December 2011 Archives by date

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Starting: Thu Dec 1 00:24:08 CET 2011
Ending: Sat Dec 31 21:45:43 CET 2011
Messages: 634

[gmx-users] control Distance between the solute and the box for 3 directions seperately mu xiaojia
[gmx-users] control Distance between the solute and the box for 3 directions seperately Mark Abraham
[gmx-users] how to understand this sentence Mark Abraham
[gmx-users] control Distance between the solute and the box for 3 directions seperately Justin A. Lemkul
[gmx-users] g_select dynamic indices Yao Yao
[gmx-users] g_select dynamic indices Justin A. Lemkul
[gmx-users] how to understand this sentence lina
[gmx-users] how to understand this sentence lina
[gmx-users] Analysis of Protein Complex Saba Ferdous
[gmx-users] Analysis of Protein Complex Tsjerk Wassenaar
[gmx-users] Partial atomic charge parto haghighi
[gmx-users] Re: Looking for potential phosphate binding sites bharat gupta
[gmx-users] Postdoctoral and staff scientist positions in the Gromacs teams Erik Lindahl
[gmx-users] Re: Looking for potential phosphate binding sites Justin A. Lemkul
[gmx-users] Partial atomic charge Justin A. Lemkul
[gmx-users] Re: couple-moltype of FEP Justin A. Lemkul
[gmx-users] Re: Looking for potential phosphate binding sites bharat gupta
[gmx-users] Re: Looking for potential phosphate binding sites Justin A. Lemkul
[gmx-users] Re: Looking for potential phosphate binding sites bharat gupta
[gmx-users] Re: Looking for potential phosphate binding sites Justin A. Lemkul
[gmx-users] how can i merge several trajectory files to one? Hyunsik
[gmx-users] how can i merge several trajectory files to one? Justin A. Lemkul
[gmx-users] how can i merge several trajectory files to one? Hyunsik
[gmx-users] compiling with the PGI compiler Szilárd Páll
[gmx-users] compiling with the PGI compiler Teemu Murtola
[gmx-users] compiling with the PGI compiler Szilárd Páll
[gmx-users] density map in 3 Dimension jagannath mondal
[gmx-users] editconf -d mohammad agha
[gmx-users] Fw: editconf -d mohammad agha
[gmx-users] editconf -d Justin A. Lemkul
[gmx-users] density map in 3 Dimension Justin A. Lemkul
[gmx-users] compiling with the PGI compiler chris.neale at utoronto.ca
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Mark Abraham
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Justin A. Lemkul
[gmx-users] Failed to lock .log. Already running simulation? chris.neale at utoronto.ca
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Dallas Warren
[gmx-users] Re: Protein ligand simulation bharat gupta
[gmx-users] Re: Protein ligand simulation Mark Abraham
[gmx-users] (no subject) abdullah ahmed
[gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul) Chunxia Gao
[gmx-users] Pdb2gmx with Amber99SB-ILDN Alberto Arrigoni
[gmx-users] postdoctoral vacancy in computational biochemistry/biophysics David van der Spoel
[gmx-users] compiling with the PGI compiler Szilárd Páll
[gmx-users] PhD position Kukol, Andreas
[gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o Szilárd Páll
[gmx-users] Harmonic potentials -- Lagrangian multipliers Emanuel Peter
[gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul) Justin A. Lemkul
[gmx-users] Pdb2gmx with Amber99SB-ILDN Justin A. Lemkul
[gmx-users] A special case of cutoffs related to mdrun with -rerun option Ioannis Beis
[gmx-users] QMMM Compilation Ravi Kumar Venkatraman
[gmx-users] Job announcement at University of Regensburg Emanuel Peter
[gmx-users] can not restart a simulation from the checkpoint file Chen, Zhihong (chenz2)
[gmx-users] restraints between two molecules lq z
[gmx-users] restraints between two molecules Justin A. Lemkul
[gmx-users] Re: restraints between two molecules lq z
[gmx-users] Re: restraints between two molecules Justin A. Lemkul
[gmx-users] can not restart a simulation from the checkpoint file Justin A. Lemkul
[gmx-users] QM calculation parto haghighi
[gmx-users] QM calculation Justin A. Lemkul
[gmx-users] Half double pair list method in GROMACS [update] Sai Kumar Ramadugu
[gmx-users] Half double pair list method in GROMACS [update] Chris Neale
[gmx-users] A special case of cutoffs related to mdrun with -rerun option Mark Abraham
[gmx-users] Check for bad contacts and/or reduce the timestep pragna lakshmi
[gmx-users] Check for bad contacts and/or reduce the timestep Justin A. Lemkul
[gmx-users] Check for bad contacts and/or reduce the timestep pragna lakshmi
[gmx-users] Check for bad contacts and/or reduce the timestep Mark Abraham
[gmx-users] Check for bad contacts and/or reduce the timestep Mark Abraham
[gmx-users] Check for bad contacts and/or reduce the timestep pragna lakshmi
[gmx-users] Check for bad contacts and/or reduce the timestep Mark Abraham
[gmx-users] grompp error for CNT simulation niaz poorgholami
[gmx-users] Convert to Sammon map Alex Jemulin
[gmx-users] Cluster analysis Alex Jemulin
[gmx-users] grompp error for CNT simulation Justin A. Lemkul
[gmx-users] Half double pair list method in GROMACS [update] ABEL Stephane 175950
[gmx-users] output logfile Sanku M
[gmx-users] output logfile Broadbent, Richard
[gmx-users] Re: grompp error for CNT simulation Dr. Vitaly V. Chaban
[gmx-users] Convert xpm to matrix Alex Jemulin
[gmx-users] Edit on-the-fly topology files (stateA->stateB) Vasileios Tatsis
[gmx-users] Convert xpm to matrix lina
[gmx-users] output logfile Sanku M
[gmx-users] Edit on-the-fly topology files (stateA->stateB) Mark Abraham
[gmx-users] output logfile Mark Abraham
[gmx-users] MSD normalization Sławomir Stachura
[gmx-users] mdrun stuck with PME on BlueGene/P Rongliang Wu
[gmx-users] Putting back the images of residues and atoms in the box Justin A. Lemkul
[gmx-users] mdrun stuck with PME on BlueGene/P Mark Abraham
[gmx-users] RMDS calculation vferrario at units.it
[gmx-users] RMDS calculation Tsjerk Wassenaar
[gmx-users] Re: MSD normalization Sławomir Stachura
[gmx-users] Putting back the images of residues and atoms in the box Rohit Farmer
[gmx-users] setenv: Too many arguments Mehdi Talebzadeh Farooji
[gmx-users] File input/output error pdb2gmx command nbhutwal at uci.edu
[gmx-users] File input/output error pdb2gmx command Dallas Warren
[gmx-users] File input/output error pdb2gmx command Justin A. Lemkul
[gmx-users] Re: MSD normalization Mark Abraham
[gmx-users] setenv: Too many arguments Mark Abraham
[gmx-users] setenv: Too many arguments Mehdi Talebzadeh Farooji
[gmx-users] Simulation in different PH Sathish
[gmx-users] Simulation in different PH Justin A. Lemkul
[gmx-users] setenv: Too many arguments Mark Abraham
[gmx-users] gromacs installation error aiswarya pawar
[gmx-users] RE: logfile size lloyd riggs
[gmx-users] problem installing gromacs Efrat Exlrod
[gmx-users] mmView - a tool for mmCIF exploration Daniel Svozil
[gmx-users] gromacs installation error Javier Cerezo
[gmx-users] RMDS calculation vferrario at units.it
[gmx-users] problem installing gromacs Mark Abraham
[gmx-users] RE: logfile size Mark Abraham
[gmx-users] RE: logfile size Mark Abraham
[gmx-users] gromacs installation error aiswarya.pawar at gmail.com
[gmx-users] dihedral format in top file? Markus K. Dahlgren
[gmx-users] RE: logfile size Javier Cerezo
[gmx-users] intel grompp with pathscale mdrun Chris Neale
[gmx-users] dihedral format in top file? Dallas Warren
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 30 lloyd riggs
[gmx-users] Simulation of a charged system Surya Prakash Tiwari
[gmx-users] itp file for D2O cuong nguyen
[gmx-users] Can Gromacs do Targeted MD simulation? DeChang Li
[gmx-users] itp file for D2O Surya Prakash Tiwari
[gmx-users] itp file for D2O Justin A. Lemkul
[gmx-users] itp file for D2O Surya Prakash Tiwari
[gmx-users] intel grompp with pathscale mdrun Matthew Zwier
[gmx-users] intel grompp with pathscale mdrun chris.neale at utoronto.ca
[gmx-users] intel grompp with pathscale mdrun Rasale, Anupama
[gmx-users] intel grompp with pathscale mdrun Mark Abraham
[gmx-users] Simulation of a charged system Mark Abraham
[gmx-users] Re: itp file for D2O (cuong nguyen) Gerrit Groenhof
[gmx-users] Simulation in different PH Sathish
[gmx-users] RE: logfile size lloyd riggs
[gmx-users] gromacs installation error Javier Cerezo
[gmx-users] RE: logfile size Mark Abraham
[gmx-users] gromacs installation error aiswarya pawar
[gmx-users] gromacs installation error Mark Abraham
[gmx-users] Regarding Improper Dihedral Ravi Kumar Venkatraman
[gmx-users] Regarding Improper Dihedral Justin A. Lemkul
[gmx-users] Re: RE: logfile size lloyd riggs
[gmx-users] Gromacs 4.5.4 on multi-node cluster Nikos Papadimitriou
[gmx-users] Gromacs 4.5.4 on multi-node cluster Mark Abraham
[gmx-users] Newbie: Which implicit solvent force field to choose? Jose Borreguero
[gmx-users] Newbie: How to modify the topology file after adding ions? Jose Borreguero
[gmx-users] Newbie: How to modify the topology file after adding ions? Justin A. Lemkul
[gmx-users] Newbie: How to modify the topology file after adding ions? Jose Borreguero
[gmx-users] box vectors Chandan Choudhury
[gmx-users] g_msd and pbc Chandan Choudhury
[gmx-users] Charmm Sugars/carbohydrates Michael McGovern
[gmx-users] Newbie: How to modify the topology file after adding ions? Justin A. Lemkul
[gmx-users] Charmm Sugars/carbohydrates Andrew Paluch
[gmx-users] box vectors Justin A. Lemkul
[gmx-users] box vectors Tsjerk Wassenaar
[gmx-users] g_msd and pbc Tsjerk Wassenaar
[gmx-users] box vectors Matthew Zwier
[gmx-users] Reg: RMSD calculation of a certain portion of protein Justin A. Lemkul
[gmx-users] Newbie: How to modify the topology file after adding ions? Jose Borreguero
[gmx-users] Segmentation fault error from mdrun rainy908
[gmx-users] box vectors Mark Abraham
[gmx-users] Segmentation fault error from mdrun Mark Abraham
[gmx-users] Problem with computing graphite-water surface tension WU Yanbin
[gmx-users] Reg: RMSD calculation of a certain portion of protein Rohit Farmer
[gmx-users] box vectors Chandan Choudhury
[gmx-users] g_msd and pbc Chandan Choudhury
[gmx-users] Simulation of a charged system Surya Prakash Tiwari
[gmx-users] Re: g_msd and pbc Dr. Vitaly V. Chaban
[gmx-users] I want only coordinates in md.xtc/md.pdb Saba Ferdous
[gmx-users] I want only coordinates in md.xtc/md.pdb Chandan Choudhury
[gmx-users] I want only coordinates in md.xtc/md.pdb Mark Abraham
[gmx-users] box vectors Mark Abraham
[gmx-users] Simulation of a charged system Mark Abraham
[gmx-users] mdrun_mpi error aiswarya pawar
[gmx-users] Membrane Proteins & pdb2gmx Anirban Ghosh
[gmx-users] restart does not automatically use checkpoint? Peter C. Lai
[gmx-users] Re: Gromacs 4.5.4 on multi-node cluster Nikos Papadimitriou
[gmx-users] Membrane Proteins & pdb2gmx Peter C. Lai
[gmx-users] Re: Gromacs 4.5.4 on multi-node cluster Dimitris Dellis
[gmx-users] Membrane Proteins & pdb2gmx Anirban Ghosh
[gmx-users] No automatic terminus detection Matthias Ernst
[gmx-users] how to set the BASENAME in QMMM simualtions using gromacs/orca Qinghua Liao
[gmx-users] how to set the BASENAME in QMMM simualtions using gromacs/orca Christoph Riplinger
[gmx-users] restart does not automatically use checkpoint? Justin A. Lemkul
[gmx-users] No automatic terminus detection Mark Abraham
[gmx-users] mdrun_mpi error Mark Abraham
[gmx-users] box vectors Chandan Choudhury
[gmx-users] Postdoc and PhD positions in Denmark Himanshu Khandelia
[gmx-users] box vectors Mark Abraham
[gmx-users] Implicit solvent tutorial Gianluca Santoni
[gmx-users] Implicit solvent tutorial Justin A. Lemkul
[gmx-users] No automatic terminus detection Matthias Ernst
[gmx-users] box vectors Tsjerk Wassenaar
[gmx-users] No automatic terminus detection Mark Abraham
[gmx-users] Re: Gromacs 4.5.4 on multi-node cluster Nikos Papadimitriou
[gmx-users] Implicit solvent tutorial lina
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 44 Qinghua Liao
[gmx-users] Implicit solvent tutorial Justin A. Lemkul
[gmx-users] Implicit solvent tutorial lina
[gmx-users] Newbie: How to modify the topology file after adding ions? Tsjerk Wassenaar
[gmx-users] freezing grps during em Saman Mandegar
[gmx-users] Re:Newbie: How to modify the topology file after adding ions? lloyd riggs
[gmx-users] Aminoacids.hdb problem Alberto Arrigoni
[gmx-users] Aminoacids.hdb problem Justin A. Lemkul
[gmx-users] REST simulation Otto Master
[gmx-users] Re:Re:Re: MSD normalization Sławomir Stachura
[gmx-users] Newbie: How to modify the topology file after adding ions? Tsjerk Wassenaar
[gmx-users] Newbie: How to modify the topology file after adding ions? Jose Borreguero
[gmx-users] Re:Re:Re: MSD normalization Mark Abraham
[gmx-users] diffusion coefficient Ruhollah Moussavi-Baygi
[gmx-users] diffusion coefficient Mark Abraham
[gmx-users] diffusion coefficient David van der Spoel
[gmx-users] Is openmp necessary? Hsin-Lin Chiang
[gmx-users] Is openmp necessary? Mark Abraham
[gmx-users] Re: Is openmp necessary? Hsin-Lin Chiang
[gmx-users] Fwd: Check for bad contacts and/or reduce the timestep Mark Abraham
[gmx-users] Gromos parameters for atom type OA Samuli Ollila
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 49 Sławomir Stachura
[gmx-users] gromacs/orca--qmmm li yan
[gmx-users] Gromos parameters for atom type OA Javier Cerezo
[gmx-users] Problem with GDP parameters generation neeru sharma
[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC Ruhollah Moussavi-Baygi
[gmx-users] Problem with GDP parameters generation Mark Abraham
[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC Matthew Zwier
[gmx-users] mdrun_mpi error aiswarya pawar
[gmx-users] mdrun_mpi error aiswarya pawar
[gmx-users] mdrun_mpi error Mark Abraham
[gmx-users] mdrun_mpi error aiswarya pawar
[gmx-users] qm/mm(orca/gromacs) li yan
[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC David van der Spoel
[gmx-users] No such moleculetype Na Setare Jiji
[gmx-users] No such moleculetype Na Tsjerk Wassenaar
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 56 Gerrit Groenhof
[gmx-users] No such moleculetype Na cuong nguyen
[gmx-users] Problem with GDP parameters generation neeru sharma
[gmx-users] Problem with GDP parameters generation Mark Abraham
[gmx-users] mdrun_mpi error Mark Abraham
[gmx-users] No such moleculetype Na Setare Jiji
[gmx-users] No such moleculetype Na Mark Abraham
[gmx-users] coordinate number aroud the first shell mohammad agha
[gmx-users] trjconv -pbc mol/nojump Efrat Exlrod
回复： [gmx-users] No such moleculetype Na yp sun
[gmx-users] trjconv -pbc mol/nojump Mark Abraham
[gmx-users] trjconv -pbc mol/nojump leila karami
回复： [gmx-users] No such moleculetype Na Mark Abraham
[gmx-users] No such moleculetype Na m_p
[gmx-users] coordinate number aroud the first shell Dallas Warren
[gmx-users] coordinate number aroud the first shell mohammad agha
[gmx-users] Information about g_sas Alex Jemulin
[gmx-users] g_hbond sulatha M. S
[gmx-users] Gromacs Installation error aiswarya pawar
[gmx-users] g_hbond David van der Spoel
[gmx-users] g_hbond sulatha M. S
[gmx-users] g_hbond David van der Spoel
[gmx-users] REST simulation Patrick Fuchs
[gmx-users] Gromos parameters for atom type OA Patrick Fuchs
[gmx-users] REST simulation Mark Abraham
[gmx-users] REST simulation Otto Master
[gmx-users] Information about g_sas Justin A. Lemkul
[gmx-users] REST simulation Otto Master
[gmx-users] REST simulation Patrick Fuchs
[gmx-users] REST simulation Patrick Fuchs
[gmx-users] g_hbond sulatha M. S
[gmx-users] error while adding charges to the system using genion Nishith Saurav Topno
[gmx-users] Force field for polymer molecule - tips Jernej Zidar
[gmx-users] error while adding charges to the system using genion Mark Abraham
[gmx-users] Force field for polymer molecule - tips Mark Abraham
[gmx-users] Coupling groups for nvt equilibration neeru sharma
[gmx-users] g_rms on large amount of data khuchtumur bumerdene
Re[2]: 回复： [gmx-users] No such moleculetype Na Иимяа Фаамиилиияа
[gmx-users] REST simulation Otto Master
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 66 Rongliang Wu
[gmx-users] How to neutralize 0.748e system charge Sundargenesan
[gmx-users] How to neutralize 0.748e system charge Tsjerk Wassenaar
[gmx-users] analysis the results of melocular dynamics simulation yp sun
[gmx-users] REST simulation Patrick Fuchs
[gmx-users] analysis the results of melocular dynamics simulation Javier Cerezo
[gmx-users] REST simulation Otto Master
[gmx-users] REST simulation Patrick Fuchs
[gmx-users] antifreeze particle in martini coarse-grained mohammad agha
[gmx-users] Protein encapsulation Anthony Cruz Balberdi
[gmx-users] antifreeze particle in martini coarse-grained XAvier Periole
[gmx-users] Coupling groups for nvt equilibration Justin A. Lemkul
[gmx-users] RE: Gromos parameters for atom type OA Samuli Ollila
[gmx-users] antifreeze particle in martini coarse-grained XAvier Periole
[gmx-users] Pull error message eva.pluharova at marge.uochb.cas.cz
[gmx-users] antifreeze particle in martini coarse-grained mohammad agha
[gmx-users] How to neutralize 0.748e system charge Mark Abraham
[gmx-users] Cosine content R.S.K.Vijayan
[gmx-users] Pme on gpu performance Szilárd Páll
[gmx-users] Cosine content Francesco Oteri
[gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham) Jernej Zidar
[gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham) Justin A. Lemkul
[gmx-users] Re: Coupling groups for nvt equilibration neeru sharma
[gmx-users] Re: Coupling groups for nvt equilibration Justin A. Lemkul
[gmx-users] calculation of standard deviation of SASA per residue Harpreet Basra
[gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham) Tsjerk Wassenaar
[gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham) Mark Abraham
[gmx-users] calculation of standard deviation of SASA per residue Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 73 Jernej Zidar
[gmx-users] Cosine content Tsjerk Wassenaar
[gmx-users] Re: Coupling groups for nvt equilibration neeru sharma
[gmx-users] submission error aiswarya pawar
[gmx-users] submission error Mark Abraham
[gmx-users] (no subject) Linder Tobias
[gmx-users] XYZ-Direction of eigenvector Linder Tobias
[gmx-users] XYZ-Direction of eigenvector Mark Abraham
[gmx-users] Re: Coupling groups for nvt equilibration Justin A. Lemkul
[gmx-users] submission error aiswarya.pawar at gmail.com
[gmx-users] submission error Justin A. Lemkul
[gmx-users] Help with g_rmsf Carla Jamous
[gmx-users] topology and parameter for cobalt metal shahid nayeem
[gmx-users] Help with g_rmsf Tsjerk Wassenaar
[gmx-users] topology and parameter for cobalt metal Justin A. Lemkul
[gmx-users] nrexcl = 2 or 3? lq z
[gmx-users] how to use g_dipoles 李浩
[gmx-users] submission error aiswarya.pawar at gmail.com
[gmx-users] Protein-MG-GDP (Protein-Ion-ligand) system simulation neeru sharma
[gmx-users] Protein-MG-GDP (Protein-Ion-ligand) system simulation Justin A. Lemkul
[gmx-users] how to use g_dipoles Mark Abraham
[gmx-users] nrexcl = 2 or 3? Mark Abraham
[gmx-users] nrexcl = 2 or 3? Yun Shi
[gmx-users] nrexcl = 2 or 3? Mark Abraham
[gmx-users] MD simulation of Glycoproteion 陈应广
[gmx-users] Glycoproteion MD 陈应广
[gmx-users] MD simulation of Glycoproteion 陈应广
[gmx-users] MD simulation of Glycoproteion Yun Shi
回复： [gmx-users] MD simulation of Glycoproteion 陈应广
[gmx-users] MD simulation of Glycoproteion Mark Abraham
[gmx-users] Re: submission error aiswarya pawar
[gmx-users] Re: submission error Mark Abraham
[gmx-users] Re: Re: calculation of standard deviation of SASA per residue Harpreet Basra
[gmx-users] calculation of density for martini coarse-grained mohammad agha
[gmx-users] calculation of density for martini coarse-grained Mark Abraham
[gmx-users] mdrun_mpi -rerun bonded interactions Vasileios Tatsis
[gmx-users] calculation of density for martini coarse-grained mohammad agha
[gmx-users] calculation of density for martini coarse-grained Mark Abraham
Fw: [gmx-users] Re: submission error aiswarya.pawar at gmail.com
[gmx-users] calculation of density for martini coarse-grained mohammad agha
[gmx-users] calculation of density for martini coarse-grained mohammad agha
[gmx-users] calculation of density for martini coarse-grained Justin A. Lemkul
[gmx-users] calculation of density for martini coarse-grained Justin A. Lemkul
[gmx-users] calculation of density for martini coarse-grained mohammad agha
[gmx-users] Eigenvalue values from PCA (a general question) R.S.K.Vijayan
[gmx-users] free energy and UB term lq z
[gmx-users] Eigenvalue values from PCA (a general question) Tsjerk Wassenaar
[gmx-users] Eigenvalue values from PCA (a general question) R.S.K.Vijayan
[gmx-users] Eigenvalue values from PCA (a general question) Tsjerk Wassenaar
[gmx-users] Eigenvalue values from PCA (a general question) R.S.K.Vijayan
[gmx-users] Re: Eigenvalue values from PCA (a general question) Niesen, Michiel
[gmx-users] Re: Eigenvalue values from PCA (a general question) R.S.K.Vijayan
[gmx-users] free energy and UB term Mark Abraham
[gmx-users] good reference for PCA in gromacs Sanku M
[gmx-users] good reference for PCA in gromacs Mark Abraham
[gmx-users] Re: Eigenvalue values from PCA (a general question) Tsjerk Wassenaar
[gmx-users] compatible gromacs aiswarya pawar
[gmx-users] calculation of density for martini coarse-grained mohammad agha
[gmx-users] Re: Eigenvalue values from PCA (a general question) Niesen, Michiel
[gmx-users] Regarding free energy calculation bipin singh
[gmx-users] Re: Eigenvalue values from PCA (a general question) Tsjerk Wassenaar
[gmx-users] calculation of density for martini coarse-grained Tsjerk Wassenaar
[gmx-users] compatible gromacs Mark Abraham
[gmx-users] compatible gromacs aiswarya pawar
[gmx-users] tip3p water in gromacs_4.5.4 shahid nayeem
[gmx-users] tip3p water in gromacs_4.5.4 Tomek Wlodarski
[gmx-users] Regarding free energy calculation Justin A. Lemkul
[gmx-users] Voronoi tessellation Ramya Parthasarathi
[gmx-users] Voronoi tessellation Justin A. Lemkul
[gmx-users] About plumed gromacs umbrella pulling vidhya sankar
[gmx-users] pressure coupling mohammad agha
[gmx-users] pressure coupling Mark Abraham
[gmx-users] energy_terms balaji nagarajan
[gmx-users] energy_terms Mark Abraham
[gmx-users] pressure coupling mohammad agha
[gmx-users] pressure coupling Mark Abraham
[gmx-users] pressure coupling mohammad agha
[gmx-users] Coulomb Energies Saba Ferdous
[gmx-users] Test mail priya thiyagarajan
[gmx-users] energy_terms balaji nagarajan
[gmx-users] energy_terms Mark Abraham
[gmx-users] energy_terms Mark Abraham
[gmx-users] Coulomb Energy Saba Ferdous
[gmx-users] Information about boxX,boxY e boxZ Alex Jemulin
[gmx-users] Coulomb Energy Mark Abraham
[gmx-users] Information about boxX,boxY e boxZ Mark Abraham
[gmx-users] LINCS error aiswarya pawar
[gmx-users] LINCS error Mark Abraham
[gmx-users] Invitation to connect on LinkedIn ram prasad via LinkedIn
[gmx-users] maxh not causing termination Ben Reynwar
[gmx-users] regarding x2top error priya thiyagarajan
[gmx-users] regarding x2top error David van der Spoel
[gmx-users] h-bonds constraints Gavin Melaugh
[gmx-users] regarding x2top priya thiyagarajan
[gmx-users] regarding x2top Justin A. Lemkul
[gmx-users] Metal Ion Position simon sham
[gmx-users] Metal Ion Position Justin A. Lemkul
[gmx-users] Regarding free energy calculation David Mobley
[gmx-users] About restraint for umbrella sampling vidhya sankar
[gmx-users] Reg: Parallel run Rohit Farmer
[gmx-users] regarding rtp file priya thiyagarajan
[gmx-users] regarding rtp file Justin A. Lemkul
[gmx-users] Reg: Parallel run Justin A. Lemkul
[gmx-users] Help with g_density Alex Jemulin
[gmx-users] Help with g_density Dallas Warren
[gmx-users] which may caused this error lina
[gmx-users] which may caused this error Justin A. Lemkul
[gmx-users] regarding topology priya thiyagarajan
[gmx-users] regarding topology Justin A. Lemkul
[gmx-users] LINCS error aiswarya pawar
[gmx-users] LINCS error Justin A. Lemkul
[gmx-users] Regarding free energy calculation bipin singh
[gmx-users] select groups in g_rms yp sun
[gmx-users] select groups in g_rms Gianluca Santoni
[gmx-users] EM curve question parto haghighi
[gmx-users] regarding rtp file priya thiyagarajan
[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges Thomas Evangelidis
[gmx-users] Possible typo in "nb_kernel_x86_64_sse.c" (4.5.5) Daniel Adriano Silva M
[gmx-users] regarding rtp file Mark Abraham
[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges Mark Abraham
[gmx-users] EM curve question Mark Abraham
[gmx-users] Re: LINCS error aiswarya pawar
[gmx-users] Re: LINCS error Mark Abraham
[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges Thomas Evangelidis
[gmx-users] A simulation of pure chloroform with AMBER compatible parameters never gives the right density anaome at fundp.ac.be
[gmx-users] A simulation of pure chloroform with AMBER compatible parameters never gives the right density David van der Spoel
[gmx-users] a doubt about pbc nojump or mol or whole Anna Marabotti
[gmx-users] [Fwd: h-bonds constraints] Gavin Melaugh
[gmx-users] About conformation choice for Umbrella sampling vidhya sankar
[gmx-users] umbrella sampling with replica exchange Sanku M
[gmx-users] [Fwd: h-bonds constraints] Justin A. Lemkul
[gmx-users] About conformation choice for Umbrella sampling Justin A. Lemkul
[gmx-users] a doubt about pbc nojump or mol or whole Tsjerk Wassenaar
[gmx-users] Voronoi tessellation Ramya Parthasarathi
[gmx-users] pressure profiles Ramya Parthasarathi
[gmx-users] pressure profiles Dallas Warren
[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges Mark Abraham
[gmx-users] CTAB force field cuong nguyen
[gmx-users] Possible typo in "nb_kernel_x86_64_sse.c" (4.5.5) Roland Schulz
[gmx-users] maxh not causing termination Mark Abraham
[gmx-users] Possible typo in "nb_kernel_x86_64_sse.c" (4.5.5) Daniel Adriano Silva M
[gmx-users] regarding rtp file priya thiyagarajan
[gmx-users] regarding rtp file Justin A. Lemkul
[gmx-users] g_hbond sulatha M. S
[gmx-users] Re:Getting energy values in kcal/mol Sairam Tatikonda
[gmx-users] Re:Getting energy values in kcal/mol Mark Abraham
[gmx-users] regarding itp priya thiyagarajan
[gmx-users] regarding itp Mark Abraham
[gmx-users] restraint force and free enrgy code. sunhanzi at nibs.ac.cn
[gmx-users] Re: LINCS error aiswarya.pawar at gmail.com
[gmx-users] Protein Chains Spatially Separated After Energy Minimization Benjamin Er
[gmx-users] Protein Chains Spatially Separated After Energy Minimization Justin A. Lemkul
[gmx-users] discrepancy between ED motions and the MD motion R.S.K.Vijayan
[gmx-users] about umbrella sampling vidhya sankar
[gmx-users] EM curve question parto haghighi
[gmx-users] discrepancy between ED motions and the MD motion Tsjerk Wassenaar
[gmx-users] about umbrella sampling Justin A. Lemkul
[gmx-users] EM curve question Justin A. Lemkul
[gmx-users] discrepancy between ED motions and the MD motion R.S.K.Vijayan
[gmx-users] About Choice PDB vidhya sankar
[gmx-users] energy_terms balaji nagarajan
[gmx-users] g_angle calculation SebastianWaltz
[gmx-users] energy_terms Justin A. Lemkul
[gmx-users] About Choice PDB Justin A. Lemkul
[gmx-users] Gromacs is aborting without error during nvt equilibration Bodmer, Nicholas (bodmernk)
[gmx-users] Test mail victor doss
[gmx-users] regarding top file priya thiyagarajan
[gmx-users] Re:comparison of energy between GROMACS and NAMD Sairam Tatikonda
[gmx-users] Re:comparison of energy between GROMACS and NAMD Mark Abraham
[gmx-users] regarding top file Mark Abraham
[gmx-users] Re:comparison of energy between GROMACS and NAMD David van der Spoel
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 116 Sairam Tatikonda
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 116 David van der Spoel
[gmx-users] Reg: Langevine Thermostat Rohit Farmer
[gmx-users] calculation of concentration mohammad agha
[gmx-users] calculation of concentration Tsjerk Wassenaar
[gmx-users] pressure profiles Ramya Parthasarathi
[gmx-users] Reg: Langevine Thermostat Mark Abraham
[gmx-users] Ice Surface Binding Simulations Nancy
[gmx-users] RDF: mol_com and atom at the same time Thomas Schlesier
[gmx-users] Temperature de-coupling in Langevin Dynamics Inon Sharony
[gmx-users] micelle clustering mohammad agha
[gmx-users] micelle clustering Mark Abraham
[gmx-users] Temperature de-coupling in Langevin Dynamics Mark Abraham
[gmx-users] micelle clustering mohammad agha
[gmx-users] calculation charges copmatible with GROMOS Su Nh
[gmx-users] calculation charges copmatible with GROMOS David van der Spoel
[gmx-users] (no subject) banafsheh mehrazma
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] Fw: modifying the mutated DNA parameters banafsheh mehrazma
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] Fw: modifying the mutated DNA parameters Mark Abraham
[gmx-users] how to obtain error bar for plotting? Mark Abraham
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] Re: topology file David van der Spoel
[gmx-users] Regarding Benzene Simulation Ravi Kumar Venkatraman
[gmx-users] Fw: calculation charges copmatible with GROMOS Su Nh
[gmx-users] Fw: calculation charges copmatible with GROMOS Justin A. Lemkul
[gmx-users] Fw: modifying the mutated DNA parameters banafsheh mehrazma
[gmx-users] Fw: modifying the mutated DNA parameters Mark Abraham
[gmx-users] Temperature de-coupling in Langevin Dynamics Inon Sharony
[gmx-users] oligosaccharide oplsaa .itp Ashalatha Sreshty
[gmx-users] Temperature de-coupling in Langevin Dynamics David van der Spoel
[gmx-users] Fw: modifying the mutated DNA parameters banafsheh mehrazma
[gmx-users] Announcing the GROMACS Molecule & Liquid Database David van der Spoel
[gmx-users] how to use gromacs 4.5.5's temple? 杜波
[gmx-users] Gravity or weightlessness condition Shahrbanoo Karbalaee
[gmx-users] Gravity or weightlessness condition David van der Spoel
[gmx-users] Atomtype not found - grompp - charmm27 and charmm22 Lara Bunte
[gmx-users] Atomtype not found - grompp - charmm27 and charmm22 Justin A. Lemkul
[gmx-users] General Questions about Molecular Dynamics Lara Bunte
[gmx-users] Atomtype not found - grompp - charmm27 and charmm22 Justin A. Lemkul
[gmx-users] General Questions about Molecular Dynamics Justin A. Lemkul
[gmx-users] General Questions about Molecular Dynamics Mark Abraham
[gmx-users] General Questions about Molecular Dynamics Jussi Lehtola
[gmx-users] trjconv and g_clustsize mohammad agha
[gmx-users] No default Angle types and Improper Dih. types Lara Bunte
[gmx-users] average pressure using g_energy Efrat Exlrod
[gmx-users] average pressure using g_energy Mark Abraham
[gmx-users] No default Angle types and Improper Dih. types Mark Abraham
[gmx-users] trjconv and g_clustsize Mark Abraham
[gmx-users] Problem with umbrella sampling and g_wham Eric LeGresley
[gmx-users] Problem with umbrella sampling and g_wham Justin A. Lemkul
[gmx-users] how to use gromacs 4.5.5's temple? Mark Abraham
[gmx-users] oligosaccharide oplsaa .itp Mark Abraham
[gmx-users] (no subject) Nidhi Katyal
[gmx-users] exploding system lina
[gmx-users] TI results parto haghighi
[gmx-users] (no subject) Mark Abraham
[gmx-users] problem with access to Gromacs after installation Sylwia Chmielewska
[gmx-users] Intel composer vs. Intel Studio Sudip Roy
[gmx-users] exploding system Mark Abraham
[gmx-users] problem with access to Gromacs after installation Mark Abraham
[gmx-users] Intel composer vs. Intel Studio Mark Abraham
[gmx-users] g_angle calculation Bogdan Costescu
[gmx-users] TI results Justin A. Lemkul
[gmx-users] SPC density Theodora García
[gmx-users] SPC density David van der Spoel
[gmx-users] trjconv and g_clustsize mohammad agha
[gmx-users] Problem with umbrella sampling and g_wham Eric LeGresley
[gmx-users] Modify charge groups parto haghighi
[gmx-users] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np' David Perel
[gmx-users] Modify charge groups Justin A. Lemkul
[gmx-users] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np' Justin A. Lemkul
[gmx-users] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np' David Perel
[gmx-users] dodecahedron box Zahra M
[gmx-users] dodecahedron box Tsjerk Wassenaar
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] how to obtain error bar for plotting? Mark Abraham
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] how to obtain error bar for plotting? Mark Abraham
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] SPC density Theodora García
[gmx-users] how to obtain error bar for plotting? leila karami
[gmx-users] trjconv -nojump mohammad agha
[gmx-users] SPC density Theodora García
[gmx-users] how to use the modified gromacs 4.5.5's temple 杜波
[gmx-users] (no subject) Olivia Waring
[gmx-users] Re: Olivia Waring
[gmx-users] -pbc nojump mohammad agha
[gmx-users] Ligand-Ligand interaction Hovakim Grabski
[gmx-users] Ligand-Ligand interaction Justin A. Lemkul
[gmx-users] -pbc nojump Tsjerk Wassenaar
[gmx-users] Coulomb Energies afsaneh maleki
[gmx-users] Coulomb Energies Justin A. Lemkul
[gmx-users] Intel composer vs. Intel Studio Peter C. Lai
[gmx-users] -pbc nojump Tsjerk Wassenaar
[gmx-users] SPC density Mark Abraham
[gmx-users] Re: Mark Abraham
[gmx-users] how to obtain error bar for plotting? Mark Abraham
[gmx-users] how to use the modified gromacs 4.5.5's temple Mark Abraham
[gmx-users] Intel composer vs. Intel Studio Mark Abraham
[gmx-users] -pbc nojump mohammad agha
[gmx-users] positive potential energy Zahra M
[gmx-users] Re: positive potential energy Zahra M
[gmx-users] Re: positive potential energy Mark Abraham
[gmx-users] shell molecular dynamics michael zhenin
[gmx-users] how to obtain error bar for plotting? Tsjerk Wassenaar
[gmx-users] shell molecular dynamics Mark Abraham
[gmx-users] g_analyze -ee leila karami
[gmx-users] Re: Generating Pairs with a Buckingham Potential Olivia Waring
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 138 Zahra M
[gmx-users] what is a "central structure" Yun Shi
[gmx-users] what is a "central structure" Mark Abraham
[gmx-users] Re: Generating Pairs with a Buckingham Potential Mark Abraham
[gmx-users] g_analyze -ee Mark Abraham
[gmx-users] trjconv in martini mohammad agha
[gmx-users] trjconv in martini Tsjerk Wassenaar
Fw: [gmx-users] trjconv in martini mohammad agha
[gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5 Rashek Kazi
Fw: [gmx-users] trjconv in martini Tsjerk Wassenaar
[gmx-users] where are GB parameters stored? David Mobley
[gmx-users] Warning: g_sas Vdwradii.dat afsaneh maleki
[gmx-users] where are GB parameters stored? Justin A. Lemkul
[gmx-users] Configurations stored in REMD trajectories César Ávila
[gmx-users] Re: Folding rate bharat gupta
[gmx-users] Re: Folding rate Justin A. Lemkul
[gmx-users] Re: Folding rate bharat gupta
[gmx-users] Re: Folding rate KS Rotondi
[gmx-users] Configurations stored in REMD trajectories Mark Abraham
[gmx-users] Re: Folding rate Justin A. Lemkul
[gmx-users] Re: Folding rate KS Rotondi
[gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5 Mark Abraham
[gmx-users] Re: Folding rate bharat gupta
[gmx-users] Re: Folding rate KS Rotondi
[gmx-users] Re: Folding rate João M. Damas
[gmx-users] Re: Folding rate felmerino at uchile.cl
[gmx-users] Re: Folding rate bharat gupta
[gmx-users] Re: Folding rate felmerino at uchile.cl
[gmx-users] About restraints vidhya sankar
Fw: [gmx-users] trjconv in martini mohammad agha
[gmx-users] g_sas vdwradii.dat afsaneh maleki
[gmx-users] g_sas vdwradii.dat Mark Abraham
[gmx-users] g_analyze -ee leila karami
Fw: [gmx-users] trjconv in martini Tsjerk Wassenaar
Fw: [gmx-users] trjconv in martini mohammad agha
Fw: [gmx-users] trjconv in martini mohammad agha
Fw: [gmx-users] trjconv in martini Tsjerk Wassenaar
Fw: [gmx-users] trjconv in martini mohammad agha
Fw: [gmx-users] trjconv in martini Tsjerk Wassenaar
Fw: [gmx-users] trjconv in martini mohammad agha
[gmx-users] After installation help Willian Pereira Felix
[gmx-users] Configurations stored in REMD trajectories César Ávila
[gmx-users] Re: Dr. Vitaly V. Chaban
[gmx-users] Re: cnt topology Dr. Vitaly V. Chaban
[gmx-users] detective work before or after creating a topology? Lara Bunte

Last message date: Sat Dec 31 21:45:43 CET 2011
Archived on: Thu Nov 14 12:12:07 CET 2013

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