November 2011 Archives by author

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Starting: Tue Nov 1 00:56:25 CET 2011
Ending: Wed Nov 30 23:00:10 CET 2011
Messages: 949

[gmx-users] diffusion of the water at the micelle surface ABEL Stephane 175950
[gmx-users] segmentation fault from power6 kernel Fabio AFFINITO
[gmx-users] segmentation fault from power6 kernel Fabio AFFINITO
[gmx-users] Re: how to calculate the force between two groups (Mark Abraham) Mark Abraham
[gmx-users] LINCS crushes Mark Abraham
[gmx-users] unknown cmap torsion between atoms Mark Abraham
[gmx-users] unknown cmap torsion between atoms Mark Abraham
[gmx-users] xtc vs. trr file Mark Abraham
[gmx-users] setting working directory Mark Abraham
[gmx-users] grompp: "invalid bond type" error Mark Abraham
[gmx-users] Simulation of membrane protein Mark Abraham
[gmx-users] discrepancy trjconv and gmxdump Mark Abraham
[gmx-users] tc_grps Justin Tutorial Mark Abraham
[gmx-users] how to make top and gro file for acid hexanoic Mark Abraham
[gmx-users] segmentation fault from power6 kernel Mark Abraham
[gmx-users] remd- Function not implemented Mark Abraham
[gmx-users] Simulation of membrane protein Mark Abraham
[gmx-users] segmentation fault from power6 kernel Mark Abraham
[gmx-users] Gromacs query for vaccum medium Mark Abraham
[gmx-users] Regarding Minimization Mark Abraham
[gmx-users] Regarding error in ion neutralization step Mark Abraham
[gmx-users] Regarding Extension of the potential lookup tables Mark Abraham
[gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of Mark Abraham
[gmx-users] refcoord_scaling Mark Abraham
[gmx-users] PBC - Protein - ligand Mark Abraham
[gmx-users] gromacs query for force field in vaccum and liquid Mark Abraham
[gmx-users] B-factor to large? Input for TLS Mark Abraham
[gmx-users] how to make topol.top file for mixed solution Mark Abraham
[gmx-users] remd with different potential at different temperature Mark Abraham
[gmx-users] how to do remd with different tabulated potentials Mark Abraham
[gmx-users] CygWin and Gromacs 4.5.5 Mark Abraham
[gmx-users] newbie question about GROMACS input files Mark Abraham
[gmx-users] How to list OPLS parameters Mark Abraham
[gmx-users] where is Coul-LR? Mark Abraham
[gmx-users] Normal Mode Analysis Mark Abraham
[gmx-users] g_mindist -on Mark Abraham
[gmx-users] Normal Mode Analysis Mark Abraham
[gmx-users] Parametrisation of the heteroatomic pdb Mark Abraham
[gmx-users] Parametrisation of the heteroatomic pdb Mark Abraham
[gmx-users] Converting of itp topology files Mark Abraham
[gmx-users] Disulphur bridge parameters Mark Abraham
[gmx-users] Converting of itp topology files Mark Abraham
[gmx-users] about the velocity output from leap-frog integrators Mark Abraham
[gmx-users] Problems with g_membed tools Mark Abraham
[gmx-users] Parametrisation of the heteroatomic pdb Mark Abraham
[gmx-users] Parametrisation of the heteroatomic pdb Mark Abraham
[gmx-users] Re: Problems with g_membed tools Mark Abraham
[gmx-users] Re: Problems with g_membed tools Mark Abraham
[gmx-users] Positive potential energy for TFE solvent Mark Abraham
[gmx-users] several itp Mark Abraham
[gmx-users] remd :One of the processes started by mpirun has exited with a nonzero exit code. Mark Abraham
[gmx-users] Time unit issue with g_anaeig Mark Abraham
[gmx-users] Atomtype 'CR' not found Mark Abraham
[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures Mark Abraham
[gmx-users] mpirun with remd Mark Abraham
[gmx-users] Units of Buckingham potential Mark Abraham
[gmx-users] The equilibrium before REMD simulations Mark Abraham
[gmx-users] Query on restraining center of mass of a protein Mark Abraham
[gmx-users] import force field Mark Abraham
[gmx-users] The equilibrium before REMD simulations Mark Abraham
[gmx-users] Positive potential energy for TFE solvent Mark Abraham
[gmx-users] Units of Buckingham potential Mark Abraham
[gmx-users] Units of Buckingham potential Mark Abraham
[gmx-users] Re: Positive potential energy for TFE solvent Mark Abraham
[gmx-users] about tabulated potentials Mark Abraham
[gmx-users] dihedral angle Mark Abraham
[gmx-users] Re: Re: Positive potential energy for TFE solvent Mark Abraham
[gmx-users] import force field Mark Abraham
[gmx-users] Gromacs 3D maps Mark Abraham
[gmx-users] problem obtaining similar force fields for protein and ligand Mark Abraham
[gmx-users] analysing helix dynamics Mark Abraham
[gmx-users] non-specific protein-protein interactions Mark Abraham
[gmx-users] query for energy minimization in solvent Mark Abraham
[gmx-users] what's the math algorithm? Mark Abraham
[gmx-users] Hydrogen database Mark Abraham
[gmx-users] Poor exchange probability for REMD Mark Abraham
[gmx-users] REMD: when it exchange the replica, it will be bombed!! Mark Abraham
[gmx-users] non-specific protein-protein interactions Mark Abraham
[gmx-users] Reproducable MD runs on two PCs Mark Abraham
[gmx-users] Reproducable MD runs on two PCs Mark Abraham
[gmx-users] Reproducable MD runs on two PCs Mark Abraham
[gmx-users] about temperature coupling Mark Abraham
[gmx-users] maybe you are out of quota? Mark Abraham
[gmx-users] Topology error Mark Abraham
[gmx-users] Potential Energy Landscape Mark Abraham
[gmx-users] Ligand charge assignment Mark Abraham
[gmx-users] Error when try obtain protein energies instead of system energies Mark Abraham
[gmx-users] Trajectory to matrix Mark Abraham
[gmx-users] do_dssp segmentation fault Mark Abraham
[gmx-users] Force equations of virtual site type 4fdn Mark Abraham
[gmx-users] Box in Implicit Solvent Simulations Mark Abraham
[gmx-users] Rv: g_helixorient question Mark Abraham
[gmx-users] Regarding Dimer calculations Mark Abraham
[gmx-users] Cavity detection on membrane protein surface Mark Abraham
[gmx-users] how to edit a .xvg file? Mark Abraham
[gmx-users] Visualizing g_helixorient output Mark Abraham
[gmx-users] Visualizing g_helixorient output Mark Abraham
[gmx-users] grompp line too long error Mark Abraham
[gmx-users] Adding ions using "genion" Mark Abraham
[gmx-users] do remd in the npt ensemble:Warning: pressure scaling more than 1%, mu: 333821 333821 333821 Mark Abraham
[gmx-users] centroid clustering Mark Abraham
[gmx-users] mdrun -rerun (not reproducible energy values?) Mark Abraham
[gmx-users] Pressure stabilization during NPT phase Mark Abraham
[gmx-users] Pressure stabilization during NPT phase Mark Abraham
[gmx-users] Pressure stabilization during NPT phase Mark Abraham
[gmx-users] grompp error Mark Abraham
[gmx-users] making movie from trajectories Mark Abraham
[gmx-users] to gro or not to gro Mark Abraham
[gmx-users] to gro or not to gro Mark Abraham
[gmx-users] Add ligand molecules in a lipid bilayer Mark Abraham
[gmx-users] .top to .itp file conversion Mark Abraham
[gmx-users] .top to .itp file conversion Mark Abraham
[gmx-users] Atom not found in residue while adding hydrogens Mark Abraham
[gmx-users] Atom not found in residue while adding hydrogens Mark Abraham
[gmx-users] remd in the npt ensemble: When the exchange, the temperature abruptly surge . Mark Abraham
[gmx-users] restoration of crashed simulation Mark Abraham
[gmx-users] File input/output error: 1OTI.pdb Mark Abraham
[gmx-users] frames in 2 trajectory files Mark Abraham
[gmx-users] Limit on energygrp_table Mark Abraham
[gmx-users] Limit on energygrp_table Mark Abraham
[gmx-users] Limit on energygrp_table Mark Abraham
[gmx-users] Suppress writing step*.pdb files Mark Abraham
[gmx-users] segmentation fault from power6 kernel Fabio Affinito
[gmx-users] re: Phosphate esters Ben Ahmady
[gmx-users] Re: Phosphate esters Ben Ahmady
[gmx-users] cutting a trajectory and continuing from a part of it Sajad Ahrari
[gmx-users] Method insert ion Saeid Akbarshahi
[gmx-users] Generating topology file Alan
[gmx-users] Re: PDB structure quality Alan
[gmx-users] about relaxation protocol Albert
[gmx-users] about relaxation protocol Albert
[gmx-users] g_analyze errors Alex
[gmx-users] How to use deuterium order parameters Alex
[gmx-users] Problems with deuterium graphs Alex
[gmx-users] A question about deuteriu order parameters graph Alex
[gmx-users] Sorry for posting twice Alex
[gmx-users] Remove water from membrane protein Alex
[gmx-users] Gromacs 3D maps Alex
[gmx-users] Pme on gpu performance Jones de Andrade
[gmx-users] request for comments on profile.xvg (PMF) courve Przemek Bartha
[gmx-users] Positive potential energy for TFE solvent Harpreet Basra
[gmx-users] Positive potential energy for TFE solvent Harpreet Basra
[gmx-users] Re: Positive potential energy for TFE solvent Harpreet Basra
[gmx-users] Re: Positive potential energy for TFE solvent Harpreet Basra
[gmx-users] Re: gmx-users Digest, Vol 91, Issue 105 Harpreet Basra
[gmx-users] Re: Re: Positive potential energy for TFE solvent Harpreet Basra
[gmx-users] Time step problem on coarse-grained LJ chain Tomy van Batis
[gmx-users] How to make coordinate file with correct numbering in the atoms when inbetween atoms are removed Ioannis Beis
[gmx-users] about the velocity output from leap-frog integrators Ravi Bhadauria
[gmx-users] about the velocity output from leap-frog integrators Ravi Bhadauria
[gmx-users] PLUMED release 1.3 available Massimiliano Bonomi
[gmx-users] how to obtain NOEs from MD trajectory ? Jose Borreguero
[gmx-users] g_helixorient Sebastian Breuers
[gmx-users] disable-nice Scott Brozell
[gmx-users] Error with pdb input Lara Bunte
[gmx-users] orca and qm/mm Javier Cerezo
[gmx-users] A question about deuteriu order parameters graph Javier Cerezo
[gmx-users] A question about deuteriu order parameters graph Javier Cerezo
[gmx-users] gromacs/mopac compilation: linking libmopac Javier Cerezo
[gmx-users] gromacs/mopac compilation: linking libmopac Javier Cerezo
[gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo) Javier Cerezo
[gmx-users] Re: problem while running production md Dr. Vitaly V. Chaban
[gmx-users] barostat for gases Dr. Vitaly V. Chaban
[gmx-users] barostat for gases Dr. Vitaly V. Chaban
[gmx-users] How DispCorr influsnces pressure Dr. Vitaly V. Chaban
[gmx-users] Re: NPT or NVT for calculating averaged experimental parameters Dr. Vitaly V. Chaban
[gmx-users] Re: gmx-users Digest, Vol 91, Issue 191 Dr. Vitaly V. Chaban
[gmx-users] Using CHARMM 36 for DPPC simulation Amit Choubey
[gmx-users] Re: Using CHARMM 36 for DPPC simulation Amit Choubey
[gmx-users] newbie question about GROMACS input files Markus K. Dahlgren
[gmx-users] dihedral angle Nilesh Dhumal
[gmx-users] Reproducable MD runs on two PCs Igor Druz
[gmx-users] Speeding up g_angle calculations Igor Druz
[gmx-users] Reproducable MD runs on two PCs Igor Druz
[gmx-users] Reproducable MD runs on two PCs Igor Druz
[gmx-users] NPT or NVT for calculating averaged experimental parameters Igor Druz
[gmx-users] vol in mdrun output Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] to gro or not to gro Igor Druz
[gmx-users] Small molecule - CHARMM EGY
[gmx-users] g_lie question EGY
[gmx-users] Re: g_lie question EGY
[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER Thomas Evangelidis
[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER Thomas Evangelidis
[gmx-users] setting working directory Efrat Exlrod
[gmx-users] gromacs 4.5.3 and GCC 4.1.x Efrat Exlrod
[gmx-users] Error when try obtain protein energies instead of system energies Rodrigo Faccioli
[gmx-users] Error when try obtain protein energies instead of system energies Rodrigo Faccioli
[gmx-users] Reg : Simulating heterologous protein complex with bound ligand Rohit Farmer
[gmx-users] Reg : Simulating heterologous protein complex with bound ligand Rohit Farmer
[gmx-users] Reg : Protein-ligand complex using Amber force field Rohit Farmer
[gmx-users] Strange problem.complex out of Box after EM Saba Ferdous
[gmx-users] Re: gmx-users Digest, Vol 91, Issue 119 Saba Ferdous
[gmx-users] Protein Complex simulation Saba Ferdous
[gmx-users] Increasing time for simulation Saba Ferdous
[gmx-users] restoration of crashed simulation Saba Ferdous
[gmx-users] frames in 2 trajectory files Saba Ferdous
[gmx-users] q4md-forcefieldtools.org announcement FyD
[gmx-users] what's the parameters for angle restraints in mdp file Chunxia Gao
[gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 " Chunxia Gao
[gmx-users] g_helixorientation question Javier Romero Garcia
[gmx-users] g_helixorient Javier Romero Garcia
[gmx-users] Rv: g_helixorient question Javier Romero Garcia
[gmx-users] Rv: g_helixorient question Javier Romero Garcia
[gmx-users] *** Extended deadline Dec 6 *** CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012 Daniele Gianni
[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER Oliver Grant
[gmx-users] Re 1. orca and qm/mm (xi zhao) Gerrit Groenhof
[gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao) Gerrit Groenhof
[gmx-users] Re: orca and Segmentation fault (xi zhao) Gerrit Groenhof
[gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo) Gerrit Groenhof
[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Gerrit Groenhof
[gmx-users] Gromacs error message Salvatore Guccione
[gmx-users] pyroglutamate in gromos53a6 Henry Hocking
[gmx-users] pyroglutamate in gromos53a6 Henry Hocking
[gmx-users] pyroglutamate in gromos53a6 Henry Hocking
[gmx-users] Question about simulated annealing w/ implicit solvent model Wonseok Hwang
[gmx-users] Write the total dipole moment on-the-fly? HAO JIANG
[gmx-users] Re: gmx-users Dipole HAO JIANG
[gmx-users] UNK not found in residue topology Janowicz, Adrianna C.
[gmx-users] UNK not found in residue topology Janowicz, Adrianna C.
[gmx-users] UNK not found Janowicz, Adrianna C.
[gmx-users] A question about deuteriu order parameters graph Alex Jemulin
[gmx-users] Extract van der waals surface atoms coordinates Alex Jemulin
[gmx-users] Problems with g_filter Alex Jemulin
[gmx-users] Trajectory to matrix Alex Jemulin
[gmx-users] do_dssp segmentation fault Alex Jemulin
[gmx-users] Trajectory to matrix Alex Jemulin
[gmx-users] Cavity detection on membrane protein surface Alex Jemulin
[gmx-users] NVT Equilibration Alex Jemulin
[gmx-users] NVT Equilibration Alex Jemulin
[gmx-users] user contribution Thorsten Koeddermann
[gmx-users] barostat for gases Krzysztof Kuczera
[gmx-users] Simulation of membrane protein Kukol, Andreas
[gmx-users] orca and qm/mm Micha Ben Achim Kunze
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) Micha Ben Achim Kunze
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) Micha Ben Achim Kunze
[gmx-users] orca question and LA Micha Ben Achim Kunze
[gmx-users] orca question and LA Micha Ben Achim Kunze
[gmx-users] Running QM/MM in parallel (ORCA/GMX) Micha Ben Achim Kunze
[gmx-users] do_dssp segmentation fault Carsten Kutzner
[gmx-users] do_dssp segmentation fault Carsten Kutzner
[gmx-users] modify the gromacs4.5.5 code: using cout Carsten Kutzner
[gmx-users] Hydrogen database Peter C. Lai
[gmx-users] Pme on gpu performance Peter C. Lai
[gmx-users] Pme on gpu performance Peter C. Lai
[gmx-users] CHARMMff using GROMACS 4.5.3 Gideon Lapidoth
[gmx-users] Pme on gpu performance Matt Larson
[gmx-users] MM/PBSA Gromacs Per Larsson
[gmx-users] equilbium convergence and RMSD structure Justin A. Lemkul
[gmx-users] Re: Structure preparation for the simulation Justin A. Lemkul
[gmx-users] Justin Tutorial - Protein-Ligand Justin A. Lemkul
[gmx-users] Ligand topology in topol.top Justin A. Lemkul
[gmx-users] Ligand topology in topol.top Justin A. Lemkul
[gmx-users] grompp: "invalid bond type" error Justin A. Lemkul
[gmx-users] grompp: "invalid bond type" error Justin A. Lemkul
[gmx-users] Problem regarding Simulation Justin A. Lemkul
[gmx-users] Method insert ion Justin A. Lemkul
[gmx-users] Adding Hydrogens by pdb2gmx Justin A. Lemkul
[gmx-users] tc_grps Justin Tutorial Justin A. Lemkul
[gmx-users] Regarding Gromacs Algorithms Justin A. Lemkul
[gmx-users] re: Phosphate esters Justin A. Lemkul
[gmx-users] Re: Phosphate esters Justin A. Lemkul
[gmx-users] grompp: "invalid bond type" error Justin A. Lemkul
[gmx-users] grompp: "invalid bond type" error Justin A. Lemkul
[gmx-users] how to make top and gro file for acid hexanoic Justin A. Lemkul
[gmx-users] Energy Minimisation Justin A. Lemkul
[gmx-users] umbrella sampling restart Justin A. Lemkul
[gmx-users] www.gromacs.org down? Justin A. Lemkul
[gmx-users] Steered MD in reverse direction? Justin A. Lemkul
[gmx-users] Gromacs query for vaccum medium Justin A. Lemkul
[gmx-users] Thioester bond problem Justin A. Lemkul
[gmx-users] PMF when pulling in -Z direction Justin A. Lemkul
[gmx-users] PMF when pulling in -Z direction Justin A. Lemkul
[gmx-users] query for energy minimization in solvent Justin A. Lemkul
[gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of Justin A. Lemkul
[gmx-users] cutting a trajectory and continuing from a part of it Justin A. Lemkul
[gmx-users] pressure scaling more than 1% Justin A. Lemkul
[gmx-users] fudge QQ values Justin A. Lemkul
[gmx-users] how to make topol.top file for mixed solution Justin A. Lemkul
[gmx-users] how to make topol.top file for mixed solution Justin A. Lemkul
[gmx-users] Regarding Table Extension Justin A. Lemkul
[gmx-users] how to make topol.top file for mixed solution Justin A. Lemkul
[gmx-users] PBC - Protein - ligand Justin A. Lemkul
[gmx-users] Re: umbrella sampling with "pull=constraint" Justin A. Lemkul
[gmx-users] lipid bilayer and umbrella sampling Justin A. Lemkul
[gmx-users] Re: umbrella sampling with "pull=constraint" Justin A. Lemkul
[gmx-users] request for comments on profile.xvg (PMF) courve Justin A. Lemkul
[gmx-users] problem while running production md Justin A. Lemkul
[gmx-users] Re: PBC - Protein - ligand Justin A. Lemkul
[gmx-users] g_hbond -hbn Justin A. Lemkul
[gmx-users] mdp file problem Justin A. Lemkul
[gmx-users] mdp file problem Justin A. Lemkul
[gmx-users] where is Coul-LR? Justin A. Lemkul
[gmx-users] newbie question about GROMACS input files Justin A. Lemkul
[gmx-users] MD structure analysis Justin A. Lemkul
[gmx-users] Error with pdb input Justin A. Lemkul
[gmx-users] Parametrisation of the heteroatomic pdb Justin A. Lemkul
[gmx-users] Error with pdb input Justin A. Lemkul
[gmx-users] what's the meaning of g_msd's -trestart Justin A. Lemkul
[gmx-users] Insertion of the protein into membrane with Gmembed Justin A. Lemkul
[gmx-users] Re: mdp file problem Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] pull_distance Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] UNK not found in residue topology Justin A. Lemkul
[gmx-users] Simulation of membrane protein Justin A. Lemkul
[gmx-users] picking out resident water molecule? Justin A. Lemkul
[gmx-users] Remove water from membrane protein Justin A. Lemkul
[gmx-users] several itp Justin A. Lemkul
[gmx-users] Topology dihedral or improper dihedral Justin A. Lemkul
[gmx-users] The equilibrium before REMD simulations Justin A. Lemkul
[gmx-users] The equilibrium before REMD simulations Justin A. Lemkul
[gmx-users] GMX to remove clashes? Justin A. Lemkul
[gmx-users] UNK not found in residue topology Justin A. Lemkul
[gmx-users] GMX to remove clashes? Justin A. Lemkul
[gmx-users] GMX to remove clashes? Justin A. Lemkul
[gmx-users] how to select option for genion command automatically? Justin A. Lemkul
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION Justin A. Lemkul
[gmx-users] Problem during GROMACS 4.5.5 installation Justin A. Lemkul
[gmx-users] Pressure change after NPT equilibriation Justin A. Lemkul
[gmx-users] Pressure change after NPT equilibriation Justin A. Lemkul
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION Justin A. Lemkul
[gmx-users] Pressure change after NPT equilibriation Justin A. Lemkul
[gmx-users] Umbrella Sampling - Justin tutorial Justin A. Lemkul
[gmx-users] pulling force vs free energy Justin A. Lemkul
[gmx-users] Umbrella Sampling - Justin tutorial Justin A. Lemkul
[gmx-users] pulling force vs free energy Justin A. Lemkul
[gmx-users] calculate potentials of structure Justin A. Lemkul
[gmx-users] H bonds Justin A. Lemkul
[gmx-users] Strange problem.complex out of Box after EM Justin A. Lemkul
[gmx-users] Regarding TIP4P structure Justin A. Lemkul
[gmx-users] Re: Umbrella Sampling - Justin tutorial Justin A. Lemkul
[gmx-users] calculate potential with tabulated non-bonded interactions Justin A. Lemkul
[gmx-users] calculate potential with tabulated non-bonded interactions Justin A. Lemkul
[gmx-users] user contribution Justin A. Lemkul
[gmx-users] Strange problem.complex out of Box after EM Justin A. Lemkul
[gmx-users] calculate potential with tabulated non-bonded interactions Justin A. Lemkul
[gmx-users] GROMACS/ORCA QMMM Justin A. Lemkul
[gmx-users] GROMACS/ORCA QMMM Justin A. Lemkul
[gmx-users] query for energy minimization in solvent Justin A. Lemkul
[gmx-users] fatal occur occuring Justin A. Lemkul
[gmx-users] difference in force fields. Justin A. Lemkul
[gmx-users] problem in NVT equilibration Justin A. Lemkul
[gmx-users] PRODRG2.5 server not found. Justin A. Lemkul
[gmx-users] .rtp file Justin A. Lemkul
[gmx-users] PRODRG server Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] fatal error occuring. Justin A. Lemkul
[gmx-users] fatal error occuring. Justin A. Lemkul
[gmx-users] Extract van der waals surface atoms coordinates Justin A. Lemkul
[gmx-users] Re: g_lie question Justin A. Lemkul
[gmx-users] .ppa file Justin A. Lemkul
[gmx-users] afm simulation Justin A. Lemkul
[gmx-users] simulation of a simple, solvated DPPC membrane Justin A. Lemkul
[gmx-users] afm simulation Justin A. Lemkul
[gmx-users] How to make coordinate file with correct numbering in the atoms when inbetween atoms are removed Justin A. Lemkul
[gmx-users] restraining the ligand. Justin A. Lemkul
[gmx-users] nvt equilibration Justin A. Lemkul
[gmx-users] g_wham error Justin A. Lemkul
[gmx-users] NVT simulation Justin A. Lemkul
[gmx-users] pull parameters Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Index file Justin A. Lemkul
[gmx-users] Protein Complex simulation Justin A. Lemkul
[gmx-users] g_wham error Justin A. Lemkul
[gmx-users] g_wham error Justin A. Lemkul
[gmx-users] query on partial charge entry in topology Justin A. Lemkul
[gmx-users] g_wham error Justin A. Lemkul
[gmx-users] g_wham error Justin A. Lemkul
[gmx-users] g_wham error Justin A. Lemkul
[gmx-users] about temperature coupling Justin A. Lemkul
[gmx-users] GROMACS/ORCA QMMM Justin A. Lemkul
[gmx-users] Increasing time for simulation Justin A. Lemkul
[gmx-users] atomtype OW is not found Justin A. Lemkul
[gmx-users] PRODRG charges Justin A. Lemkul
[gmx-users] removing dihedral Justin A. Lemkul
[gmx-users] force vs displacement Justin A. Lemkul
[gmx-users] removing dihedral Justin A. Lemkul
[gmx-users] UNK not found Justin A. Lemkul
[gmx-users] disable-nice Justin A. Lemkul
[gmx-users] removing dihedral Justin A. Lemkul
[gmx-users] Create gro and top file for hexanoic acid Justin A. Lemkul
[gmx-users] gromacs 4.5.3 and GCC 4.1.x Justin A. Lemkul
[gmx-users] unity in ffbonded.itp Justin A. Lemkul
[gmx-users] CHARMMff using GROMACS 4.5.3 Justin A. Lemkul
[gmx-users] how to edit a .xvg file? Justin A. Lemkul
[gmx-users] Umbrella Sampling tutorial Justin A. Lemkul
[gmx-users] Regarding KALP-15 Simulation Justin A. Lemkul
[gmx-users] Reg : Simulating heterologous protein complex with bound ligand Justin A. Lemkul
[gmx-users] NVT Equilibration Justin A. Lemkul
[gmx-users] Reg : Protein-ligand complex using Amber force field Justin A. Lemkul
[gmx-users] REMD: NPT being +-Infinity or NaN Justin A. Lemkul
[gmx-users] restoration of crashed simulation Justin A. Lemkul
[gmx-users] questions about steer molecular dynamics by using gromacs4 Justin A. Lemkul
[gmx-users] protein hydration shell water Justin A. Lemkul
[gmx-users] how to know the pH of a solution Justin A. Lemkul
[gmx-users] how to know the pH of a solution Justin A. Lemkul
[gmx-users] Regarding inter helical distance using g_bundle Justin A. Lemkul
[gmx-users] Suppress writing step*.pdb files Justin A. Lemkul
[gmx-users] Unit of r in radial distribution function Justin A. Lemkul
[gmx-users] g_select Justin A. Lemkul
[gmx-users] Hydrophobic cores Justin A. Lemkul
[gmx-users] g_select Justin A. Lemkul
[gmx-users] gas-phase protein simulation Justin A. Lemkul
[gmx-users] gas-phase protein simulation Justin A. Lemkul
[gmx-users] g_select dynamic indices Justin A. Lemkul
[gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 " Justin A. Lemkul
[gmx-users] Problems with g_membed tools LindaSong
[gmx-users] Re: Problems with g_membed tools LindaSong
[gmx-users] Re: Problems with g_membed tools LindaSong
[gmx-users] GMX to remove clashes? Liu, Liang
[gmx-users] GMX to remove clashes? Liu, Liang
[gmx-users] GMX to remove clashes? Liu, Liang
[gmx-users] import force field Liu, Liang
[gmx-users] how to select option for genion command automatically? Liu, Liang
[gmx-users] how to select option for genion command automatically? Liu, Liang
[gmx-users] import force field Liu, Liang
[gmx-users] about tabulated potentials Liu, Liang
[gmx-users] about tabulated potentials Liu, Liang
[gmx-users] about tabulated potentials Liu, Liang
[gmx-users] calculate potentials of structure Liu, Liang
[gmx-users] calculate potential with tabulated non-bonded interactions Liu, Liang
[gmx-users] calculate potential with tabulated non-bonded interactions Liu, Liang
[gmx-users] calculate potential with tabulated non-bonded interactions Liu, Liang
[gmx-users] what's the math algorithm? Liu, Liang
[gmx-users] Limit on energygrp_table Liu, Liang
[gmx-users] Limit on energygrp_table Liu, Liang
[gmx-users] Limit on energygrp_table Liu, Liang
[gmx-users] GB implicit solvent - non polar solvation forces Hari Shankar M
[gmx-users] Steered MD in reverse direction? Sanku M
[gmx-users] Steered MD in reverse direction? Sanku M
[gmx-users] Steered MD in reverse direction? Sanku M
[gmx-users] How to calculate work Sanku M
[gmx-users] Gromacs error message Sanku M
[gmx-users] g_wham and entropic subtraction Sanku M
[gmx-users] Query on restraining center of mass of a protein Sanku M
[gmx-users] query on partial charge entry in topology Sanku M
[gmx-users] density of confined water Sanku M
[gmx-users] Cuda not detected Ye MEI
[gmx-users] lipid bilayer and umbrella sampling Giovanni Mancini
[gmx-users] making movie from trajectories Saman Mandegar
[gmx-users] How to use deuterium order parameters Igor Marques
[gmx-users] about tabulated potentials Sikandar Mashayak
[gmx-users] discrepancy trjconv and gmxdump Gavin Melaugh
[gmx-users] discrepancy trjconv and gmxdump Gavin Melaugh
[gmx-users] discrepancy trjconv and gmxdump Gavin Melaugh
[gmx-users] B-factor to large? Input for TLS Henri Mone
[gmx-users] B-factor to large? Input for TLS Henri Mone
[gmx-users] QM/MM energies Jon Mujika
[gmx-users] xtc vs. trr file Juliette N.
[gmx-users] Ice Crystal Structure Nancy
[gmx-users] Ice Crystal Structure Nancy
[gmx-users] lipid bilayer and umbrella sampling Chris Neale
[gmx-users] compiling with the PGI compiler Chris Neale
[gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o Chris Neale
[gmx-users] Justin Tutorial - Protein-Ligand Steven Neumann
[gmx-users] Ligand topology in topol.top Steven Neumann
[gmx-users] Ligand topology in topol.top Steven Neumann
[gmx-users] Ligand topology in topol.top Steven Neumann
[gmx-users] tc_grps Justin Tutorial Steven Neumann
[gmx-users] tc_grps Justin Tutorial Steven Neumann
[gmx-users] Small molecule - CHARMM Steven Neumann
[gmx-users] PBC - Protein - ligand Steven Neumann
[gmx-users] PBC - Protein - ligand Steven Neumann
[gmx-users] Re: PBC - Protein - ligand Steven Neumann
[gmx-users] Re: PBC - Protein - ligand Steven Neumann
[gmx-users] Re: PBC - Protein - ligand Steven Neumann
[gmx-users] g_mindist -on Steven Neumann
[gmx-users] Charged wall Steven Neumann
[gmx-users] Umbrella Sampling - Justin tutorial Steven Neumann
[gmx-users] Umbrella Sampling - Justin tutorial Steven Neumann
[gmx-users] Umbrella Sampling - Justin tutorial Steven Neumann
[gmx-users] Re: Umbrella Sampling - Justin tutorial Steven Neumann
[gmx-users] Re: Umbrella Sampling - Justin tutorial Steven Neumann
[gmx-users] Charged tube Steven Neumann
[gmx-users] Umbrella Sampling tutorial Steven Neumann
[gmx-users] Simulations with unknown structure Steven Neumann
[gmx-users] removing dihedral Francesco Oteri
[gmx-users] removing dihedral Francesco Oteri
[gmx-users] calculating the pmf in constrained force simulations Ramya Parthasarathi
[gmx-users] calculating the pmf in constrained force simulations Ramya Parthasarathi
[gmx-users] Regarding ngmx Luís Pereira
[gmx-users] source of opls Mg2+ parameters? Thomas Piggot
[gmx-users] Parametrisation of the heteroatomic pdb Thomas Piggot
[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs Elizabeth Ploetz
[gmx-users] Re: pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs (Tsjerk Wassenaar) Elizabeth Ploetz
[gmx-users] g_helixorient Poojari, Chetan
[gmx-users] Link to Intel MKL (fftw) via cmake options Szilárd Páll
[gmx-users] Link to Intel MKL (fftw) via cmake options Szilárd Páll
[gmx-users] CygWin and Gromacs 4.5.5 Szilárd Páll
[gmx-users] CygWin and Gromacs 4.5.5 Szilárd Páll
[gmx-users] gromacs 4.5.3 and GCC 4.1.x Szilárd Páll
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Output of g_hbond Hu Qiu
[gmx-users] SASA query R.S.K.Vijayan
[gmx-users] MM/PBSA Gromacs R.S.K.Vijayan
[gmx-users] atomtype OW is not found Doaa Ragab
[gmx-users] How to calculate work Sai Kumar Ramadugu
[gmx-users] pulling force vs free energy Sai Kumar Ramadugu
[gmx-users] CygWin and Gromacs 4.5.5 Mr Bernard Ramos
[gmx-users] CG representation for Organic molecules Venkat Reddy
[gmx-users] non-specific protein-protein interactions Ben Reynwar
[gmx-users] non-specific protein-protein interactions Ben Reynwar
[gmx-users] non-specific protein-protein interactions Ben Reynwar
[gmx-users] Poor exchange probability for REMD Ben Reynwar
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) Christoph Riplinger
[gmx-users] Running QM/MM in parallel (ORCA/GMX) Christoph Riplinger
[gmx-users] orca and Segmentation fault Christoph Riplinger
[gmx-users] GROMACS/ORCA QMMM Christoph Riplinger
[gmx-users] GROMACS/ORCA QMMM Christoph Riplinger
[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Christoph Riplinger
[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Christoph Riplinger
[gmx-users] QM/MM energies Christoph Riplinger
[gmx-users] Hi X Rules
[gmx-users] hi X Rules
[gmx-users] hi X Rules
[gmx-users] I DID IT! X Rules
[gmx-users] Cuda not detected Andrzej Rzepiela
[gmx-users] Cuda not detected Andrzej Rzepiela
[gmx-users] Pme on gpu performance Andrzej Rzepiela
[gmx-users] Pme on gpu performance Andrzej Rzepiela
[gmx-users] Pme on gpu performance Andrzej Rzepiela
[gmx-users] RMSD Gianluca Santoni
[gmx-users] How to obtain .gro file from unfinished simulation? Gianluca Santoni
[gmx-users] H bonds Gianluca Santoni
[gmx-users] Cuda not detected Gianluca Santoni
[gmx-users] Issue in membrane simulation How To Gianluca Santoni
[gmx-users] Output of g_hbond Gianluca Santoni
[gmx-users] T-coupling Gianluca Santoni
[gmx-users] grompp line too long error Gianluca Santoni
[gmx-users] grompp error Gianluca Santoni
[gmx-users] g(r) and <ρB>local Gianluca Santoni
[gmx-users] Regarding inter helical distance using g_bundle Gianluca Santoni
[gmx-users] multiple molecules simulations Gloria Saracino
[gmx-users] multiple molecules simulations Gloria Saracino
[gmx-users] multiple molecules simulations Gloria Saracino
[gmx-users] Re:umbrella sampling with "pull=constraint" Thomas Schlesier
[gmx-users] How to list OPLS parameters Thomas Schlesier
[gmx-users] N-Acetylglucosamine (NAG) in OPLS-AA Ehud Schreiber
[gmx-users] Hydrogen database Ehud Schreiber
[gmx-users] CygWin and Gromacs 4.5.5 Roland Schulz
[gmx-users] remd with different potential at different temperature Roland Schulz
[gmx-users] how to do remd with different tabulated potentials Roland Schulz
[gmx-users] CygWin and Gromacs 4.5.5 Roland Schulz
[gmx-users] No locks available. Roland Schulz
[gmx-users] No locks available. Roland Schulz
[gmx-users] MDRun -append error Roland Schulz
[gmx-users] Re: Restarting a crashed run Roland Schulz
[gmx-users] gas-phase protein simulation Shi, Huilin
[gmx-users] gas-phase protein simulation Shi, Huilin
[gmx-users] Thioester bond problem Yun Shi
[gmx-users] fudge QQ values Yun Shi
[gmx-users] where is Coul-LR? Yun Shi
[gmx-users] where is Coul-LR? Yun Shi
[gmx-users] sudden drop of minimal periodic distance Yun Shi
[gmx-users] Re: sudden drop of minimal periodic distance Yun Shi
[gmx-users] Re: sudden drop of minimal periodic distance Yun Shi
[gmx-users] picking out resident water molecule? Yun Shi
[gmx-users] the force constant in constant speed umbrella pulling Yun Shi
[gmx-users] how to edit a .xvg file? Yun Shi
[gmx-users] how to edit a .xvg file? Yun Shi
[gmx-users] Re: how to edit a .xvg file? Yun Shi
[gmx-users] How DispCorr influsnces pressure Michael Shirts
[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER Michael Shirts
[gmx-users] Pme on gpu performance Alexey Shvetsov
[gmx-users] Time unit issue with g_anaeig Kei Sit
[gmx-users] Time unit issue with g_anaeig Kei Sit
[gmx-users] Time unit issue with g_anaeig Kei Sit
[gmx-users] Dual Processor Intel Xeon X5650 (6 core) versus Quad Processor Opteron series 6100 (12 core) Claudio M. Soares
[gmx-users] Spherical Position Restrain from the center of the Box Ricardo O. S. Soares
[gmx-users] Hbond occupancy Larif Sofiene
[gmx-users] (no subject) Larif Sofiene
[gmx-users] Re: Problems with g_membed tools Wanling Song
[gmx-users] FEP instability David van der Spoel
[gmx-users] Shell MD David van der Spoel
[gmx-users] g_wham and entropic subtraction David van der Spoel
[gmx-users] How DispCorr influsnces pressure David van der Spoel
[gmx-users] Poor exchange probability for REMD David van der Spoel
[gmx-users] Using tables to construct a z-dependent 12-3 potential David van der Spoel
[gmx-users] to gro or not to gro David van der Spoel
[gmx-users] to gro or not to gro David van der Spoel
[gmx-users] g_clustsize David van der Spoel
[gmx-users] to gro or not to gro David van der Spoel
[gmx-users] Using tables to construct a z-dependent 12-3 potential David van der Spoel
[gmx-users] to gro or not to gro David van der Spoel
[gmx-users] g_rdf -com David van der Spoel
[gmx-users] to gro or not to gro David van der Spoel
[gmx-users] Re: gmx-users Dipole David van der Spoel
[gmx-users] .top to .itp file conversion David van der Spoel
[gmx-users] gas-phase protein simulation David van der Spoel
[gmx-users] Questionable van der waals volumes from g_sas Jacob Alan Spooner
[gmx-users] Re: gmx-users Digest, Vol 91, Issue 184 Sławomir Stachura
[gmx-users] Charmm27 ff for membrane protein simulation James Starlight
[gmx-users] Re: Structure preparation for the simulation James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Adding Hydrogens by pdb2gmx James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Normal Mode Analysis James Starlight
[gmx-users] Parametrisation of the heteroatomic pdb James Starlight
[gmx-users] Normal Mode Analysis James Starlight
[gmx-users] Normal Mode Analysis James Starlight
[gmx-users] Normal Mode Analysis James Starlight
[gmx-users] Parametrisation of the heteroatomic pdb James Starlight
[gmx-users] Parametrisation of the heteroatomic pdb James Starlight
[gmx-users] Converting of itp topology files James Starlight
[gmx-users] Converting of itp topology files James Starlight
[gmx-users] Parametrisation of the heteroatomic pdb James Starlight
[gmx-users] Parametrisation of the heteroatomic pdb James Starlight
[gmx-users] Insertion of the protein into membrane with Gmembed James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] Simulation of membrane protein James Starlight
[gmx-users] How to obtain .gro file from unfinished simulation? James Starlight
[gmx-users] Folding of small globular peptide James Starlight
[gmx-users] Pressure stabilization during NPT phase James Starlight
[gmx-users] Pressure stabilization during NPT phase James Starlight
[gmx-users] Pressure stabilization during NPT phase James Starlight
[gmx-users] Potential Energy Landscape Natalie Stephenson
[gmx-users] Potential Energy Landscape Natalie Stephenson
[gmx-users] Potential Energy Landscape Natalie Stephenson
[gmx-users] Topology dihedral or improper dihedral XUEMING TANG
[gmx-users] Topology dihedral or improper dihedral XUEMING TANG
[gmx-users] Estimation of free energy using Linear Response method Vasileios Tatsis
[gmx-users] maybe you are out of quota? Vasileios Tatsis
[gmx-users] mdrun -rerun (not reproducible energy values?) Vasileios Tatsis
[gmx-users] how to edit a .xvg file? Robel Teklebrhan
[gmx-users] how to select option for genion command automatically? Terry
[gmx-users] Gromacs query for vaccum medium Anushree Tripathi
[gmx-users] Gromacs query for vaccum medium Anushree Tripathi
[gmx-users] query for energy minimization in solvent Anushree Tripathi
[gmx-users] gromacs query for force field in vaccum and liquid Anushree Tripathi
[gmx-users] query for energy minimization in solvent Anushree Tripathi
[gmx-users] problem in NVT equilibration Anushree Tripathi
[gmx-users] query regarding source of error Anushree Tripathi
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] GROMACS/ORCA QMMM Jose Tusell
[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Jose Tusell
[gmx-users] Regarding Gromacs Algorithms Ravi Kumar Venkatraman
[gmx-users] Energy Minimisation Ravi Kumar Venkatraman
[gmx-users] Regarding Minimization Ravi Kumar Venkatraman
[gmx-users] Regarding Extension of the potential lookup tables Ravi Kumar Venkatraman
[gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of Ravi Kumar Venkatraman
[gmx-users] Regarding Table Extension Ravi Kumar Venkatraman
[gmx-users] Regarding TIP4P structure Ravi Kumar Venkatraman
[gmx-users] Thanks Justin Lemkul Ravi Kumar Venkatraman
[gmx-users] Regarding Shell Molecular Dynamics Ravi Kumar Venkatraman
[gmx-users] Regarding Dimer calculations Ravi Kumar Venkatraman
[gmx-users] Regarding Simulation of KALP-15 in DPPC Ravi Kumar Venkatraman
[gmx-users] Regarding KALP-15 Simulation Ravi Kumar Venkatraman
[gmx-users] Regarding ngmx Ravi Kumar Venkatraman
[gmx-users] umbrella sampling convergence Vijayaraj
[gmx-users] umbrella sampling restart Vijayaraj
[gmx-users] umbrella sampling with "pull=constraint" Vijayaraj
[gmx-users] Re: umbrella sampling with "pull=constraint" Vijayaraj
[gmx-users] Re: umbrella sampling with "pull=constraint" Vijayaraj
[gmx-users] Re: umbrella sampling with "pull=constraint" Vijayaraj
[gmx-users] diffusion through nanotube Vijayaraj
[gmx-users] pulling force vs free energy Vijayaraj
[gmx-users] pulling force vs free energy Vijayaraj
[gmx-users] PMF with nanotube Vijayaraj
[gmx-users] PMF curve Vijayaraj
[gmx-users] PMF curve Vijayaraj
[gmx-users] Visualizing g_helixorient output NG HUI WEN
[gmx-users] Visualizing g_helixorient output NG HUI WEN
[gmx-users] Regarding Gromacs Algorithms Mirco Wahab
[gmx-users] CygWin and Gromacs 4.5.5 Mirco Wahab
[gmx-users] CygWin and Gromacs 4.5.5 Mirco Wahab
[gmx-users] Kinetic Energy in FEP calculations Connie Wang
[gmx-users] grompp: "invalid bond type" error Olivia Waring
[gmx-users] grompp: "invalid bond type" error Olivia Waring
[gmx-users] grompp: "invalid bond type" error Olivia Waring
[gmx-users] grompp: "invalid bond type" error Olivia Waring
[gmx-users] Using tables to construct a z-dependent 12-3 potential Olivia Waring
[gmx-users] Using tables to construct a z-dependent 12-3 potential Olivia Waring
[gmx-users] Using walls and user defined potentials Olivia Waring
[gmx-users] Regarding Table Extension Dallas Warren
[gmx-users] Re: PBC - Protein - ligand Dallas Warren
[gmx-users] RE: Questionable van der waals volumes from g_sas Dallas Warren
[gmx-users] RE: Questionable van der waals volumes from g_sas Dallas Warren
[gmx-users] The time correlation functions for the orientation of the C-H Dallas Warren
[gmx-users] NVT simulation Dallas Warren
[gmx-users] density Dallas Warren
[gmx-users] density Dallas Warren
[gmx-users] UNK not found Dallas Warren
[gmx-users] Error when try obtain protein energies instead of system energies Dallas Warren
[gmx-users] glutamic acid protonation Dallas Warren
[gmx-users] Regarding Simulation of KALP-15 in DPPC Dallas Warren
[gmx-users] how to know the pH of a solution Dallas Warren
[gmx-users] how to know the pH of a solution Dallas Warren
[gmx-users] Ice Crystal Structure Dallas Warren
[gmx-users] how to understand this sentence Dallas Warren
[gmx-users] PCA on secondary structure of protein. Tsjerk Wassenaar
[gmx-users] PBC - Protein - ligand Tsjerk Wassenaar
[gmx-users] PBC - Protein - ligand Tsjerk Wassenaar
[gmx-users] Re: sudden drop of minimal periodic distance Tsjerk Wassenaar
[gmx-users] Normal Mode Analysis Tsjerk Wassenaar
[gmx-users] Normal Mode Analysis Tsjerk Wassenaar
[gmx-users] Re: sudden drop of minimal periodic distance Tsjerk Wassenaar
[gmx-users] Regarding cosine content Tsjerk Wassenaar
[gmx-users] query regarding source of error Tsjerk Wassenaar
[gmx-users] pyroglutamate in gromos53a6 Tsjerk Wassenaar
[gmx-users] how to obtain NOEs from MD trajectory ? Tsjerk Wassenaar
[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs Tsjerk Wassenaar
[gmx-users] Re: how to edit a .xvg file? Tsjerk Wassenaar
[gmx-users] grompp line too long error Tsjerk Wassenaar
[gmx-users] Time step problem on coarse-grained LJ chain Tsjerk Wassenaar
[gmx-users] pyroglutamate in gromos53a6 Tsjerk Wassenaar
[gmx-users] about relaxation protocol Tsjerk Wassenaar
[gmx-users] Pressure stabilization during NPT phase Tsjerk Wassenaar
[gmx-users] Pressure stabilization during NPT phase Tsjerk Wassenaar
[gmx-users] multiple molecules simulations Tsjerk Wassenaar
[gmx-users] Pressure stabilization during NPT phase Tsjerk Wassenaar
[gmx-users] to gro or not to gro Tsjerk Wassenaar
[gmx-users] to gro or not to gro Tsjerk Wassenaar
[gmx-users] .top to .itp file conversion Tsjerk Wassenaar
[gmx-users] frames in 2 trajectory files Tsjerk Wassenaar
[gmx-users] Suppress writing step*.pdb files Tsjerk Wassenaar
[gmx-users] Suppress writing step*.pdb files Tsjerk Wassenaar
[gmx-users] Unit of r in radial distribution function Tsjerk Wassenaar
[gmx-users] Spherical Position Restrain from the center of the Box Tsjerk Wassenaar
[gmx-users] nonbonded/bonded interactions and the pressure tensor West, Ana
[gmx-users] Water Liquid-vapor interface: Negative surface tension by virial formula? WU Yanbin
[gmx-users] g_hbond -hbn Yao Yao
[gmx-users] protein hydration shell water Yao Yao
[gmx-users] g_select dynamic indices Yao Yao
[gmx-users] about temperature coupling RuiTing Zhang
[gmx-users] about temperature coupling RuiTing Zhang
[gmx-users] density mohammad agha
[gmx-users] density mohammad agha
[gmx-users] g_clustsize mohammad agha
[gmx-users] g_clustsize mohammad agha
[gmx-users] editconf -d mohammad agha
[gmx-users] g_rdf -com mohammad agha
[gmx-users] g_rdf -com mohammad agha
[gmx-users] g_select mohammad agha
[gmx-users] g_select mohammad agha
[gmx-users] problem with extr of g_anaeig agnes
[gmx-users] Thioester bond problem alberto arrigoni
[gmx-users] Disulphur bridge parameters alberto arrigoni
[gmx-users] -ter flag, pdb2gmx alberto arrigoni
[gmx-users] unknown cmap torsion between atoms ram bio
[gmx-users] unknown cmap torsion between atoms ram bio
[gmx-users] charmm 27 gromacs version mdp query ram bio
[gmx-users] charmm 27 FF mdp query ram bio
[gmx-users] PRODRG charges gpat at bioacademy.gr
[gmx-users] refcoord_scaling khuchtumur bumerdene
[gmx-users] Problem regarding Simulation madhumita das
[gmx-users] mdp file problem madhumita das
[gmx-users] mdp file problem madhumita das
[gmx-users] Re: mdp file problem madhumita das
[gmx-users] Generating topology file madhumita das
[gmx-users] g_wham error rajat desikan
[gmx-users] g_wham error rajat desikan
[gmx-users] g_wham error rajat desikan
[gmx-users] g_wham error rajat desikan
[gmx-users] Units of Buckingham potential xiaojing gong
[gmx-users] Units of Buckingham potential xiaojing gong
[gmx-users] Units of Buckingham potential xiaojing gong
[gmx-users] Units of Buckingham potential xiaojing gong
[gmx-users] Units of Buckingham potential xiaojing gong
[gmx-users] Units of Buckingham potential xiaojing gong
[gmx-users] Re: Restarting a crashed run bharat gupta
[gmx-users] Fwd: Restarting a crashed run bharat gupta
[gmx-users] Add ligand molecules in a lipid bilayer parto haghighi
[gmx-users] Add ligand molecules in a lipid bilayer parto haghighi
[gmx-users] .rtp file ibi2010004 at iiita.ac.in
[gmx-users] (no subject) ibi2010004 at iiita.ac.in
[gmx-users] fatal error occuring. ibi2010004 at iiita.ac.in
[gmx-users] .ppa file ibi2010004 at iiita.ac.in
[gmx-users] afm simulation ibi2010004 at iiita.ac.in
[gmx-users] restraining the ligand. ibi2010004 at iiita.ac.in
[gmx-users] pull parameters ibi2010004 at iiita.ac.in
[gmx-users] force vs displacement ibi2010004 at iiita.ac.in
[gmx-users] The time correlation functions for the orientation of the C-H intra\sa175950
[gmx-users] translational diffusion of the water at the micelle surface intra\sa175950
[gmx-users] how to know the pH of a solution baptista at itqb.unl.pt
[gmx-users] simulation of a simple, solvated DPPC membrane undergrad j
[gmx-users] analysing helix dynamics jayant james
[gmx-users] Atomtype 'CR' not found radhika jaswal
[gmx-users] Could g_order be used to calculate the order parameters for the two bonds C1'-H1', C3'-H3' in DNA? jnsong
[gmx-users] T-coupling sarah k
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION arun kumar
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION arun kumar
[gmx-users] (no subject) sangeeta kundu
[gmx-users] g(r) and <ρB>local anna_gromacs at libero.it
[gmx-users] setting working directory lina
[gmx-users] Topology dihedral or improper dihedral lina
[gmx-users] No locks available. lina
[gmx-users] No locks available. lina
[gmx-users] No locks available. lina
[gmx-users] Adding ions using "genion" lina
[gmx-users] diffusion of the water at the micelle surface lina
[gmx-users] how to understand this sentence lina
[gmx-users] Re: how to understand this sentence lina
[gmx-users] PMF when pulling in -Z direction nahren manuel
[gmx-users] PMF when pulling in -Z direction nahren manuel
[gmx-users] PCA on secondary structure of protein. vivek modi
[gmx-users] Re:Re: PCA on secondary structure of protein. vivek modi
[gmx-users] 3D density Map jagannath mondal
[gmx-users] RMSD shahid nayeem
[gmx-users] RMSD shahid nayeem
[gmx-users] how to make top and gro file for acid hexanoic cuong nguyen
[gmx-users] Regarding Table Extension cuong nguyen
[gmx-users] how to make topol.top file for mixed solution cuong nguyen
[gmx-users] how to make topol.top file for mixed solution cuong nguyen
[gmx-users] how to make topol.top file for mixed solution cuong nguyen
[gmx-users] Create gro and top file for hexanoic acid cuong nguyen
[gmx-users] Adding ions using "genion" cuong nguyen
[gmx-users] how to know the pH of a solution cuong nguyen
[gmx-users] Problem during GROMACS 4.5.5 installation sai nitin
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION sai nitin
[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION sai nitin
[gmx-users] removing dihedral francesco oteri
[gmx-users] unity in ffbonded.itp francesco oteri
[gmx-users] Regarding error in ion neutralization step kirubakaran palani
[gmx-users] Regarding error in ion neutralization step kirubakaran palani
[gmx-users] GROMACS/ORCA QMMM swati patel
[gmx-users] fatal occur occuring swati patel
[gmx-users] difference in force fields. swati patel
[gmx-users] PRODRG2.5 server not found. swati patel
[gmx-users] problem obtaining similar force fields for protein and ligand swati patel
[gmx-users] difference in forcefields. swati patel
[gmx-users] PRODRG server swati patel
[gmx-users] fatal error occuring. swati patel
[gmx-users] afm simulation swati patel
[gmx-users] Fwd: afm simulation swati patel
[gmx-users] nvt equilibration swati patel
[gmx-users] NVT simulation swati patel
[gmx-users] (no subject) swati patel
[gmx-users] Index file swati patel
[gmx-users] problem while running production md ansuman at physics.iisc.ernet.in
[gmx-users] glutamic acid protonation quantrum75
[gmx-users] .top to .itp file conversion neeru sharma
[gmx-users] Box in Implicit Solvent Simulations ifat shub
[gmx-users] Regarding cosine content bipin singh
[gmx-users] Regarding cosine content bipin singh
[gmx-users] Regarding cosine content bipin singh
[gmx-users] Regarding inter helical distance using g_bundle bipin singh
[gmx-users] Regarding inter helical distance using g_bundle bipin singh
[gmx-users] Unit of r in radial distribution function bipin singh
[gmx-users] Unit of r in radial distribution function bipin singh
[gmx-users] questions about steer molecular dynamics by using gromacs4 mircial at sjtu.edu.cn
[gmx-users] equilbium convergence and RMSD structure larif sofiene
[gmx-users] MD structure analysis larif sofiene
[gmx-users] H bonds larif sofiene
[gmx-users] Hbond occupancy reference rate larif sofiene
[gmx-users] Topology error archana sonawani
[gmx-users] Ligand charge assignment archana sonawani
[gmx-users] grompp error yp sun
[gmx-users] grompp error yp sun
[gmx-users] grompp error yp sun
[gmx-users] .top to .itp file conversion yp sun
[gmx-users] Atom not found in residue while adding hydrogens yp sun
[gmx-users] Atom not found in residue while adding hydrogens yp sun
[gmx-users] RMSD felmerino at uchile.cl
[gmx-users] File input/output error: 1OTI.pdb nbhutwal at uci.edu
[gmx-users] CygWin and Gromacs 4.5.5 bhf70 at udsu.ru
[gmx-users] CygWin and Gromacs 4.5.5 bhf70 at udsu.ru
[gmx-users] Pme on gpu performance rafapa at us.es
[gmx-users] umbrella sampling convergence chris.neale at utoronto.ca
[gmx-users] source of opls Mg2+ parameters? chris.neale at utoronto.ca
[gmx-users] source of opls Mg2+ parameters? chris.neale at utoronto.ca
[gmx-users] umbrella sampling with "pull=constraint" chris.neale at utoronto.ca
[gmx-users] Charged wall chris.neale at utoronto.ca
[gmx-users] calculating the pmf in constrained force simulations chris.neale at utoronto.ca
[gmx-users] to gro or not to gro chris.neale at utoronto.ca
[gmx-users] diffusion of the water at the micelle surface chris.neale at utoronto.ca
[gmx-users] to gro or not to gro chris.neale at utoronto.ca
[gmx-users] to gro or not to gro chris.neale at utoronto.ca
[gmx-users] diffusion of the water at the micelle surface chris.neale at utoronto.ca
[gmx-users] do_dssp normalization error loan.huynh at utoronto.ca
[gmx-users] restart the mdrun with the checkpoint file xianqiang
[gmx-users] MDRun -append error xianqiang
[gmx-users] MDRun -append error xianqiang
[gmx-users] www.gromacs.org down? mu xiaojia
[gmx-users] calculation equation of g_vanhove xiaowu759
[gmx-users] Force equations of virtual site type 4fdn xuji
[gmx-users] Pressure change after NPT equilibriation shilpa yadahalli
[gmx-users] Shell MD yiran870804
[gmx-users] Shell MD yiran870804
[gmx-users] Shell MD yiran870804
[gmx-users] orca and qm/mm xi zhao
[gmx-users] orca and qm/mm xi zhao
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) xi zhao
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) xi zhao
Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) xi zhao
Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) xi zhao
[gmx-users] ORCA and dummy atom in the gromacs xi zhao
回复： [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao) xi zhao
[gmx-users] orca question and LA xi zhao
[gmx-users] orca question and LA xi zhao
[gmx-users] orca question and LA xi zhao
[gmx-users] orca and Segmentation fault xi zhao
[gmx-users] orca and Segmentation fault xi zhao
[gmx-users] how to set files for free energy caculation? zhongjin
[gmx-users] The equilibrium before REMD simulations ÏéÇ« ¿×
[gmx-users] The equilibrium before REMD simulations ÏéÇ« ¿×
[gmx-users] The equilibrium before REMD simulations ÏéÇ« ¿×
[gmx-users] Poor exchange probability for REMD ÏéÇ« ¿×
[gmx-users] Poor exchange probability for REMD ÏéÇ« ¿×
[gmx-users] pull_distance Алексей Раевский
[gmx-users] several itp Алексей Раевский
[gmx-users] remd- Function not implemented 杜波
[gmx-users] pressure scaling more than 1% 杜波
[gmx-users] remd with different potential at different temperature 杜波
[gmx-users] remd with different potential at different temperature 杜波
[gmx-users] how to do remd with different tabulated potentials 杜波
[gmx-users] what's the meaning of g_msd's -trestart 杜波
[gmx-users] remd :One of the processes started by mpirun has exited with a nonzero exit code. 杜波
[gmx-users] mpirun with remd 杜波
[gmx-users] REMD: when it exchange the replica, it will be bombed!! 杜波
[gmx-users] Re: do remd in npt enmable with warning :pressure scaling more than 1%, mu: 1.01087 1.01087 1.01087 杜波
[gmx-users] do remd in the npt ensemble:Warning: pressure scaling more than 1%, mu: 333821 333821 333821 杜波
[gmx-users] remd :Step 1000002 Warning: pressure scaling more than 1%, mu: 333821 333821 333821 杜波
[gmx-users] REMD: NPT being +-Infinity or NaN 杜波
[gmx-users] remd in the npt ensemble: When the exchange, the temperature abruptly surge . 杜波
[gmx-users] modify the gromacs4.5.5 code: using cout 杜波
[gmx-users] grompp line too long error 杨伟
[gmx-users] grompp line too long error 杨伟
[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures 蕭翔駿
[gmx-users] Hydrophobic cores 김현식

Last message date: Wed Nov 30 23:00:10 CET 2011
Archived on: Thu Nov 14 12:11:57 CET 2013

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