx-users] binding_affinity shahid nayeem
[gmx-users] binding_affinity shahid nayeem
[gmx-users] binding_affinity shahid nayeem
[gmx-users] simulation with ligand at the active site onetwo
[gmx-users] Installtion of gromacs-4.5.3 parichita parichita
[gmx-users] Installation error pawan raghav
[gmx-users] Is there still interest in rigid-body simulation? mohsen ramezanpour
[gmx-users] domain decomposition mohsen ramezanpour
[gmx-users] domain decomposition mohsen ramezanpour
[gmx-users] domain decomposition mohsen ramezanpour
[gmx-users] How to remove charge of 5e-2 ?? mohsen ramezanpour
[gmx-users] How to remove charge of 5e-2 ?? mohsen ramezanpour
[gmx-users] How to remove charge of 5e-2 ?? mohsen ramezanpour
[gmx-users] How to remove charge of 5e-2 ?? mohsen ramezanpour
[gmx-users] How to remove charge of 5e-2 ?? mohsen ramezanpour
[gmx-users] not enough space mohsen ramezanpour
[gmx-users] Re: not enough space mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Umberella sampling mohsen ramezanpour
[gmx-users] Extending Simulation mohsen ramezanpour
[gmx-users] NPT.mdp parameters NOTE mohsen ramezanpour
[gmx-users] Extending Simulation mohsen ramezanpour
[gmx-users] Extending Simulation mohsen ramezanpour
[gmx-users] converging value mohsen ramezanpour
[gmx-users] converging value mohsen ramezanpour
[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL mohsen ramezanpour
[gmx-users] Articles using Gromacs to do simulation, calculation, evaluation mohsen ramezanpour
[gmx-users] Docking mohsen ramezanpour
[gmx-users] Docking mohsen ramezanpour
[gmx-users] Docking mohsen ramezanpour
[gmx-users] Protein_thermal_Unfolding satya s
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC sa
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC sa
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC sa
[gmx-users] Error while performing a REMD simulation massimo sandal
[gmx-users] Error while performing a REMD simulation massimo sandal
[gmx-users] reg pulling of o2 towards fe atom vidhya sankar
[gmx-users] g_sasa deisy yurley rodriguez sarmiento
[gmx-users] genbox leila separdar
[gmx-users] Fwd: genbox leila separdar
[gmx-users] g_chi simon sham
[gmx-users] g_chi simon sham
[gmx-users] g_cluster warning message simon sham
[gmx-users] g_saltbr simon sham
[gmx-users] FW: protein split over boundary ravi sharma
[gmx-users] Error while compiling gromacs-4.5.4 vivek sharma
[gmx-users] Regarding g_enemat bipin singh
[gmx-users] Regarding g_enemat bipin singh
[gmx-users] Residue 'HEM' not found in residue topology database hui sun
[gmx-users] VDW parameters: Martini Forcefield + Implicit Solvation emendez at ucalgary.ca
[gmx-users] RE: VDW parameters: Martini Forcefield + Implicit Solvation emendez at ucalgary.ca
[gmx-users] VDW parameters: Martini Forcefield + Implicit Solvation emendez at ucalgary.ca
[gmx-users] Umbrella Sampling chris.neale at utoronto.ca
[gmx-users] FEP and loss of performance chris.neale at utoronto.ca
[gmx-users] minimization and simulation problems chris.neale at utoronto.ca
[gmx-users] FEP and loss of performance chris.neale at utoronto.ca
[gmx-users] converging value chris.neale at utoronto.ca
[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL chris.neale at utoronto.ca
[gmx-users] Unexpected results arising from T- and P-coupling methods chris.neale at utoronto.ca
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 chris.neale at utoronto.ca
[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3 chris.neale at utoronto.ca
[gmx-users] Cylinder Pulling output file pullx.xvg wron chris.neale at utoronto.ca
[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field chris.neale at utoronto.ca
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 :ERROR christopher.yip at utoronto.ca
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 :ERROR christopher.yip at utoronto.ca
[gmx-users] sugar force fields nishap.patel at utoronto.ca
[gmx-users] Re: NPT issue in 4.0.7 and 4.5.3 xiaowu759
[gmx-users] The solvent group Water is not continuous ahmet yıldırım
[gmx-users] The solvent group Water is not continuous ahmet yıldırım
[gmx-users] The solvent group Water is not continuous ahmet yıldırım
[gmx-users] The solvent group Water is not continuous ahmet yıldırım
[gmx-users] The solvent group Water is not continuous ahmet yıldırım
[gmx-users] the total charge of system is not an integer ahmet yıldırım
[gmx-users] the total charge of system is not an integer ahmet yıldırım
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology ahmet yıldırım
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology ahmet yıldırım
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology ahmet yıldırım
[gmx-users] the ligand have more than one molecules ahmet yıldırım
[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology ahmet yıldırım
[gmx-users] ions problem ahmet yıldırım
[gmx-users] Re: ions problem ahmet yıldırım
[gmx-users] ions problem ahmet yıldırım
[gmx-users] the ligand have more than one molecules ahmet yıldırım
[gmx-users] protein-ligand complex tutorial ahmet yıldırım
[gmx-users] protein-ligand complex tutorial ahmet yıldırım
[gmx-users] protein-ligand complex tutorial ahmet yıldırım
[gmx-users] protein-ligand complex tutorial ahmet yıldırım
[gmx-users] protein-ligand complex tutorial ahmet yıldırım
[gmx-users] what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy zhongjin
[gmx-users] the gmx-4.5.4 can not be compiled but the gmx-4.5.3 can 英雄不再寂寞
[gmx-users] Unexpected results arising from T- and P-coupling methods 英雄不再寂寞
[gmx-users] How to remove charge of 5e-2 ?? 김현식
[gmx-users] how to prepare implicit solvent system?? 김현식

Last message date: Sat Apr 30 22:56:40 CEST 2011
Archived on: Thu Nov 14 12:10:43 CET 2013

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