May 2017 Archives by author

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Starting: Mon May 1 13:55:26 CEST 2017
Ending: Wed May 31 23:22:58 CEST 2017
Messages: 634

[gmx-users] regarding posting queries in gromacs mailing list Abhinav Srivastava (P14CHM002)
[gmx-users] B-FACTOR Kingsley Theras Primus Dass .
[gmx-users] B-FACTOR Kingsley Theras Primus Dass .
[gmx-users] 2016.3 installation Mark Abraham
[gmx-users] gmx hbond -tu error Mark Abraham
[gmx-users] gmx sorient interpretation Mark Abraham
[gmx-users] Fwd: Domain decomposition error Mark Abraham
[gmx-users] 2016.3 installation Mark Abraham
[gmx-users] Adding buffer to simulation box Mark Abraham
[gmx-users] Different number of molecules in simulation box. Mark Abraham
[gmx-users] Different number of molecules in simulation box. Mark Abraham
[gmx-users] Installatoin error Mark Abraham
[gmx-users] Lennard Jones and Buckingham potential together in one simulation Mark Abraham
[gmx-users] protein ligand complex Energy Minimisation Mark Abraham
[gmx-users] Grommp Fatal Error Mark Abraham
[gmx-users] Adding buffer to simulation box Mark Abraham
[gmx-users] mixed 1-4 scaling factor Mark Abraham
[gmx-users] mixed 1-4 scaling factor Mark Abraham
[gmx-users] Continuation mdp flag Mark Abraham
[gmx-users] Continuation mdp flag Mark Abraham
[gmx-users] (Opt.) indication to gmx cluster -s doesn't seem to be optional Mark Abraham
[gmx-users] Grommp Fatal Error (Syed Azeem) Mark Abraham
[gmx-users] regarding posting queries in gromacs mailing list Mark Abraham
[gmx-users] Error In Umbrella sampling. Mark Abraham
[gmx-users] How to use "gmx view" on Ubuntu? Mark Abraham
[gmx-users] How to use "gmx view" on Ubuntu? Mark Abraham
[gmx-users] How to compile Mopac7 with Gromacs_2016.3 release? Mark Abraham
[gmx-users] -1.8 Equilibration pressure during MD simulation Mark Abraham
[gmx-users] How to use "gmx view" on Ubuntu? Mark Abraham
[gmx-users] How to use "gmx view" on Ubuntu? Mark Abraham
[gmx-users] A simple question Mark Abraham
[gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs Mark Abraham
[gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs Mark Abraham
[gmx-users] GROMACS INPUT FILE Mark Abraham
[gmx-users] soft "exit" Mark Abraham
[gmx-users] Running Gromacs on GPUs Mark Abraham
[gmx-users] Running Gromacs on GPUs Mark Abraham
[gmx-users] regarding tha langevin thermostat (integrator sd) Mark Abraham
[gmx-users] New residue for custom capping Mark Abraham
[gmx-users] New residue for custom capping Mark Abraham
[gmx-users] New residue for custom capping Mark Abraham
[gmx-users] RMSF problem Mark Abraham
[gmx-users] NVML does not come separate starting from Cuda 8.0 Mark Abraham
[gmx-users] forcefield parameter missing Mark Abraham
[gmx-users] Doubts about g_lie and g_bar Mark Abraham
[gmx-users] forcefield parameter missing Mark Abraham
[gmx-users] Doubts about g_lie and g_bar Mark Abraham
[gmx-users] Unreasonably high pressure values Mark Abraham
[gmx-users] Unreasonably high pressure values Mark Abraham
[gmx-users] topol files Mark Abraham
[gmx-users] Perturbation Thermodynamic Integration Mark Abraham
[gmx-users] NMA eigenvectors doubts Mark Abraham
[gmx-users] Unreasonably high pressure values Mark Abraham
[gmx-users] Perturbation Thermodynamic Integration Mark Abraham
[gmx-users] Perturbation Thermodynamic Integration Mark Abraham
[gmx-users] Fwd: Issue with parallel simulations in vacuum Mark Abraham
[gmx-users] NMA eigenvectors doubts Mark Abraham
[gmx-users] symmetrical LJ binary mixture simulation Mark Abraham
[gmx-users] symmetrical LJ binary mixture simulation Mark Abraham
[gmx-users] NMA eigenvectors doubts Mark Abraham
[gmx-users] md continuation Mark Abraham
[gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Mark Abraham
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Mark Abraham
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Mark Abraham
[gmx-users] Error message Mark Abraham
[gmx-users] Error message Mark Abraham
[gmx-users] I tried all the suggestions; but no improvement..! Fwd: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Mark Abraham
[gmx-users] I tried all the suggestions; but no improvement..! Fwd: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Mark Abraham
[gmx-users] Error with moleculetype Mark Abraham
[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22 Mark Abraham
[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22 Mark Abraham
[gmx-users] Error with moleculetype Mark Abraham
[gmx-users] pdb2gmx do not work for unstable conformations Mark Abraham
[gmx-users] Regarding extending simulations with change in .mdp file Mark Abraham
[gmx-users] Problem with accelerations Mark Abraham
[gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1 Mark Abraham
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Mark Abraham
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Mark Abraham
[gmx-users] gromacs-5.1.4 installation issue Mark Abraham
[gmx-users] gromacs-5.1.4 installation issue Mark Abraham
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Mark Abraham
[gmx-users] sequential simulations with mdrun -multi option Mark Abraham
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Mark Abraham
[gmx-users] gromacs-5.1.4 installation issue Mark Abraham
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? Mark Abraham
[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option. Abhishek Acharya
[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option. Abhishek Acharya
[gmx-users] g_rms using a structure in trajectory as reference Abhishek Acharya
[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option. Abhishek Acharya
[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option. Abhishek Acharya
[gmx-users] (no subject) Shivangi Agarwal
[gmx-users] (no subject) Shivangi Agarwal
[gmx-users] PBC Alex
[gmx-users] Internal energy Alex
[gmx-users] Fwd: Internal energy Alex
[gmx-users] (no subject) Alex
[gmx-users] A simple question Alex
[gmx-users] A simple question Alex
[gmx-users] A simple question Alex
[gmx-users] pullx/pullf and COM energy Alex
[gmx-users] pullx/pullf and COM energy Alex
[gmx-users] topol files Alex
[gmx-users] Problem in Bootstrapping of PMF Alex
[gmx-users] Grommp Fatal Error Syed Azeem
[gmx-users] Grommp Fatal Error (Syed Azeem) Syed Azeem
[gmx-users] Reg: creation of separate chains in .pdb file Syed Azeem
[gmx-users] Reg: creation of separate chains in .pdb file Syed Azeem
[gmx-users] NVML does not come separate starting from Cuda 8.0 Mat B
[gmx-users] Increasing sigma Pallavi Banerjee
[gmx-users] Calculation of nematic order parameter using gromacs Antonio Baptista
[gmx-users] Need to confirm parameters. Sailesh Bataju
[gmx-users] Need to confirm parameters. Sailesh Bataju
[gmx-users] Need to confirm parameters. Sailesh Bataju
[gmx-users] Need to confirm parameters. Sailesh Bataju
[gmx-users] Need to confirm parameters. Sailesh Bataju
[gmx-users] Need to confirm parameters. Sailesh Bataju
[gmx-users] CHARMM36 and energygroup exclusions Daniel Bauer
[gmx-users] CHARMM36 and energygroup exclusions Daniel Bauer
[gmx-users] CHARMM36 and energygroup exclusions Daniel Bauer
[gmx-users] Continuation mdp flag Daniel Bauer
[gmx-users] Continuation mdp flag Daniel Bauer
[gmx-users] Lipid Simulation Analysis Daniel Bauer
[gmx-users] sequential simulations with mdrun -multi option Debdip Bhandary
[gmx-users] Problem setting up SMD simulation for DNA Nicholus Bhattacharjee
[gmx-users] g_rms using a structure in trajectory as reference Francesca Lønstad Bleken
[gmx-users] sampling convergence of FEL Subhomoi Borkotoky
[gmx-users] Regarding sampling convergence Subhomoi Borkotoky
[gmx-users] How to use "gmx view" on Ubuntu? ZHANG Cheng
[gmx-users] How to use "gmx view" on Ubuntu? ZHANG Cheng
[gmx-users] How to use "gmx view" on Ubuntu? ZHANG Cheng
[gmx-users] How to use "gmx view" on Ubuntu? ZHANG Cheng
[gmx-users] How to use "gmx view" on Ubuntu? ZHANG Cheng
[gmx-users] How to use "gmx view" on Ubuntu? ZHANG Cheng
[gmx-users] How the pH is reflected in Gromacs? ZHANG Cheng
[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file ZHANG Cheng
[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file ZHANG Cheng
[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file ZHANG Cheng
[gmx-users] pdb2gmx do not work for unstable conformations ZHANG Cheng
[gmx-users] pdb2gmx do not work for unstable conformations ZHANG Cheng
[gmx-users] mdp file for 370 K MD based on Justin's tutorial ZHANG Cheng
[gmx-users] mdp file for 370 K MD based on Justin's tutorial ZHANG Cheng
[gmx-users] New residue for custom capping Simon Kit Sang Chu
[gmx-users] New residue for custom capping Simon Kit Sang Chu
[gmx-users] New residue for custom capping Simon Kit Sang Chu
[gmx-users] forcefield parameter missing Simon Kit Sang Chu
[gmx-users] forcefield parameter missing Simon Kit Sang Chu
[gmx-users] Parameterizing Acetylated lysine: need for impropers? Ramon Crehuet
[gmx-users] B-FACTOR Ramon Crehuet
[gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB Ramon Crehuet
[gmx-users] Is dssp required with CG ElNeDyn model? Sudip Das
[gmx-users] Difference in alpha and thole terms for drudeFF Dayhoff, Guy
[gmx-users] Gromacs on Ubuntu 17.04 De Crisci, Antonio (NRCan/RNCan)
[gmx-users] gmx hbond -tu error Marcelo Depólo
[gmx-users] gmx sorient interpretation Marcelo Depólo
[gmx-users] atomname2types.n2t explanation Marcelo Depólo
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Marcelo Depólo
[gmx-users] Martini Website is not accessible Anurag Dobhal
[gmx-users] Martini Website is not accessible Anurag Dobhal
[gmx-users] Martini Website is not accessible Anurag Dobhal
[gmx-users] Fwd: Issue with parallel simulations in vacuum Agusti Emperador
[gmx-users] Fwd: Issue with parallel simulations in vacuum Agusti Emperador
[gmx-users] Free energy calculations using tabulated potential Gianluca DEL FRATE
[gmx-users] Ligand Boron parameters Pedro Fernandes
[gmx-users] Hydroxyl bonds rotating too much Juan José Galano Frutos
[gmx-users] Hydroxyl bonds rotating too much Juan José Galano Frutos
[gmx-users] Hydroxyl bonds rotating too much Juan José Galano Frutos
[gmx-users] gmx freevolume Federico Gallino
[gmx-users] MD at different pH Anu George
[gmx-users] MD at different pH Anu George
[gmx-users] MD at different pH Anu George
[gmx-users] MD at different pH Anu George
[gmx-users] Regarding conversion of .trr file to readable file Bappa Ghosh
[gmx-users] Fwd: Broken chain / fragmentation Biplab Ghosh
[gmx-users] Using the md integrator for calculating free energy of solvation Dan Gil
[gmx-users] Using the md integrator for calculating free energy of solvation Dan Gil
[gmx-users] Using the md integrator for calculating free energy of solvation Dan Gil
[gmx-users] Using the md integrator for calculating free energy of solvation Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Perturbation Thermodynamic Integration Dan Gil
[gmx-users] Running Gromacs on GPUs Giannis Gl
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Steffen Graether
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Steffen Graether
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Steffen Graether
[gmx-users] GROMACS INPUT FILE Neha Gupta
[gmx-users] strange behavior during energy minimization Gergely Gyimesi
[gmx-users] Lipid Simulation Analysis Mr. Zaved Hazarika
[gmx-users] Lipid Simulation Analysis Mr. Zaved Hazarika
[gmx-users] lipid / -OH oscillation period Tamas Hegedus
[gmx-users] RMSF problem Franco Henrique
[gmx-users] RMSF problem Franco Henrique
[gmx-users] MD at different pH João Henriques
[gmx-users] MD at different pH João Henriques
[gmx-users] MD at different pH João Henriques
[gmx-users] HPC resources in Europe (preferably Northern/Central Europe) João Henriques
[gmx-users] HPC resources in Europe (preferably Northern/Central Europe) João Henriques
[gmx-users] mdp file for 370 K MD based on Justin's tutorial João Henriques
[gmx-users] Positive potential energy Emran Heshmati
[gmx-users] Positive potential energy Emran Heshmati
[gmx-users] Positive potential energy Emran Heshmati
[gmx-users] System Crashes Sheikh Imamul Hossain
[gmx-users] Strange energy minimization problem with large Martini box Jochen Hub
[gmx-users] Heavy atom - hydrogens bond lengths constraints. Jochen Hub
[gmx-users] Tetrahedral orientational order parameter ISHRAT JAHAN
[gmx-users] symmetrical LJ binary mixture simulation Hyuntae Jung
[gmx-users] symmetrical LJ binary mixture simulation Hyuntae Jung
[gmx-users] -1.8 Equilibration pressure during MD simulation Quin K
[gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Adarsh V. K.
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Adarsh V. K.
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Adarsh V. K.
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? Adarsh V. K.
[gmx-users] column no 1 , 2 and 3? of " hbnum.xvg " file? Re: gromacs.org_gmx-users Digest, Vol 157, Issue 135 Adarsh V. K.
[gmx-users] How to perform final MD simulation after extending a NPT simulation Adarsh V. K.
[gmx-users] Unreasonably high pressure values Kamps, M.
[gmx-users] Unreasonably high pressure values Kamps, M.
[gmx-users] Unreasonably high pressure values Kamps, M.
[gmx-users] Problem with accelerations Kamps, M.
[gmx-users] Problem with accelerations Kamps, M.
[gmx-users] Problem with accelerations Kamps, M.
[gmx-users] md continuation Kashif
[gmx-users] md continuation Kashif
[gmx-users] Domain decomposition error Kashif
[gmx-users] md continuation Kashif
[gmx-users] Check stability of complex Kashif
[gmx-users] em and nvt problem Kashif
[gmx-users] Atom type CB ERROR Kashif
[gmx-users] Atom type CB ERROR Kashif
[gmx-users] Using the md integrator for calculating free energy of solvation Tasneem Kausar
[gmx-users] Hydration shell Tasneem Kausar
[gmx-users] Water molecules present at the protein-protein interface. Tasneem Kausar
[gmx-users] pdb2gmx handle the dna structure containing potassium Tasneem Kausar
[gmx-users] md continuation Tasneem Kausar
[gmx-users] md continuation Tasneem Kausar
[gmx-users] Fwd: Broken chain / fragmentation Tasneem Kausar
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Mohammad Hassan Khatami
[gmx-users] CHARMM36 parameter for polysaccharide branching Mohammad Hassan Khatami
[gmx-users] CHARMM36 parameter for polysaccharide branching Mohammad Hassan Khatami
[gmx-users] Lennard Jones and Buckingham potential together in one simulation Narjes Khosravian
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Daniel Kozuch
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Daniel Kozuch
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Daniel Kozuch
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Daniel Kozuch
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Daniel Kozuch
[gmx-users] em and nvt problem Daniel Kozuch
[gmx-users] Fwd: Topology error Jai Krishna
[gmx-users] Martini Website is not accessible Peter Kroon
[gmx-users] Regarding centering the molecule/protein during Simulation Peter Kroon
[gmx-users] Regarding centering the molecule/protein during Simulation Peter Kroon
[gmx-users] Regarding centering the molecule/protein during Simulation Peter Kroon
[gmx-users] pdb2gmx handle the dna structure containing potassium Changdong LIU
[gmx-users] 答复: Re: pdb2gmx handle the dna structure containing potassium Changdong LIU
[gmx-users] (no subject) Anshul Lahariya
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Anshul Lahariya
[gmx-users] gmx hbond -tu error Justin Lemkul
[gmx-users] Polymer topology file Justin Lemkul
[gmx-users] The Rationality of Position Restrain in Umbrella Sampling Justin Lemkul
[gmx-users] GAAMP parameterization Justin Lemkul
[gmx-users] The Rationality of Position Restrain in Umbrella Sampling Justin Lemkul
[gmx-users] GAAMP parameterization Justin Lemkul
[gmx-users] CHARMM36 and energygroup exclusions Justin Lemkul
[gmx-users] CHARMM36 and energygroup exclusions Justin Lemkul
[gmx-users] MD at different pH Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] position of water molecules during the simulation time Justin Lemkul
[gmx-users] Different number of molecules in simulation box. Justin Lemkul
[gmx-users] MD at different pH Justin Lemkul
[gmx-users] Using the md integrator for calculating free energy of solvation Justin Lemkul
[gmx-users] MD at different pH Justin Lemkul
[gmx-users] Increasing sigma Justin Lemkul
[gmx-users] PBC Justin Lemkul
[gmx-users] From: Graduate Student protein active site inquiry Justin Lemkul
[gmx-users] From: Graduate Student protein active site inquiry Justin Lemkul
[gmx-users] question about applying surface tension Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] lipid / -OH oscillation period Justin Lemkul
[gmx-users] question about applying surface tension Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Ligand Boron parameters Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Difference in alpha and thole terms for drudeFF Justin Lemkul
[gmx-users] How to use "gmx view" on Ubuntu? Justin Lemkul
[gmx-users] pdb2gmx handle the dna structure containing potassium Justin Lemkul
[gmx-users] Fwd: Simulation Justin Lemkul
[gmx-users] A simple question Justin Lemkul
[gmx-users] Regarding simulation radioactive material Justin Lemkul
[gmx-users] A simple question Justin Lemkul
[gmx-users] How to use "gmx view" on Ubuntu? Justin Lemkul
[gmx-users] A simple question Justin Lemkul
[gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs Justin Lemkul
[gmx-users] assignment of atomname1 and atomname2 in param_example file in GridMAT-MD Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Using the md integrator for calculating free energy of solvation Justin Lemkul
[gmx-users] Regarding simulation radioactive material Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] RMSF problem Justin Lemkul
[gmx-users] RMSF problem Justin Lemkul
[gmx-users] question about applying surface tension Justin Lemkul
[gmx-users] Using the md integrator for calculating free energy of solvation Justin Lemkul
[gmx-users] question about applying surface tension Justin Lemkul
[gmx-users] Graphene modeling Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Perturbation Thermodynamic Integration Justin Lemkul
[gmx-users] Hydroxyl bonds rotating too much Justin Lemkul
[gmx-users] Graphene modeling Justin Lemkul
[gmx-users] Fwd: Issue with parallel simulations in vacuum Justin Lemkul
[gmx-users] Problem in Bootstrapping of PMF Justin Lemkul
[gmx-users] genion command Justin Lemkul
[gmx-users] 1-4 interactions in CHARMM force field Justin Lemkul
[gmx-users] Protein-Ligand Justin Lemkul
[gmx-users] Problems with large molecule simulation Justin Lemkul
[gmx-users] Problems with large molecule simulation Justin Lemkul
[gmx-users] Protein-Ligand Justin Lemkul
[gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB Justin Lemkul
[gmx-users] Problem setting up SMD simulation for DNA Justin Lemkul
[gmx-users] md continuation Justin Lemkul
[gmx-users] Domain decomposition error Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Error message Justin Lemkul
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Justin Lemkul
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] Need to confirm parameters. Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Error with moleculetype Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] Need to confirm parameters. Justin Lemkul
[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file Justin Lemkul
[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file Justin Lemkul
[gmx-users] Error with moleculetype Justin Lemkul
[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22 Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] ligand moving out during umbrella sampling Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] mdp file for 370 K MD based on Justin's tutorial Justin Lemkul
[gmx-users] Minimisation Justin Lemkul
[gmx-users] Fwd: Topology error Justin Lemkul
[gmx-users] Minimisation Justin Lemkul
[gmx-users] Need to confirm parameters. Justin Lemkul
[gmx-users] Minimisation Justin Lemkul
[gmx-users] Minimisation Justin Lemkul
[gmx-users] Need to confirm parameters. Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] atomname2types.n2t explanation Justin Lemkul
[gmx-users] Need to confirm parameters. Justin Lemkul
[gmx-users] high temperature during mdrun Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides Justin Lemkul
[gmx-users] RMSF per residue Justin Lemkul
[gmx-users] simulating AMP covalently linked to a protein Justin Lemkul
[gmx-users] gromacs bond energy calculate Justin Lemkul
[gmx-users] Check stability of complex Justin Lemkul
[gmx-users] em and nvt problem Justin Lemkul
[gmx-users] DSSP Justin Lemkul
[gmx-users] CHARMM36 parameter for polysaccharide branching Justin Lemkul
[gmx-users] simulating AMP covalently linked to a protein Justin Lemkul
[gmx-users] RMSF per residue Justin Lemkul
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? Justin Lemkul
[gmx-users] RMSF per residue Justin Lemkul
[gmx-users] Grompp error for graphene modeling Justin Lemkul
[gmx-users] Fwd: Broken chain / fragmentation Justin Lemkul
[gmx-users] Genion error Justin Lemkul
[gmx-users] Invalid directive impropers Justin Lemkul
[gmx-users] Genion error Justin Lemkul
[gmx-users] Atom type CB ERROR Justin Lemkul
[gmx-users] Reg: creation of separate chains in .pdb file Justin Lemkul
[gmx-users] g_rms using a structure in trajectory as reference Justin Lemkul
[gmx-users] Making a move using command gromacs/vmd Justin Lemkul
[gmx-users] Non-bonded interaction energy Justin Lemkul
[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option. Justin Lemkul
[gmx-users] calculation of energy of individual water molecules in gromacs Justin Lemkul
[gmx-users] destruction of the structure of a molecule in water after energy minimization Justin Lemkul
[gmx-users] Write force on a single particle Justin Lemkul
[gmx-users] Doubt about gmx wham analysis Justin Lemkul
[gmx-users] Deuterium Order Parameter Calculations Justin Lemkul
[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS Justin Lemkul
[gmx-users] How to perform final MD simulation after extending a NPT simulation Justin Lemkul
[gmx-users] calculation of energy of individual water molecules in gromacs Justin Lemkul
[gmx-users] Atom type CB ERROR Justin Lemkul
[gmx-users] Need to confirm parameters. Justin Lemkul
[gmx-users] Reg: creation of separate chains in .pdb file Justin Lemkul
[gmx-users] Doubt about gmx wham analysis Justin Lemkul
[gmx-users] mixed 1-4 scaling factor Qinghua Liao
[gmx-users] Open GROMACS researcher position in Stockholm Erik Lindahl
[gmx-users] Calculation of dielectric constant Philip Loche
[gmx-users] Increasing sigma Hannes Loeffler
[gmx-users] Perturbation Thermodynamic Integration Hannes Loeffler
[gmx-users] Perturbation Thermodynamic Integration Hannes Loeffler
[gmx-users] Perturbation Thermodynamic Integration Hannes Loeffler
[gmx-users] Anyone use FMA (Functional Mode Analysis) ? Qing Lv
[gmx-users] Anyone use FMA (Functional Mode Analysis) ? Qing Lv
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? Erik Marklund
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? Erik Marklund
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? Erik Marklund
[gmx-users] MD at different pH Nikhil Maroli
[gmx-users] position of water molecules during the simulation time Nikhil Maroli
[gmx-users] Installatoin error Nikhil Maroli
[gmx-users] Suggestion for workstation configurations Nikhil Maroli
[gmx-users] protein ligand complex Energy Minimisation Nikhil Maroli
[gmx-users] Gromacs on Ubuntu 17.04 Nikhil Maroli
[gmx-users] Regarding python program/code for Hydrogen bond lifetime Nikhil Maroli
[gmx-users] Lipid Simulation Analysis Nikhil Maroli
[gmx-users] Radial distribution function Sohaib. Mohammed
[gmx-users] choosing confs for Umbrella sampling abhisek Mondal
[gmx-users] choosing confs for Umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] Error In Umbrella sampling. abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] ligand moving out during umbrella sampling abhisek Mondal
[gmx-users] gromacs-5.1.4 installation issue abhisek Mondal
[gmx-users] gromacs-5.1.4 installation issue abhisek Mondal
[gmx-users] Biasing potential query abhisek Mondal
[gmx-users] Biasing potential query abhisek Mondal
[gmx-users] Doubt about gmx wham analysis abhisek Mondal
[gmx-users] Calculation of volume of protein hydration layer Saumyak Mukherjee
[gmx-users] Calculation of volume of protein hydration layer Saumyak Mukherjee
[gmx-users] Calculation of dielectric constant Saumyak Mukherjee
[gmx-users] Calculation of dielectric constant Saumyak Mukherjee
[gmx-users] genion command Saumyak Mukherjee
[gmx-users] Regarding centering the molecule/protein during Simulation Saumyak Mukherjee
[gmx-users] calculation of energy of individual water molecules in gromacs Saumyak Mukherjee
[gmx-users] calculation of energy of individual water molecules in gromacs Saumyak Mukherjee
[gmx-users] calculation of energy of individual water molecules in gromacs Saumyak Mukherjee
[gmx-users] Regarding conversion of .trr file to readable file Dilip H N
[gmx-users] Regarding extending simulations Dilip H N
[gmx-users] Regarding extending simulations Dilip H N
[gmx-users] Regarding extending simulations with change in .mdp file Dilip H N
[gmx-users] Regarding centering the molecule/protein during Simulation Dilip H N
[gmx-users] Regarding python program/code for Hydrogen bond lifetime Dilip H N
[gmx-users] Regarding python program/code for Hydrogen bond lifetime Dilip H N
[gmx-users] Invalid directive impropers Saeed Nasiri
[gmx-users] destruction of the structure of a molecule in water after energy minimization Saeed Nasiri
[gmx-users] Invalid directive impropers Saeed Nasiri
[gmx-users] (Opt.) indication to gmx cluster -s doesn't seem to be optional Christopher Neale
[gmx-users] mixed 1-4 scaling factor Christopher Neale
[gmx-users] gmx cluster -binary flag to get the "centroid" as the member that has max neighbours < cutoff ? Christopher Neale
[gmx-users] Regarding simulation radioactive material Christopher Neale
[gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy Christopher Neale
[gmx-users] System volume "jumps" on exact continuations Christopher Neale
[gmx-users] Adding buffer to simulation box Pandya, Akash
[gmx-users] Adding buffer to simulation box Pandya, Akash
[gmx-users] Calculating the number of ligand molecules needed inside the simulation box Pandya, Akash
[gmx-users] Calculating number of molecules to add in simulation box Pandya, Akash
[gmx-users] Error message Pandya, Akash
[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4 Pandya, Akash
[gmx-users] Error message Pandya, Akash
[gmx-users] Error message Pandya, Akash
[gmx-users] Error with moleculetype Pandya, Akash
[gmx-users] Error with moleculetype Pandya, Akash
[gmx-users] Error with moleculetype Pandya, Akash
[gmx-users] Minimisation Pandya, Akash
[gmx-users] Minimisation Pandya, Akash
[gmx-users] Minimisation Pandya, Akash
[gmx-users] Minimisation Pandya, Akash
[gmx-users] Minimisation Pandya, Akash
[gmx-users] protein ligand complex Energy Minimisation Patel, Hershna
[gmx-users] From: Graduate Student protein active site inquiry Sajeewa Pemasinghe
[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS Tomasz Piskorz
[gmx-users] System volume "jumps" on exact continuations Elizabeth Ploetz
[gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1 Harry Ponce
[gmx-users] gromacs.org_gmx-users Digest, Vol 157, Issue 112 Harry Ponce
[gmx-users] Different number of molecules in simulation box. B Prakash
[gmx-users] Different number of molecules in simulation box. B Prakash
[gmx-users] Different number of molecules in simulation box. B Prakash
[gmx-users] Polymer topology file Chetan Puri
[gmx-users] Gromacs on Ubuntu 17.04 Szilárd Páll
[gmx-users] NVML does not come separate starting from Cuda 8.0 Szilárd Páll
[gmx-users] NVML does not come separate starting from Cuda 8.0 Szilárd Páll
[gmx-users] (no subject) Szilárd Páll
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Szilárd Páll
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Szilárd Páll
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Szilárd Páll
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Szilárd Páll
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Szilárd Páll
[gmx-users] System volume "jumps" on exact continuations Szilárd Páll
[gmx-users] Deuterium Order Parameter Analysis Sanim Rahman
[gmx-users] Deuterium Order Parameter Calculations Sanim Rahman
[gmx-users] Deuterium Order Parameter Calculations Sanim Rahman
[gmx-users] Doubts about g_lie and g_bar Varvdekar Bhagyesh Rajendra
[gmx-users] Doubts about g_lie and g_bar Varvdekar Bhagyesh Rajendra
[gmx-users] Doubts about g_lie and g_bar Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about gmx wham analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about constrained NM Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about gmx wham analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about gmx wham analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about gmx wham analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Vytautas Rakeviius
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Vytautas Rakeviius
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Vytautas Rakeviius
[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04 Vytautas Rakeviius
[gmx-users] gromacs-5.1.4 installation issue Vytautas Rakeviius
[gmx-users] gromacs-5.1.4 installation issue Vytautas Rakeviius
[gmx-users] Simulated annealing Venkat Raman
[gmx-users] GAAMP parameterization Mohsen Ramezanpour
[gmx-users] GAAMP parameterization Mohsen Ramezanpour
[gmx-users] GAAMP parameterization Mohsen Ramezanpour
[gmx-users] PBC fix for visualization Mohsen Ramezanpour
[gmx-users] PBC fix for visualization Mohsen Ramezanpour
[gmx-users] RMSF per residue Mohsen Ramezanpour
[gmx-users] RMSF per residue Mohsen Ramezanpour
[gmx-users] RMSF per residue Mohsen Ramezanpour
[gmx-users] RMSF per residue Mohsen Ramezanpour
[gmx-users] About using GLYCAM force field in Gromacs WT Ren
[gmx-users] -1.8 Equilibration pressure during MD simulation Dries Van Rompaey
[gmx-users] 2016.3 installation RAHUL SURESH
[gmx-users] 2016.3 installation RAHUL SURESH
[gmx-users] 2016.3 installation RAHUL SURESH
[gmx-users] 2016.3 installation RAHUL SURESH
[gmx-users] Installatoin error RAHUL SURESH
[gmx-users] Installatoin error RAHUL SURESH
[gmx-users] Simulation RAHUL SURESH
[gmx-users] B-FACTOR RAHUL SURESH
[gmx-users] Fwd: Simulation RAHUL SURESH
[gmx-users] Protein-Ligand RAHUL SURESH
[gmx-users] Protein-Ligand RAHUL SURESH
[gmx-users] Gromacs on Ubuntu 17.04 Åke Sandgren
[gmx-users] NVML does not come separate starting from Cuda 8.0 Åke Sandgren
[gmx-users] question about applying surface tension Ali Shomali
[gmx-users] question about applying surface tension Ali Shomali
[gmx-users] question about applying surface tension Ali Shomali
[gmx-users] question about applying surface tension Ali Shomali
[gmx-users] question about applying surface tension Ali Shomali
[gmx-users] appropriate tau-p for surface tension coupling Ali Shomali
[gmx-users] em and nvt problem Marlon Sidore
[gmx-users] AMBER LIPID14 ff in GROMACS Amit Singh
[gmx-users] MD at different pH Smith, Micholas D.
[gmx-users] MD at different pH Smith, Micholas D.
[gmx-users] Calculating number of molecules to add in simulation box Smith, Micholas D.
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Smith, Micholas D.
[gmx-users] Poor GPU Performance with GROMACS 5.1.4 Smith, Micholas D.
[gmx-users] CELLmicrocosmos MembraneEditor: Quad-2 Release Björn Sommer
[gmx-users] Calculation of volume of protein hydration layer David van der Spoel
[gmx-users] GAAMP parameterization David van der Spoel
[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ? David van der Spoel
[gmx-users] column no 1 , 2 and 3? of " hbnum.xvg " file? Re: gromacs.org_gmx-users Digest, Vol 157, Issue 135 David van der Spoel
[gmx-users] HPC resources in Europe (preferably Northern/Central Europe) ABEL Stephane
[gmx-users] NMA eigenvectors doubts Peter Stern
[gmx-users] NMA eigenvectors doubts Peter Stern
[gmx-users] How to find free energy barriers between conformational sub-states of simulation? Seera Suryanarayana
[gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs ZUO Taisen
[gmx-users] gromacs.org_gmx-users Digest, Vol 157, Issue 42 ZUO Taisen
[gmx-users] Problems with large molecule simulation Ben Tam
[gmx-users] Problems with large molecule simulation Tam, Benjamin
[gmx-users] Problems with large molecule simulation Tam, Benjamin
[gmx-users] simulating AMP covalently linked to a protein Gilberto Valdes
[gmx-users] simulating AMP covalently linked to a protein Gilberto Valdes
[gmx-users] soft "exit" Daskalakis Vangelis
[gmx-users] soft "exit" Daskalakis Vangelis
[gmx-users] g_densmap with Cartesian coordinates results in segvault, cylindrical does not Vis, van der, J.S.
[gmx-users] Suggestion for workstation configurations Johannes Wagner
[gmx-users] PBC fix for visualization Dallas Warren
[gmx-users] DSSP Mariusz Wierzbowski
[gmx-users] From: Graduate Student protein active site inquiry Felix Y Yang
[gmx-users] From: Graduate Student protein active site inquiry Felix Y Yang
[gmx-users] regarding tha langevin thermostat (integrator sd) Felix Y Yang
[gmx-users] How the pH is reflected in Gromacs? Zhi Yue
[gmx-users] Making a move using command gromacs/vmd Poncho Arvayo Zatarain
[gmx-users] How to compile Mopac7 with Gromacs_2016.3 release? Frank Zhou
[gmx-users] How to compile Mopac7 with Gromacs_2016.3 release? Frank Zhou
[gmx-users] How to use "gmx view" on Ubuntu? Frank Zhou
[gmx-users] How to use "gmx view" on Ubuntu? Frank Zhou
[gmx-users] The Rationality of Position Restrain in Umbrella Sampling Jason Zhu
[gmx-users] The Rationality of Position Restrain in Umbrella Sampling Jason Zhu
[gmx-users] Nonequilibrium simulations jwillcox at andrew.cmu.edu
[gmx-users] Nonequilibrium simulations jwillcox at andrew.cmu.edu
[gmx-users] Nose-Hoover + acc-grps jwillcox at andrew.cmu.edu
[gmx-users] Suggestion for workstation configurations deepak bapat
[gmx-users] Heavy atom - hydrogens bond lengths constraints. Dawid das
[gmx-users] Heavy atom - hydrogens bond lengths constraints. Dawid das
[gmx-users] 1-4 interactions in CHARMM force field Dawid das
[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22 Dawid das
[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22 Dawid das
[gmx-users] gromacs bond energy calculate Dawid das
[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22 Dawid das
[gmx-users] Write force on a single particle simon.grosse-holz at fau.de
[gmx-users] Mail list shivani gupta
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA eigenvectors doubts luca maggi
[gmx-users] NMA Hessian Sub-matrix luca maggi
[gmx-users] genion command diana p
[gmx-users] assignment of atomname1 and atomname2 in param_example file in GridMAT-MD manindersingh rajawat
[gmx-users] mdrun failure fatemeh ramezani
[gmx-users] Fw: mdrun failure fatemeh ramezani
[gmx-users] mdrun failed fatemeh ramezani
[gmx-users] mdrun failed fatemeh ramezani
[gmx-users] mdrun failure fatemeh ramezani
[gmx-users] high temperature during mdrun fatemeh ramezani
[gmx-users] Calculation of nematic order parameter using gromacs nidhi sorout
[gmx-users] Non-bonded interaction energy Мижээ Батсайхан
[gmx-users] Call for testing: trajectory analysis framework in Python Максим Кольцов
[gmx-users] Graphene modeling ‪Mohammad Roostaie‬ ‪
[gmx-users] Graphene modeling ‪Mohammad Roostaie‬ ‪
[gmx-users] Graphene modeling ‪Mohammad Roostaie‬ ‪
[gmx-users] Graphene modeling ‪Mohammad Roostaie‬ ‪
[gmx-users] Graphene ‪Mohammad Roostaie‬ ‪
[gmx-users] grompp error ‪Mohammad Roostaie‬ ‪
[gmx-users] Grompp error for graphene modeling ‪Mohammad Roostaie‬ ‪
[gmx-users] Grompp error for graphene modeling ‪Mohammad Roostaie‬ ‪
[gmx-users] Genion error ‪Mohammad Roostaie‬ ‪
[gmx-users] Genion error ‪Mohammad Roostaie‬ ‪
[gmx-users] Genion error ‪Mohammad Roostaie‬ ‪
[gmx-users] EM error ‪Mohammad Roostaie‬ ‪
[gmx-users] gromacs bond energy calculate 王珍
[gmx-users] About using GLYCAM force field in Gromacs 维维

Last message date: Wed May 31 23:22:58 CEST 2017
Archived on: Wed May 31 23:22:59 CEST 2017

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