June 2010 Archives by author

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Starting: Tue Jun 1 00:22:36 CEST 2010
Ending: Wed Jun 30 23:53:58 CEST 2010
Messages: 813

[gmx-users] water clusters MD Mark Abraham
[gmx-users] vibrational spectra of glucose Mark Abraham
Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. Mark Abraham
[gmx-users] water clusters MD Mark Abraham
[gmx-users] Constraint causing system to explode Mark Abraham
[gmx-users] g_energy & graph .xvg Mark Abraham
[gmx-users] C-alpha group Mark Abraham
Re: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. Mark Abraham
[gmx-users] Forces on atom which is shifted out of the minimum Mark Abraham
[gmx-users] Visualizing of a peptide in a water box - using trjconv Mark Abraham
[gmx-users] g_covar Mark Abraham
[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms Mark Abraham
[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms Mark Abraham
[gmx-users] Running gromacs in parallel on multicore machine Mark Abraham
[gmx-users] Running gromacs in parallel on multicore machine Mark Abraham
[gmx-users] Issue with g_energy Mark Abraham
[gmx-users] water clusters MD Mark Abraham
Re: Re: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. Mark Abraham
[gmx-users] pdb2gmx renumbers the residues in my pdb file Mark Abraham
[gmx-users] Extracting enthalpies during or after MD Mark Abraham
[gmx-users] Creation of a Non-Standard Residue Mark Abraham
[gmx-users] extra non bonded interaction Mark Abraham
[gmx-users] Extracting enthalpies during or after MD Mark Abraham
[gmx-users] Creation of a Non-Standard Residue Mark Abraham
[gmx-users] Creation of a Non-Standard Residue Mark Abraham
[gmx-users] Is there a way to energy minimize only part of macromolecular structure? Mark Abraham
[gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out Mark Abraham
[gmx-users] PME problem on BG/P cluster Mark Abraham
[gmx-users] PME problem on BG/P cluster Mark Abraham
[gmx-users] Extracting enthalpies during or after MD Mark Abraham
[gmx-users] How to increase the tolerance for conjugate gradient minimization Mark Abraham
[gmx-users] Constraint causing system to explode Mark Abraham
[gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD Mark Abraham
[gmx-users] taking snapshots of the protein after simulation Mark Abraham
[gmx-users] which flag for the force Mark Abraham
[gmx-users] add external force Mark Abraham
[gmx-users] add external force Mark Abraham
[gmx-users] PME problem on BG/P cluster Mark Abraham
[gmx-users] Reduced LJ Units Mark Abraham
[gmx-users] angle restraints Mark Abraham
[gmx-users] combine position restraints and NPT equlibration in membrane Mark Abraham
[gmx-users] GROMACS on CYGWIN Mark Abraham
[gmx-users] xpm file Mark Abraham
[gmx-users] question about [ pairs ] and interaction 1-4 Mark Abraham
[gmx-users] Positive Total energy Mark Abraham
[gmx-users] sc_power Mark Abraham
[gmx-users] the box lengths Mark Abraham
[gmx-users] Parallel instalation: gmx-users Digest, Vol 74, Issue 76 Mark Abraham
[gmx-users] trjconv index file Mark Abraham
[gmx-users] nonbonded energy contributions Mark Abraham
[gmx-users] constraints bond length vari by 10% Mark Abraham
[gmx-users] trjconv index file Mark Abraham
[gmx-users] constraints bond length vari by 10% Mark Abraham
[gmx-users] covariance analysis? Mark Abraham
[gmx-users] how small rcoulomb can be Mark Abraham
[gmx-users] LIE in reruning PME NPT runs Mark Abraham
[gmx-users] Energy minimization: problems with ramachanrad score Mark Abraham
[gmx-users] 5 identical simulations --> 5 different results, why? Mark Abraham
[gmx-users] constraints bond length vari by 10% Mark Abraham
[gmx-users] git Mark Abraham
[gmx-users] Question about topologies Mark Abraham
[gmx-users] a query about analysis Mark Abraham
[gmx-users] Plotting Energies versus time Mark Abraham
[gmx-users] Installing gromacs from git Mark Abraham
[gmx-users] Installing gromacs from git Mark Abraham
[gmx-users] Re: chain ids (2) Mark Abraham
[gmx-users] Problem of reading the atom'force from trr file using template.c Mark Abraham
[gmx-users] get the mass having the atom type Mark Abraham
[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny Mark Abraham
[gmx-users] .RTP files Mark Abraham
[gmx-users] P4_error for extending coarse grained MD simulations Mark Abraham
[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells Mark Abraham
[gmx-users] Bond Energies Absent Mark Abraham
[gmx-users] Error in MD simulation Mark Abraham
[gmx-users] Problems with installing mpi-version of Gromacs Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] [ dihedraltypes ] Mark Abraham
[gmx-users] B-factor Mark Abraham
[gmx-users] Simulatimg two proteins in water system Mark Abraham
[gmx-users] g_msd and diffusion coefficent Mark Abraham
[gmx-users] g_msd and diffusion coefficent Mark Abraham
[gmx-users] g_msd and diffusion coefficent Mark Abraham
[gmx-users] mdrun_mpi issue. Mark Abraham
[gmx-users] REMD Mark Abraham
[gmx-users] the job is not being distributed Mark Abraham
[gmx-users] Re:Chain terminus Mark Abraham
[gmx-users] question about Gromacs and Spectroscopy Mark Abraham
[gmx-users] Help with defining new residue (OXY--HEME) Omololu Akin-Ojo
[gmx-users] Help with defining new residue (OXY--HEME) Omololu Akin-Ojo
[gmx-users] Re: acetonitrile from amber to gromacs Alan
[gmx-users] Re: Adding Partial Charges for Small Molecules Alan
[gmx-users] question about [ pairs ] and interaction 1-4 Alan
[gmx-users] Re: question about [ pairs ] and interaction 1-4 Alan
[gmx-users] Problems with installing mpi-version of Gromacs Pinchas Aped
[gmx-users] (no subject) Amin Arabbagheri
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134 Amin Arabbagheri
[gmx-users] multiple dihedrals Amin Arabbagheri
[gmx-users] error in hydrocarbon dihedrals of opls-aa? Vasilii Artyukhov
[gmx-users] GROMACS on CYGWIN Vasilii Artyukhov
[gmx-users] Enough hydration of the channel Aswathy
[gmx-users] Enough hydration of the channel Aswathy
[gmx-users] Enough hydration of the channel Aswathy
[gmx-users] Query on WHAM analysis Aswathy
[gmx-users] umbrella sampling-Bimodal Histograms Aswathy
[gmx-users] umbrella sampling-Bimodal Histograms Aswathy
[gmx-users] umbrella sampling-Bimodal Histograms Aswathy
[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells Marc Baaden
[gmx-users] redundancies in the .itp file Víctor Bahamonde
[gmx-users] redundancies in the .itp file Víctor Bahamonde
[gmx-users] GROMACS on CYGWIN Nasim Biglari
[gmx-users] gromacs (git) with charmm FF lipid freezing problem David Caplan
[gmx-users] Selecting specific atoms to find average energy of Jennifer Casey
[gmx-users] generation of bilayer structures Javier Cerezo
[gmx-users] Re: Simulation with CsCl Vitaly Chaban
[gmx-users] Re: printing coordinates using template.c Vitaly Chaban
[gmx-users] Re: GROMACS on CYGWIN Vitaly Chaban
[gmx-users] restraints in one direction Vitaly Chaban
[gmx-users] Re: parameters of Sodium Sulfate Vitaly Chaban
[gmx-users] Re: parameters of Sodium Sulfate Vitaly Chaban
[gmx-users] Re: write topology by hand Vitaly Chaban
[gmx-users] Re: the box lengths Vitaly Chaban
[gmx-users] Re: moleculetype CU1+ is redefined Vitaly Chaban
[gmx-users] Re: Diffusion constant Vitaly Chaban
[gmx-users] Re: g_msd and diffusion coefficent Vitaly Chaban
[gmx-users] Re: Diffusion constant Vitaly Chaban
[gmx-users] Re: Diffusion constant Vitaly Chaban
[gmx-users] Re: g_msd and diffusion coefficent Vitaly Chaban
[gmx-users] liquid-vapor Vitaly Chaban
[gmx-users] Re:g_msd and diffusion coefficent Vitaly Chaban
[gmx-users] Re: multiple time step Vitaly Chaban
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 182 Vitaly Chaban
[gmx-users] RE: g_msd and diffusion coefficent Vitaly Chaban
[gmx-users] Re: using x2top to convert a gro file to a top file Vitaly Chaban
[gmx-users] Re: using x2top to convert a gro file to a top file Vitaly Chaban
[gmx-users] preprocessing in position restrained step, problem with binary top file Xi Cheng
[gmx-users] g_ hbond on two peptides Hsin-Lin Chiang
[gmx-users] Re: g_ hbond on two peptides Hsin-Lin Chiang
[gmx-users] FEP for amino acid mutations. Matteo De Chiara
[gmx-users] FEP for amino acid mutations. Matteo De Chiara
[gmx-users] FEP for amino acid mutations Matteo De Chiara
[gmx-users] template.c Chandan Choudhury
[gmx-users] printing coordinates using template.c Chandan Choudhury
[gmx-users] standard state correction of delta G from a PMF Elio Cino
[gmx-users] standard state correction of delta G from a PMF Elio Cino
[gmx-users] standard state correction of delta G from a PMF Elio Cino
[gmx-users] Energy minimisation of solvated protein - Tutorial Nayef Daher
[gmx-users] FWSpider Tutorial Nayef Daher
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 189 Nayef Daher
[gmx-users] anisotropic pressure coupling Shuangxing Dai
[gmx-users] Re: anisotropic pressure coupling Shuangxing Dai
[gmx-users] anisotropic pressure coupling Shuangxing Dai
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84 Shuangxing Dai
[gmx-users] Overflow problem with test-particle insertion Kevin Daly
[gmx-users] vibrational spectra of glucose Nilesh Dhumal
[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms Nilesh Dhumal
[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms Nilesh Dhumal
[gmx-users] equilibration + Segmentation fault Nilesh Dhumal
[gmx-users] equilibration + Segmentation fault Nilesh Dhumal
[gmx-users] Discrete structure factor from g_rdf Florian Dommert
[gmx-users] how small rcoulomb can be Florian Dommert
[gmx-users] Non-conservation of total energy while using structure file to resume the simulation Dmitri Dubov
[gmx-users] Non-conservation of total energy while using structure file to resume the simulation Dmitri Dubov
[gmx-users] g_dipoles, average not the same as from g_analyze Dmitri Dubov
[gmx-users] 5 identical simulations --> 5 different results, why? Dmitri Dubov
[gmx-users] how to correct velocities in trajectory file Dmitri Dubov
[gmx-users] number of water molecules affects the PMF Ozge Engin
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 13 Ozge Engin
[gmx-users] number of water molecules affects the PMF Ozge Engin
[gmx-users] output of the -hist option of the g_wham command Ozge Engin
[gmx-users] Energy minimization: problems with ramachanrad score Thomas Evangelidis
[gmx-users] Energy minimization: problems with ramachanrad score Thomas Evangelidis
[gmx-users] Gromacs to APBS Rodrigo Faccioli
[gmx-users] PMF in vacuum and pull direction (chris.neale at utoronto.ca) Eudes Fileti
[gmx-users] PMF in vacuum and pull direction (chris.neale at utoronto.ca) Eudes Fileti
[gmx-users] PMF in vacuum and pull direction (chris.neale at utoronto.ca) Eudes Fileti
[gmx-users] How to increase the tolerance for conjugate gradient minimization Ran Friedman
[gmx-users] Re: Simulation with CsCl Ran Friedman
[gmx-users] Electric field, potential, dielectric constant Ran Friedman
[gmx-users] large forces and monstrous water molecules in energy minimization step Ran Friedman
[gmx-users] Constraint causing system to explode Warren Gallin
[gmx-users] Constraint causing system to explode Warren Gallin
[gmx-users] Questions about g_sham Warren Gallin
[gmx-users] Questions about g_sham Warren Gallin
[gmx-users] Questions about g_sham Warren Gallin
[gmx-users] Help! --- Permission denied (publickey, gssapi-with-mic, password). Yan Gao
[gmx-users] Simulation with CsCl Cecilia Fernándz Gauna
[gmx-users] Helix Tilt Calculation Anirban Ghosh
[gmx-users] Helix Tilt Calculation Anirban Ghosh
[gmx-users] Helix Tilt Calculation Anirban Ghosh
[gmx-users] martini nanotube parameters Umesh Ghoshdastider
[gmx-users] how small rcoulomb can be Gaurav Goel
[gmx-users] how small rcoulomb can be Gaurav Goel
[gmx-users] how small rcoulomb can be Gaurav Goel
[gmx-users] problem install gromacs in parallel Gaurav Goel
[gmx-users] vdwtype=shift Gaurav Goel
[gmx-users] Should I use separate PME nodes Gaurav Goel
[gmx-users] pdb2gmx renumbers the residues in my pdb file Oliver Grant
Subject: [gmx-users] error compiling mopac and gromacs Gerrit Groenhof
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 183 Gerrit Groenhof
[gmx-users] gromacs installation and test set Gu, Xiang
[gmx-users] gromacs installation and test set Gu, Xiang
[gmx-users] Meaning of bPBC Gu, Xiang
[gmx-users] Diffusion constant Ricardo Cuya Guizado
[gmx-users] RE: Diffusion constant Ricardo Cuya Guizado
[gmx-users] RE: Diffusion constant Ricardo Cuya Guizado
[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures Berk Hess
[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures Berk Hess
[gmx-users] constraints bond length vari by 10% Berk Hess
[gmx-users] pull_pbcatom reporting strangely when set to 0 Berk Hess
[gmx-users] fcstep value for shell particles Berk Hess
[gmx-users] multiple time step Berk Hess
[gmx-users] Visualizing of a peptide in a water box - using trjconv Birgit Hischenhuber
AW: [gmx-users] Visualizing of a peptide in a water box - usingtrjconv Birgit Hischenhuber
[gmx-users] Problem on forming bonds Kwee Hong
[gmx-users] QMMM cpmd Stefan Hoorman
[gmx-users] g_rdf has a huge memory leak. Kun Huang
[gmx-users] grompp fatal error Unknown bond_atomtype Peter Huwe
[gmx-users] grompp fatal error Unknown bond_atomtype Peter Huwe
[gmx-users] g_energy & graph .xvg Carla Jamous
[gmx-users] g_energy & graph .xvg Carla Jamous
[gmx-users] g_rmsf -res Carla Jamous
[gmx-users] g_rmsf -res Carla Jamous
[gmx-users] g_rmsf -res Carla Jamous
[gmx-users] xpm file Carla Jamous
[gmx-users] covariance analysis? Carla Jamous
[gmx-users] g_anaeig -proj Carla Jamous
[gmx-users] Dimer g_rms Carla Jamous
[gmx-users] Dimer g_rms Carla Jamous
[gmx-users] g_dihfix program VANDANA KUMARI
[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures Godwin Kanu
[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures Godwin Kanu
[gmx-users] CG (MARTINI) parameters for RNA Itamar Kass
[gmx-users] PBC Morteza Khabiri
[gmx-users] Helix Tilt Calculation George Khelashvili
[gmx-users] extra non bonded interaction Thanasis Koukoulas
[gmx-users] Coulomb (SR) problem Thanasis Koukoulas
[gmx-users] Positive Total energy Thanasis Koukoulas
[gmx-users] Positive Total energy Thanasis Koukoulas
[gmx-users] Question about topologies Thanasis Koukoulas
[gmx-users] Energy calculation Thanasis Koukoulas
[gmx-users] Energy miscalculation Thanasis Koukoulas
[gmx-users] Re: Energy miscalculation Thanasis Koukoulas
[gmx-users] Energy miscalculation Thanasis Koukoulas
[gmx-users] Re: Energy miscalculation Thanasis Koukoulas
[gmx-users] Re: Energy miscalculation Thanasis Koukoulas
[gmx-users] Re: Energy miscalculation Thanasis Koukoulas
[gmx-users] Re: Energy miscalculation Thanasis Koukoulas
[gmx-users] Visualizing of a peptide in a water box - using trjconv Kukol, Andreas
[gmx-users] Visualizing of a peptide in a water box - usingtrjconv Kukol, Andreas
[gmx-users] FES and FE molecule topology Kukol, Andreas
[gmx-users] free energy landscape question Kukol, Andreas
[gmx-users] question about how to install g_tune_pme Carsten Kutzner
[gmx-users] Parallel installation Carsten Kutzner
[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 Carsten Kutzner
[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 Carsten Kutzner
[gmx-users] (no subject) Carsten Kutzner
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134 Carsten Kutzner
[gmx-users] Should I use separate PME nodes Carsten Kutzner
[gmx-users] the job is not being distributed Carsten Kutzner
[gmx-users] the job is not being distributed Carsten Kutzner
[gmx-users] ED sampling Carsten Kutzner
[gmx-users] the job is not being distributed Carsten Kutzner
[gmx-users] velocity autocorrelation function. #ZHAO LINA#
[gmx-users] velocity autocorrelation function. #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] the box lengths #ZHAO LINA#
[gmx-users] No default Proper Dih. types #ZHAO LINA#
[gmx-users] Energy minimisation of solvated protein - Tutorial #ZHAO LINA#
[gmx-users] Electric field, potential, dielectric constant Vladimir Lankevich
[gmx-users] Gromacs to APBS Vladimir Lankevich
[gmx-users] Charmm without CMAP Per Larsson
[gmx-users] Re: gromacs with CMAP Per Larsson
[gmx-users] add missing atoms Justin A. Lemkul
[gmx-users] add missing atom(s) Justin A. Lemkul
[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ? Justin A. Lemkul
[gmx-users] anisotropic pressure coupling Justin A. Lemkul
[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms Justin A. Lemkul
[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms Justin A. Lemkul
[gmx-users] question about compass ff Justin A. Lemkul
[gmx-users] question about compass ff Justin A. Lemkul
[gmx-users] RE:Range checking error Justin A. Lemkul
[gmx-users] Strange bilayer behavior in protein-multimembrane models Justin A. Lemkul
[gmx-users] Position restraint for 2ns Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] gromacs installation and test set Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] gromacs installation and test set Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] 1-4 interaction not within cut-off Justin A. Lemkul
[gmx-users] intermolecular contributions/building up a long polymer chain Justin A. Lemkul
[gmx-users] Creation of a Non-Standard Residue Justin A. Lemkul
[gmx-users] Regarding genconf Justin A. Lemkul
[gmx-users] 1-4 interaction not within cut-off Justin A. Lemkul
[gmx-users] 1-4 interaction not within cut-off Justin A. Lemkul
[gmx-users] 1-4 interaction not within cut-off Justin A. Lemkul
[gmx-users] 1-4 interaction not within cut-off Justin A. Lemkul
[gmx-users] equilibration + Segmentation fault Justin A. Lemkul
[gmx-users] equilibration + Segmentation fault Justin A. Lemkul
[gmx-users] taking snapshots of the protein after simulation Justin A. Lemkul
[gmx-users] helical parameters for DNA Justin A. Lemkul
[gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions Justin A. Lemkul
[gmx-users] Simulation with CsCl Justin A. Lemkul
[gmx-users] 100 step md run: Infinite giga flopses error Justin A. Lemkul
[gmx-users] printing coordinates using template.c Justin A. Lemkul
[gmx-users] building long polymer chain Justin A. Lemkul
[gmx-users] Re: Simulation with CsCl Justin A. Lemkul
[gmx-users] tracking the time for an md run Justin A. Lemkul
[gmx-users] field-specified name for sulfate Justin A. Lemkul
[gmx-users] structure file long chains Justin A. Lemkul
[gmx-users] Position restrained Dynamics Justin A. Lemkul
[gmx-users] problems when using command "trjconv" Justin A. Lemkul
[gmx-users] restarting simulation Justin A. Lemkul
[gmx-users] pressure scaling more than 1% Justin A. Lemkul
[gmx-users] combine position restraints and NPT equlibration in membrane Justin A. Lemkul
[gmx-users] Selecting specific atoms to find average energy of Justin A. Lemkul
[gmx-users] write topology by hand Justin A. Lemkul
[gmx-users] Andersen thermostat Justin A. Lemkul
[gmx-users] epsilon_r Justin A. Lemkul
[gmx-users] soft-core Justin A. Lemkul
[gmx-users] Adding Partial Charges for Small Molecules Justin A. Lemkul
[gmx-users] Re:gmx-users Digest, Vol 74, Issue 73 Justin A. Lemkul
[gmx-users] position restraint....NEED URGENT HELP Justin A. Lemkul
[gmx-users] the box lengths Justin A. Lemkul
[gmx-users] the box lengths Justin A. Lemkul
[gmx-users] the box lengths Justin A. Lemkul
[gmx-users] moleculetype CU1+ is redefined Justin A. Lemkul
[gmx-users] ions.itp Justin A. Lemkul
[gmx-users] Disk Space Justin A. Lemkul
[gmx-users] Disk Space Justin A. Lemkul
[gmx-users] anisotropic pressure coupling Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84 (anisotropic pressure coupling) Justin A. Lemkul
[gmx-users] the box lengths Justin A. Lemkul
[gmx-users] martini nanotube parameters Justin A. Lemkul
[gmx-users] Re: trjconv index file Justin A. Lemkul
[gmx-users] Re: question about [ pairs ] and interaction 1-4 Justin A. Lemkul
[gmx-users] Re: question about [ pairs ] and interaction 1-4 Justin A. Lemkul
[gmx-users] redundancies in the .itp file Justin A. Lemkul
[gmx-users] trjconv index file Justin A. Lemkul
[gmx-users] trjconv index file Justin A. Lemkul
[gmx-users] redundancies in the .itp file Justin A. Lemkul
[gmx-users] 5 identical simulations --> 5 different results, why? Justin A. Lemkul
[gmx-users] redundancies in the .itp file Justin A. Lemkul
[gmx-users] redundancies in the .itp file Justin A. Lemkul
[gmx-users] question on merging trajectories files Justin A. Lemkul
[gmx-users] Forcefields for proteins Justin A. Lemkul
[gmx-users] How to update the neighbor list heuristically? Justin A. Lemkul
[gmx-users] Re: His protonation Justin A. Lemkul
[gmx-users] Re: His protonation Justin A. Lemkul
[gmx-users] System net charge Justin A. Lemkul
[gmx-users] large forces and monstrous water molecules in energy minimization step Justin A. Lemkul
[gmx-users] [pairs] and [dihedrals] Justin A. Lemkul
[gmx-users] git Justin A. Lemkul
[gmx-users] Enough hydration of the channel Justin A. Lemkul
[gmx-users] Re: His protonation Justin A. Lemkul
[gmx-users] Incomplete ring Justin A. Lemkul
[gmx-users] Plotting Energies versus time Justin A. Lemkul
[gmx-users] Charmm force field with gromacs Justin A. Lemkul
[gmx-users] building up a long polymer chain Justin A. Lemkul
[gmx-users] Charmm force field with gromacs Justin A. Lemkul
[gmx-users] selection of group in do_dssp Justin A. Lemkul
[gmx-users] No default Proper Dih. types Justin A. Lemkul
[gmx-users] Merge Trajectories Justin A. Lemkul
[gmx-users] Installing gromacs from git Justin A. Lemkul
[gmx-users] Overriding atomtype O Justin A. Lemkul
[gmx-users] A confusion about domain decomposition Justin A. Lemkul
[gmx-users] Installing gromacs from git Justin A. Lemkul
[gmx-users] Re: Exact run continuation Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Help with defining new residue (OXY--HEME) Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] building up a long polymer chain Justin A. Lemkul
[gmx-users] RE:Multiple chain ID's Justin A. Lemkul
[gmx-users] error in parallel mdrun Justin A. Lemkul
[gmx-users] PRODRG crash Justin A. Lemkul
[gmx-users] building up a long polymer chain Justin A. Lemkul
[gmx-users] Help in parametrisation Justin A. Lemkul
[gmx-users] building up a polymer chain Justin A. Lemkul
[gmx-users] Questions about g_sham Justin A. Lemkul
[gmx-users] Questions about g_sham Justin A. Lemkul
[gmx-users] Position Restrained Simulation for Coarse Grained DSPC Justin A. Lemkul
[gmx-users] Position Restrained Simulation for Coarse Grained DSPC Justin A. Lemkul
[gmx-users] grompp fatal error Unknown bond_atomtype Justin A. Lemkul
[gmx-users] Help in parametrisation Justin A. Lemkul
[gmx-users] General Question Justin A. Lemkul
[gmx-users] Making a .rtp file Justin A. Lemkul
[gmx-users] Weird error with g_sorient Justin A. Lemkul
[gmx-users] Re: vdwtype=shift Justin A. Lemkul
[gmx-users] Help in parametrisation Justin A. Lemkul
[gmx-users] Re: .RTP files Justin A. Lemkul
[gmx-users] Replicating monomer units-problem with geometry of connecting atoms Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 143 Justin A. Lemkul
[gmx-users] error while loading shared libraries: libOpenMM.so: Justin A. Lemkul
[gmx-users] g_msd and diffusion coefficent Justin A. Lemkul
[gmx-users] RE: Diffusion constant Justin A. Lemkul
[gmx-users] CL atom not being recognised Justin A. Lemkul
[gmx-users] Technical Justin A. Lemkul
[gmx-users] Re: Mixed Solvents Preparation? Justin A. Lemkul
[gmx-users] REMD Justin A. Lemkul
[gmx-users] Replicating monomer units Justin A. Lemkul
[gmx-users] automating analysis using shell scripting Justin A. Lemkul
[gmx-users] question about Gromacs and Spectroscopy Justin A. Lemkul
[gmx-users] Pull code Justin A. Lemkul
[gmx-users] Pull code Justin A. Lemkul
[gmx-users] index groups Justin A. Lemkul
[gmx-users] Using x2top to convert a gro file to a top file Justin A. Lemkul
[gmx-users] FWSpider Tutorial Justin A. Lemkul
[gmx-users] Re: using x2top to convert a gro file to a top file Justin A. Lemkul
[gmx-users] free energy landscape question Marc F. Lensink
[gmx-users] No convergence in Diffusion Coefficient Igor Leontyev
[gmx-users] No convergence in Diffusion Coefficient Igor Leontyev
[gmx-users] Temperature decreasing with NVE MARTINI lipid simulation Michael Lerner
[gmx-users] Temperature decreasing with NVE MARTINI lipid simulation Michael Lerner
[gmx-users] Re: Temperature decreasing with NVE MARTINI lipid simulation Michael Lerner
[gmx-users] Re: gromacs with CMAP Da-Wei Li
[gmx-users] Re: gromacs with CMAP Da-Wei Li
[gmx-users] Re: gromacs with CMAP Da-Wei Li
[gmx-users] Re: gromacs with CMAP Da-Wei Li
[gmx-users] what is the eigenvalue unit in Gromacs? DeChang Li
[gmx-users] How to increase the tolerance for conjugate gradient minimization Erik Lindahl
[gmx-users] Openings for talented programmers/postdocs who'd like to work on simulations Erik Lindahl
[gmx-users] PME problem on BG/P cluster LuLanyuan
[gmx-users] PME problem on BG/P cluster LuLanyuan
[gmx-users] PME problem on BG/P cluster LuLanyuan
[gmx-users] PME problem on BG/P cluster LuLanyuan
[gmx-users] combine position restraints and NPT equlibration in membrane Mahnam
[gmx-users] combine position restraints and NPT equlibration in membrane Mahnam
[gmx-users] A confusion about domain decomposition Amir Marcovitz
[gmx-users] output of the -hist option of the g_wham command Amir Marcovitz
[gmx-users] error in parallel mdrun Amir Marcovitz
[gmx-users] Query regarding g_rmsf and g_hbond Erik Marklund
[gmx-users] g_energy & graph .xvg Erik Marklund
[gmx-users] g_energy & graph .xvg Erik Marklund
[gmx-users] g_ hbond on two peptides Erik Marklund
[gmx-users] NPT system density Erik Marklund
[gmx-users] g_rmsf -res Erik Marklund
[gmx-users] Average pdb coordinates Erik Marklund
[gmx-users] Question about topologies Erik Marklund
[gmx-users] a query about analysis Erik Marklund
[gmx-users] get the mass having the atom type Erik Marklund
[gmx-users] vdwtype=shift Erik Marklund
[gmx-users] B-factor Erik Marklund
[gmx-users] B-factor Erik Marklund
Antw: [gmx-users] multiple time step Erik Marklund
[gmx-users] Re: multiple time step Erik Marklund
[gmx-users] Dimer g_rms Erik Marklund
[gmx-users] b-factor Erik Marklund
[gmx-users] Running gromacs in parallel on multicore machine Sikandar Mashayak
[gmx-users] Running gromacs in parallel on multicore machine Sikandar Mashayak
[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox Sikandar Mashayak
[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox Sikandar Mashayak
[gmx-users] tutorial on channel simulations Sikandar Mashayak
[gmx-users] restarting simulation Gavin Melaugh
[gmx-users] restarting simulation Gavin Melaugh
[gmx-users] error in parallel mdrun Gavin Melaugh
[gmx-users] Pull code Gavin Melaugh
[gmx-users] Pull code Gavin Melaugh
[gmx-users] intermolecular contributions/building up a long polymer chain Moeed
[gmx-users] NPT system density Moeed
[gmx-users] building long polymer chain Moeed
[gmx-users] structure file long chains Moeed
[gmx-users] nonbonded energy contributions Moeed
[gmx-users] building up a long polymer chain Moeed
[gmx-users] building up a long polymer chain Moeed
[gmx-users] PRODRG crash Moeed
[gmx-users] building up a long polymer chain Moeed
[gmx-users] building up a polymer chain Moeed
[gmx-users] Replicating monomer units-problem with geometry of connecting atoms Moeed
[gmx-users] Replicating monomer units Moeed
[gmx-users] index groups Moeed
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny Christian Mücksch
[gmx-users] Adding Partial Charges for Small Molecules Nancy
[gmx-users] Adding Partial Charges for Small Molecules Nancy
[gmx-users] .RTP files P.R.Anand Narayanan
[gmx-users] Re: .RTP files P.R.Anand Narayanan
[gmx-users] How to view evolution of secondary structure in a trajectory? Chris Neale
[gmx-users] question about compass ff Andrei Neamtu
[gmx-users] question about compass ff Andrei Neamtu
[gmx-users] free energy landscape question Andrei Neamtu
[gmx-users] free energy landscape question Andrei Neamtu
[gmx-users] free energy landscape question Andrei Neamtu
[gmx-users] free energy landscape question Andrei Neamtu
[gmx-users] convert traj file between diff gromacs versions Alcides Nicastro
[gmx-users] OPLS-AA topologies for ATP Efrat Noy
[gmx-users] water clusters MD Oleksandr
[gmx-users] water clusters MD Oleksandr
[gmx-users] water clusters MD Oleksandr
[gmx-users] question about how to install g_tune_pme Yi Peng
[gmx-users] g_ hbond on two peptides XAvier Periole
[gmx-users] number of water molecules affects the PMF XAvier Periole
[gmx-users] number of water molecules affects the PMF XAvier Periole
[gmx-users] Helix Tilt Calculation XAvier Periole
[gmx-users] Helix Tilt Calculation XAvier Periole
[gmx-users] problems when using command "trjconv" XAvier Periole
[gmx-users] restarting simulation XAvier Periole
[gmx-users] Selecting specific atoms to find average energy of XAvier Periole
[gmx-users] Dimer g_rms XAvier Periole
[gmx-users] -dt XAvier Periole
[gmx-users] Dimer g_rms XAvier Periole
[gmx-users] g_dipoles, take the normal of the computational box Emanuel Peter
[gmx-users] g_dipoles, average not the same as from g_analyze Emanuel Peter
[gmx-users] g_dipoles, average not the same as from g_analyze Emanuel Peter
Antw: [gmx-users] multiple time step Emanuel Peter
[gmx-users] FWSpider Tutorial Peicho Petkov
[gmx-users] OPLS-AA topologies for ATP Thomas Piggot
[gmx-users] OPLS-AA topologies for ATP Thomas Piggot
[gmx-users] Issue with g_energy Gene Polovy
[gmx-users] 100 step md run: Infinite giga flopses error Sai Pooja
[gmx-users] 100 step md run: Infinite giga flopses error Sai Pooja
[gmx-users] Reduced LJ Units Sai Pooja
[gmx-users] Reduced LJ Units Sai Pooja
[gmx-users] Andersen thermostat Sai Pooja
[gmx-users] git Sai Pooja
[gmx-users] git Sai Pooja
[gmx-users] charmm 22 all atom Sai Pooja
[gmx-users] Charmm force field with gromacs Sai Pooja
[gmx-users] Installing gromacs from git Sai Pooja
[gmx-users] Installing gromacs from git Sai Pooja
[gmx-users] Installing gromacs from git Sai Pooja
[gmx-users] Installing gromacs from git Sai Pooja
[gmx-users] Installing gromacs from git Sai Pooja
[gmx-users] Charmm without CMAP Sai Pooja
[gmx-users] Charmm without CMAP Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] error while loading shared libraries: libOpenMM.so: Szilárd Páll
[gmx-users] question about Gromacs and Spectroscopy Baofu Qiao
[gmx-users] question about Gromacs and Spectroscopy Baofu Qiao
[gmx-users] the job is not being distributed Baofu Qiao
[gmx-users] PBC Sai Kumar Ramadugu
[gmx-users] tutorial of free energy calculations Sai Kumar Ramadugu
[gmx-users] Thr -> Met in TI calculation Sai Kumar Ramadugu
[gmx-users] soft-core Sai Kumar Ramadugu
[gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat. Arthur Roberts
[gmx-users] Is there a way to energy minimize only part of macromolecular structure? Arthur Roberts
[gmx-users] After simulated annealing and then energy minimizing, a docked molecule seems to still be distorted? Arthur Roberts
[gmx-users] How to increase the tolerance for conjugate gradient minimization Arthur Roberts
[gmx-users] How to increase the tolerance for conjugate gradient minimization Arthur Roberts
[gmx-users] Strange bilayer behavior in protein-multimembrane models Thomas Schmidt
[gmx-users] large forces and monstrous water molecules in energy minimization step Ehud Schreiber
[gmx-users] QMMM cpmd Christian Seifert
[gmx-users] Re: QMMM cpmd Christian Seifert
[gmx-users] taking snapshots of the protein after simulation Hassan Shallal
[gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD Hassan Shallal
[gmx-users] taking snapshots of the protein after simulation Hassan Shallal
[gmx-users] automating analysis using shell scripting Hassan Shallal
[gmx-users] automating analysis using shell scripting Hassan Shallal
[gmx-users] 5 identical simulations --> 5 different results, why? Michael Shirts
[gmx-users] Merge Trajectories John Shultz
[gmx-users] Bond Energies Absent John Shultz
[gmx-users] Adding ideal gases to a simulation Micholas Smith
[gmx-users] Adding ideal gases to a simulation Micholas Smith
[gmx-users] 5 identical simulations --> 5 different results, why? Ricardo O. S. Soares
[gmx-users] question about compass ff David van der Spoel
[gmx-users] velocity autocorrelation function. David van der Spoel
[gmx-users] g_dipoles, take the normal of the computational box David van der Spoel
[gmx-users] Adding ideal gases to a simulation David van der Spoel
[gmx-users] PME problem on BG/P cluster David van der Spoel
[gmx-users] Coulomb (SR) problem David van der Spoel
[gmx-users] redundancies in the .itp file David van der Spoel
[gmx-users] Incomplete ring David van der Spoel
[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox David van der Spoel
[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox David van der Spoel
[gmx-users] Re: gromacs with CMAP David van der Spoel
[gmx-users] No convergence in Diffusion Coefficient David van der Spoel
[gmx-users] fcstep value for shell particles Mikhail Stukan
[gmx-users] error while loading shared libraries: libOpenMM.so: Tarsis
[gmx-users] Position restraint for 2ns Rabab Toubar
[gmx-users] 1-4 interaction not within cut-off Rabab Toubar
[gmx-users] 1-4 interaction not within cut-off Rabab Toubar
[gmx-users] 1-4 interaction not within cut-off Rabab Toubar
[gmx-users] 1-4 interaction not within cut-off Rabab Toubar
[gmx-users] tracking the time for an md run Rabab Toubar
[gmx-users] top2psf.pl Rabab Toubar
[gmx-users] trjconv index file Rabab Toubar
[gmx-users] trjconv index file Rabab Toubar
[gmx-users] trjconv index file Rabab Toubar
[gmx-users] Forcefields for proteins Rabab Toubar
[gmx-users] Re: His protonation Rabab Toubar
[gmx-users] System net charge Rabab Toubar
[gmx-users] Plotting Energies versus time Rabab Toubar
[gmx-users] Re: moleculetype CU1+ is redefined Lucio Ricardo Montero Valenzuela
[gmx-users] LIE in reruning PME NPT runs Lucio Ricardo Montero Valenzuela
[gmx-users] Energy minimization: problems with ramachanrad score Lucio Ricardo Montero Valenzuela
[gmx-users] Help with g_vanhove Juan M Vanegas
[gmx-users] Re: helical parameters for DNA Attilio Vargiu
[gmx-users] question on merging trajectories files Andrew Voronkov
[gmx-users] pdb2gmx renumbers the residues in my pdb file NG HUI WEN
[gmx-users] pdb2gmx renumbers the residues in my pdb file NG HUI WEN
[gmx-users] Forces on atom which is shifted out of the minimum Sebastian Waltz
[gmx-users] Instantenous Hessian Matrix Sebastian Waltz
[gmx-users] which flag for the force Sebastian Waltz
[gmx-users] pressure scaling more than 1% Sebastian Waltz
[gmx-users] constraints bond length vari by 10% Sebastian Waltz
[gmx-users] constraints bond length vari by 10% Sebastian Waltz
[gmx-users] constraints bond length vari by 10% Sebastian Waltz
[gmx-users] constraints bond length vari by 10% Sebastian Waltz
[gmx-users] get the mass having the atom type Sebastian Waltz
[gmx-users] Re: Problem of reading the atom'force from trr file using template.c Sebastian Waltz
[gmx-users] different ref_t Sebastian Waltz
[gmx-users] RE: [gmx-user]Error by pdb2gmx (Dallas Dallas B. Warren
[gmx-users] the box lengths Dallas B. Warren
[gmx-users] FEP for amino acid mutations. Dallas B. Warren
[gmx-users] the box lengths Dallas B. Warren
[gmx-users] the box lengths Dallas B. Warren
[gmx-users] the box lengths Dallas B. Warren
[gmx-users] git Dallas B. Warren
[gmx-users] Script for detecting interfaces Dallas B. Warren
[gmx-users] g_covar Tsjerk Wassenaar
[gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat. Tsjerk Wassenaar
[gmx-users] Non-conservation of total energy while using structure file to resume the simulation Tsjerk Wassenaar
[gmx-users] g_rmsf -res Tsjerk Wassenaar
[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures Tsjerk Wassenaar
[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures Tsjerk Wassenaar
[gmx-users] the box lengths Tsjerk Wassenaar
[gmx-users] convert traj file between diff gromacs versions Tsjerk Wassenaar
[gmx-users] Re: His protonation Tsjerk Wassenaar
[gmx-users] Energy minimisation of solvated protein - Tutorial Tsjerk Wassenaar
[gmx-users] Energy miscalculation Tsjerk Wassenaar
[gmx-users] Problem on forming bonds Tsjerk Wassenaar
[gmx-users] g_anaeig -proj Tsjerk Wassenaar
[gmx-users] g_rdf has a huge memory leak. Tsjerk Wassenaar
[gmx-users] automating analysis using shell scripting Tsjerk Wassenaar
[gmx-users] -dt Tsjerk Wassenaar
[gmx-users] g_rama / mult Tsjerk Wassenaar
[gmx-users] Dimer g_rms Tsjerk Wassenaar
[gmx-users] g_rama / mult Tsjerk Wassenaar
[gmx-users] FWSpider Tutorial Tsjerk Wassenaar
[gmx-users] Making a .rtp file Amanda Watkins
[gmx-users] Using x2top to convert a gro file to a top file Amanda Watkins
[gmx-users] b-factor Martyn Winn
[gmx-users] converting amber parameter to OPLS BIN ZHANG
[gmx-users] OPLS-AA topologies for ATP BIN ZHANG
[gmx-users] OPLS-AA topologies for ATP BIN ZHANG
[gmx-users] add external force Ting Zhou
[gmx-users] add external force Ting Zhou
[gmx-users] Creation of a Non-Standard Residue Mark Zottola
[gmx-users] Re: Creation of a Non-Standard Residue Mark Zottola
[gmx-users] Creation of a Non-Standard Residue Mark Zottola
[gmx-users] position restraints abdullah ahmed
FW: [gmx-users] position restraints abdullah ahmed
FW: [gmx-users] position restraints abdullah ahmed
[gmx-users] position restraints abdullah ahmed
[gmx-users] field-specified name for sulfate shiva birgani
[gmx-users] Regarding genconf nikhil damle
[gmx-users] Position restrained Dynamics nikhil damle
[gmx-users] Position restrained Dynamics nikhil damle
[gmx-users] position restraint....NEED URGENT HELP nikhil damle
[gmx-users] Topology Generation sonali dhindwal
[gmx-users] FES and FE molecule topology sonali dhindwal
[gmx-users] Re: Simulation with CsCl sonali dhindwal
[gmx-users] Re: acetonitrile from amber to gromacs vedat durmaz
[gmx-users] Discrete structure factor from g_rdf comcon1 at erg.biophys.msu.ru
[gmx-users] Discrete structure factor from g_rdf comcon1 at erg.biophys.msu.ru
[gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat. comcon1 at erg.biophys.msu.ru
[gmx-users] Thr -> Met in TI calculation fancy2012
[gmx-users] tutorial of free energy calculations fancy2012
[gmx-users] epsilon_r fancy2012
[gmx-users] soft-core fancy2012
[gmx-users] Re:gmx-users Digest, Vol 74, Issue 73 fancy2012
[gmx-users] sc_power fancy2012
[gmx-users] No default Proper Dih. types fancy2012
[gmx-users] Environment Day manjubfs at gmail.com
[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ? maria goranovic
[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ? maria goranovic
[gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out maria goranovic
[gmx-users] problem while removing extra waters from a simulation box, simulation explodes thereafter maria goranovic
[gmx-users] [ dihedraltypes ] akram gorji
[gmx-users] a query about analysis oguz gurbulak
[gmx-users] multiple time step oguz gurbulak
[gmx-users] free energy landscape question baptista at itqb.unl.pt
[gmx-users] CL atom not being recognised jayant james
[gmx-users] CL atom not being recognised jayant james
[gmx-users] Simulatimg two proteins in water system radhika jaswal
[gmx-users] Extracting enthalpies during or after MD lists at jsx.dk
[gmx-users] Extracting enthalpies during or after MD lists at jsx.dk
[gmx-users] Extracting enthalpies during or after MD lists at jsx.dk
[gmx-users] Extracting enthalpies during or after MD lists at jsx.dk
[gmx-users] g_msd and diffusion coefficent leila karami
[gmx-users] g_msd and diffusion coefficent leila karami
[gmx-users] g_msd and diffusion coefficent leila karami
[gmx-users] g_msd and diffusion coefficent leila karami
[gmx-users] g_msd and diffusion coefficent leila karami
[gmx-users] b-factor leila karami
[gmx-users] -dt leila karami
[gmx-users] g_msd and diffusion coefficent leila karami
[gmx-users] b-factor leila karami
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 2 manjula kasinathan
[gmx-users] moleculetype CU1+ is redefined afsaneh maleki
[gmx-users] ions.itp afsaneh maleki
[gmx-users] Re: moleculetype CU1+ is redefined afsaneh maleki
[gmx-users] Overriding atomtype O afsaneh maleki
[gmx-users] dgdl.xvg afsaneh maleki
[gmx-users] dgdl.xvg file afsaneh maleki
[gmx-users] Position Restrained Simulation for Coarse Grained DSPC sunny mishra
[gmx-users] Position Restrained Simulation for Coarse Grained DSPC sunny mishra
[gmx-users] PBC ms
[gmx-users] [slightly off topic] How to view evolution of secondary structure in a trajectory? ms
[gmx-users] How to view evolution of secondary structure in a trajectory? ms
[gmx-users] pdb2gmx: c-terminal oxygens considered duplicate atoms jak137 at o2.pl
[gmx-users] Help in parametrisation onetwo
Re: [gmx-users] Help in parametrisation onetwo
Re: [gmx-users] Help in parametrisation onetwo
Re: [gmx-users] Help in parametrisation onetwo
[gmx-users] residence time of water molecule atila petrosian
[gmx-users] a query about analysis shayamra at post.tau.ac.il
[gmx-users] Average pdb coordinates rituraj purohit
[gmx-users] mdrun_mpi issue. quantrum75
[gmx-users] C-alpha group pawan raghav
[gmx-users] g_covar pawan raghav
[gmx-users] General Question pawan raghav
[gmx-users] Technical pawan raghav
[gmx-users] REMD pawan raghav
[gmx-users] REMD pawan raghav
[gmx-users] RE:Range checking error lloyd riggs
[gmx-users] RE:Blowing up follow-up lloyd riggs
[gmx-users] RE:Multiple chain ID's lloyd riggs
[gmx-users] Re: chain ids (2) lloyd riggs
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 143 lloyd riggs
[gmx-users] Re:Chain terminus lloyd riggs
[gmx-users] PBC shahab shariati
[gmx-users] helical parameters for DNA shahab shariati
[gmx-users] selection of group in do_dssp shahab shariati
[gmx-users] B-factor shahab shariati
[gmx-users] B-factor shahab shariati
[gmx-users] B-factor shahab shariati
[gmx-users] B-factor shahab shariati
[gmx-users] g_rama / mult shahab shariati
[gmx-users] g_rama / mult shahab shariati
[gmx-users] calculate interfacial tension kecy_wu at sina.com
[gmx-users] problems when using command "trjconv" mircial at sjtu.edu.cn
[gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. xhomes at sohu.com
Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. xhomes at sohu.com
Re: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. xhomes at sohu.com
[gmx-users] Running gromacs in parallel on multicore machine xhomes at sohu.com
Re: Re: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. xhomes at sohu.com
[gmx-users] Re: QMMM cpmd stefhoor
[gmx-users] ED sampling vijaya subramanian
[gmx-users] angle restraints subarna thakur
[gmx-users] error compiling mopac and gromacs subarna thakur
Subject: [gmx-users] error compiling mopac and gromacs subarna thakur
[gmx-users] error in linking mopac and gromacs subarna thakur
[gmx-users] Disk Space teklebrh at ualberta.ca
[gmx-users] Disk Space teklebrh at ualberta.ca
[gmx-users] Disk Space teklebrh at ualberta.ca
[gmx-users] Re: Exact run continuation teklebrh at ualberta.ca
[gmx-users] Error in MD simulation teklebrh at ualberta.ca
[gmx-users] Mixed Solvents Preparation? teklebrh at ualberta.ca
[gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions Schneck at uni-heidelberg.de
[gmx-users] Re: thermodynamic integration yields different values.. Schneck at uni-heidelberg.de
[gmx-users] Re: add missing atom(s) chris.neale at utoronto.ca
[gmx-users] number of water molecules affects the PMF chris.neale at utoronto.ca
[gmx-users] PMF in vacuum and pull direction chris.neale at utoronto.ca
[gmx-users] PMF in vacuum and pull direction chris.neale at utoronto.ca
[gmx-users] PMF in vacuum and pull direction chris.neale at utoronto.ca
[gmx-users] Disk Space chris.neale at utoronto.ca
[gmx-users] Disk Space chris.neale at utoronto.ca
[gmx-users] Energy minimization: problems with ramachanrad score chris.neale at utoronto.ca
[gmx-users] Enough hydration of the channel chris.neale at utoronto.ca
[gmx-users] pull_pbcatom reporting strangely when set to 0 chris.neale at utoronto.ca
[gmx-users] Query on WHAM analysis chris.neale at utoronto.ca
[gmx-users] Energy miscalculation chris.neale at utoronto.ca
[gmx-users] umbrella sampling-Bimodal Histograms chris.neale at utoronto.ca
[gmx-users] pull_pbcatom reporting strangely when set to 0 chris.neale at utoronto.ca
[gmx-users] umbrella sampling-Bimodal Histograms chris.neale at utoronto.ca
[gmx-users] standard state correction of delta G from a PMF chris.neale at utoronto.ca
[gmx-users] grompp fatal error Unknown bond_atomtype chris.neale at utoronto.ca
[gmx-users] standard state correction of delta G from a PMF chris.neale at utoronto.ca
[gmx-users] g_anaeig -proj chris.neale at utoronto.ca
[gmx-users] multiple time step chris.neale at utoronto.ca
[gmx-users] different ref_t chris.neale at utoronto.ca
[gmx-users] multiple time step chris.neale at utoronto.ca
[gmx-users] Pull code chris.neale at utoronto.ca
[gmx-users] combining replicate xtc files nishap.patel at utoronto.ca
[gmx-users] Regarding genconf jani vinod
[gmx-users] Regarding genconf jani vinod
[gmx-users] Parallel installation abdul wadood
[gmx-users] Parallel instalation: gmx-users Digest, Vol 74, Issue 76 abdul wadood
[gmx-users] RE: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 abdul wadood
[gmx-users] P4_error for extending coarse grained MD simulations weixin
[gmx-users] How to update the neighbor list heuristically? xuji
[gmx-users] How to calculate the energy drift? xuji
[gmx-users] (no subject) munubas at yahoo.com
[gmx-users] (no subject) munubas at yahoo.com
[gmx-users] implementing a pulsed, time-dependent electric field in gromacs fangyong yan
[gmx-users] Re: parameters of Sodium Sulfate fang yuan
[gmx-users] add missing atoms you zou
[gmx-users] add missing atom(s) you zou
[gmx-users] write topology by hand you zou
[gmx-users] [pairs] and [dihedrals] you zou
[gmx-users] Incomplete ring you zou
[gmx-users] Incomplete ring you zou
[gmx-users] vdwtype=shift you zou
[gmx-users] Re: vdwtype=shift you zou
[gmx-users] (no subject) Linus Östberg
[gmx-users] P4_error for extending coarse grained MD simulations 张春雷
[gmx-users] P4_error for extending coarse grained MD simulations 张春雷
[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells 张春雷
[gmx-users] P4_error for extending coarse grained MD simulations 张春雷
[gmx-users] Re: P4_error for extending coarse grained MD simulations 张春雷
[gmx-users] Problem of reading the atom'force from trr file using template.c 聂雪川
[gmx-users] Re: Problem of reading the atom'force from trr file using template.c 聂雪川

Last message date: Wed Jun 30 23:53:58 CEST 2010
Archived on: Thu Nov 14 12:08:52 CET 2013

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