December 2011 Archives by thread

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...

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] control Distance between the solute and the box for 3 directions seperately   Justin A. Lemkul
• [gmx-users] how to understand this sentence   Mark Abraham
  • [gmx-users] how to understand this sentence   lina
    • [gmx-users] how to understand this sentence   lina
• [gmx-users] g_select dynamic indices   Yao Yao
  • [gmx-users] g_select dynamic indices   Justin A. Lemkul
• [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] Partial atomic charge   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] Re: Looking for potential phosphate binding sites   bharat gupta
      • [gmx-users] Re: Looking for potential phosphate binding sites   Justin A. Lemkul
• [gmx-users] Postdoctoral and staff scientist positions in the Gromacs teams   Erik Lindahl
• [gmx-users] Re: couple-moltype of FEP   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] density map in 3 Dimension   Justin A. Lemkul
• [gmx-users] editconf -d   mohammad agha
  • [gmx-users] Fw: editconf -d   mohammad agha
  • [gmx-users] editconf -d   Justin A. Lemkul
• [gmx-users] compiling with the PGI compiler   chris.neale at utoronto.ca
  • [gmx-users] compiling with the PGI compiler   Szilárd Páll
• [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] Re: Protein ligand simulation   bharat gupta
• [gmx-users] Failed to lock .log. Already running simulation?   chris.neale at utoronto.ca
• [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] Re: Re: couple-moltype of FEP (Justin A. Lemkul)   Justin A. Lemkul
• [gmx-users] Pdb2gmx with Amber99SB-ILDN   Alberto Arrigoni
  • [gmx-users] Pdb2gmx with Amber99SB-ILDN   Justin A. Lemkul
• [gmx-users] postdoctoral vacancy in computational biochemistry/biophysics   David van der Spoel
• [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] A special case of cutoffs related to mdrun with -rerun option   Ioannis Beis
  • [gmx-users] A special case of cutoffs related to mdrun with -rerun option   Mark Abraham
• [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] can not restart a simulation from the checkpoint file   Justin A. Lemkul
• [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] 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] 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] grompp error for CNT simulation   Justin A. Lemkul
• [gmx-users] Convert to Sammon map   Alex Jemulin
• [gmx-users] Cluster analysis   Alex Jemulin
• [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] output logfile   Sanku M
  • [gmx-users] output logfile   Mark Abraham
• [gmx-users] Re: grompp error for CNT simulation   Dr. Vitaly V. Chaban
• [gmx-users] Convert xpm to matrix   Alex Jemulin
  • [gmx-users] Convert xpm to matrix   lina
• [gmx-users] Edit on-the-fly topology files (stateA->stateB)   Vasileios Tatsis
  • [gmx-users] Edit on-the-fly topology files (stateA->stateB)   Mark Abraham
• [gmx-users] MSD normalization   Sławomir Stachura
  • [gmx-users] Re: MSD normalization   Sławomir Stachura
    • [gmx-users] Re: MSD normalization   Mark Abraham
• [gmx-users] mdrun stuck with PME on BlueGene/P   Rongliang Wu
  • [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] RMDS calculation   vferrario at units.it
• [gmx-users] Putting back the images of residues and atoms in the box   Rohit Farmer
  • [gmx-users] Putting back the images of residues and atoms in the box   Justin A. Lemkul
• [gmx-users] setenv: Too many arguments   Mehdi Talebzadeh Farooji
  • [gmx-users] setenv: Too many arguments   Mark Abraham
    • [gmx-users] setenv: Too many arguments   Mehdi Talebzadeh Farooji
      • [gmx-users] setenv: Too many arguments   Mark Abraham
• [gmx-users] File input/output error pdb2gmx command   nbhutwal at uci.edu
  • [gmx-users] File input/output error pdb2gmx command   Justin A. Lemkul
• [gmx-users] File input/output error pdb2gmx command   Dallas Warren
• [gmx-users] Simulation in different PH   Sathish
  • [gmx-users] Simulation in different PH   Justin A. Lemkul
    • [gmx-users] Simulation in different PH   Sathish
• [gmx-users] gromacs installation error   aiswarya pawar
  • [gmx-users] gromacs installation error   Javier Cerezo
    • [gmx-users] gromacs installation error   aiswarya.pawar at gmail.com
      • [gmx-users] gromacs installation error   Javier Cerezo
      • [gmx-users] gromacs installation error   aiswarya pawar
      • [gmx-users] gromacs installation error   Mark Abraham
• [gmx-users] RE: logfile size   lloyd riggs
  • [gmx-users] RE: logfile size   Mark Abraham
    • [gmx-users] RE: logfile size   Mark Abraham
      • [gmx-users] RE: logfile size   Javier Cerezo
• [gmx-users] problem installing gromacs   Efrat Exlrod
  • [gmx-users] problem installing gromacs   Mark Abraham
• [gmx-users] mmView - a tool for mmCIF exploration   Daniel Svozil
• [gmx-users] dihedral format in top file?   Markus K. Dahlgren
• [gmx-users] intel grompp with pathscale mdrun   Chris Neale
  • [gmx-users] intel grompp with pathscale mdrun   Matthew Zwier
  • [gmx-users] intel grompp with pathscale mdrun   Mark Abraham
• [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] Simulation of a charged system   Mark Abraham
    • [gmx-users] Simulation of a charged system   Surya Prakash Tiwari
      • [gmx-users] Simulation of a charged system   Mark Abraham
• [gmx-users] itp file for D2O   cuong nguyen
  • [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] Can Gromacs do Targeted MD simulation?   DeChang Li
• [gmx-users] intel grompp with pathscale mdrun   chris.neale at utoronto.ca
  • [gmx-users] intel grompp with pathscale mdrun   Rasale, Anupama
• [gmx-users] Re: itp file for D2O (cuong nguyen)   Gerrit Groenhof
• [gmx-users] RE: logfile size   lloyd riggs
  • [gmx-users] RE: logfile size   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] 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] 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] box vectors   Chandan Choudhury
  • [gmx-users] box vectors   Justin A. Lemkul
    • [gmx-users] box vectors   Tsjerk Wassenaar
      • [gmx-users] box vectors   Matthew Zwier
  • [gmx-users] box vectors   Mark Abraham
    • [gmx-users] box vectors   Chandan Choudhury
      • [gmx-users] box vectors   Mark Abraham
      • [gmx-users] box vectors   Chandan Choudhury
      • [gmx-users] box vectors   Mark Abraham
      • [gmx-users] box vectors   Tsjerk Wassenaar
• [gmx-users] g_msd and pbc   Chandan Choudhury
  • [gmx-users] g_msd and pbc   Tsjerk Wassenaar
    • [gmx-users] g_msd and pbc   Chandan Choudhury
• [gmx-users] Charmm Sugars/carbohydrates   Michael McGovern
  • [gmx-users] Charmm Sugars/carbohydrates   Andrew Paluch
• [gmx-users] Segmentation fault error from mdrun   rainy908
  • [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] Reg: RMSD calculation of a certain portion of protein   Justin A. Lemkul
• [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] mdrun_mpi error   aiswarya pawar
  • [gmx-users] mdrun_mpi error   Mark Abraham
    • [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] mdrun_mpi error   Mark Abraham
• [gmx-users] Membrane Proteins & pdb2gmx   Anirban Ghosh
  • [gmx-users] Membrane Proteins & pdb2gmx   Peter C. Lai
    • [gmx-users] Membrane Proteins & pdb2gmx   Anirban Ghosh
• [gmx-users] restart does not automatically use checkpoint?   Peter C. Lai
  • [gmx-users] restart does not automatically use checkpoint?   Justin A. Lemkul
• [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster   Nikos Papadimitriou
  • [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster   Dimitris Dellis
• [gmx-users] No automatic terminus detection   Matthias Ernst
  • [gmx-users] No automatic terminus detection   Mark Abraham
    • [gmx-users] No automatic terminus detection   Matthias Ernst
      • [gmx-users] No automatic terminus detection   Mark Abraham
• [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] Postdoc and PhD positions in Denmark   Himanshu Khandelia
• [gmx-users] Implicit solvent tutorial   Gianluca Santoni
  • [gmx-users] Implicit solvent tutorial   Justin A. Lemkul
  • [gmx-users] Implicit solvent tutorial   lina
    • [gmx-users] Implicit solvent tutorial   Justin A. Lemkul
      • [gmx-users] Implicit solvent tutorial   lina
• [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster   Nikos Papadimitriou
• [gmx-users] Re: gmx-users Digest, Vol 92, Issue 44   Qinghua Liao
• [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] REST simulation   Patrick Fuchs
    • [gmx-users] REST simulation   Mark Abraham
      • [gmx-users] REST simulation   Otto Master
      • [gmx-users] REST simulation   Patrick Fuchs
    • [gmx-users] REST simulation   Otto Master
      • [gmx-users] REST simulation   Patrick Fuchs
      • [gmx-users] REST simulation   Otto Master
      • [gmx-users] REST simulation   Patrick Fuchs
      • [gmx-users] REST simulation   Otto Master
      • [gmx-users] REST simulation   Patrick Fuchs
• [gmx-users] Re:Re:Re: MSD normalization   Sławomir Stachura
  • [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] Gromos parameters for atom type OA   Javier Cerezo
    • [gmx-users] Gromos parameters for atom type OA   Patrick Fuchs
• [gmx-users] Re: gmx-users Digest, Vol 92, Issue 49   Sławomir Stachura
• [gmx-users] gromacs/orca--qmmm   li yan
• [gmx-users] Problem with GDP parameters generation   neeru sharma
  • [gmx-users] Problem with GDP parameters generation   Mark Abraham
• [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC   Ruhollah Moussavi-Baygi
  • [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC   Matthew Zwier
    • [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC   David van der Spoel
• [gmx-users] qm/mm(orca/gromacs)   li yan
• [gmx-users] No such moleculetype Na   Setare Jiji
  • [gmx-users] No such moleculetype Na   Tsjerk Wassenaar
  • [gmx-users] No such moleculetype Na   cuong nguyen
• [gmx-users] Re: gmx-users Digest, Vol 92, Issue 56   Gerrit Groenhof
• [gmx-users] Problem with GDP parameters generation   neeru sharma
  • [gmx-users] Problem with GDP parameters generation   Mark Abraham
• [gmx-users] No such moleculetype Na   Setare Jiji
  • [gmx-users] No such moleculetype Na   Mark Abraham
  • 回复： [gmx-users] No such moleculetype Na   yp sun
    • 回复： [gmx-users] No such moleculetype Na   Mark Abraham
      • Re[2]: 回复： [gmx-users] No such moleculetype Na   Иимяа Фаамиилиияа
  • [gmx-users] No such moleculetype Na   m_p
• [gmx-users] coordinate number aroud the first shell   mohammad agha
  • [gmx-users] coordinate number aroud the first shell   Dallas Warren
    • [gmx-users] coordinate number aroud the first shell   mohammad agha
• [gmx-users] trjconv -pbc mol/nojump   Efrat Exlrod
  • [gmx-users] trjconv -pbc mol/nojump   Mark Abraham
• [gmx-users] trjconv -pbc mol/nojump   leila karami
• [gmx-users] Information about g_sas   Alex Jemulin
  • [gmx-users] Information about g_sas   Justin A. Lemkul
• [gmx-users] g_hbond   sulatha M. S
  • [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] g_hbond   sulatha M. S
      • [gmx-users] g_hbond   sulatha M. S
• [gmx-users] Gromacs Installation error   aiswarya pawar
• [gmx-users] error while adding charges to the system using genion   Nishith Saurav Topno
  • [gmx-users] error while adding charges to the system using genion   Mark Abraham
• [gmx-users] Force field for polymer molecule - tips   Jernej Zidar
  • [gmx-users] Force field for polymer molecule - tips   Mark Abraham
• [gmx-users] Coupling groups for nvt equilibration   neeru sharma
  • [gmx-users] Coupling groups for nvt equilibration   Justin A. Lemkul
• [gmx-users] g_rms on large amount of data   khuchtumur bumerdene
• [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] analysis the results of melocular dynamics simulation   Javier Cerezo
  • [gmx-users] How to neutralize 0.748e system charge   Mark Abraham
• [gmx-users] antifreeze particle in martini coarse-grained   mohammad agha
  • [gmx-users] antifreeze particle in martini coarse-grained   XAvier Periole
• [gmx-users] Protein encapsulation   Anthony Cruz Balberdi
• [gmx-users] RE: Gromos parameters for atom type OA   Samuli Ollila
• [gmx-users] antifreeze particle in martini coarse-grained   XAvier Periole
  • [gmx-users] antifreeze particle in martini coarse-grained   mohammad agha
• [gmx-users] Pull error message   eva.pluharova at marge.uochb.cas.cz
• [gmx-users] Cosine content   R.S.K.Vijayan
  • [gmx-users] Cosine content   Francesco Oteri
    • [gmx-users] Cosine content   Tsjerk Wassenaar
• [gmx-users] Pme on gpu performance   Szilárd Páll
• [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: 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] 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] calculation of standard deviation of SASA per residue   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 92, Issue 73   Jernej Zidar
• [gmx-users] Re: Coupling groups for nvt equilibration   neeru sharma
  • [gmx-users] Re: Coupling groups for nvt equilibration   Justin A. Lemkul
• [gmx-users] submission error   aiswarya pawar
  • [gmx-users] submission error   Mark Abraham
    • [gmx-users] submission error   aiswarya.pawar at gmail.com
      • [gmx-users] submission error   Justin A. Lemkul
  • [gmx-users] Re: submission error   aiswarya pawar
    • [gmx-users] Re: 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] Help with g_rmsf   Carla Jamous
  • [gmx-users] Help with g_rmsf   Tsjerk Wassenaar
• [gmx-users] topology and parameter for cobalt metal   shahid nayeem
  • [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] how to use g_dipoles   Mark Abraham
• [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] 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] MD simulation of Glycoproteion   Mark Abraham
• [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] 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] calculation of density for martini coarse-grained   mohammad agha
      • [gmx-users] calculation of density for martini coarse-grained   Mark Abraham
      • [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] mdrun_mpi -rerun bonded interactions   Vasileios Tatsis
• Fw: [gmx-users] Re: submission error   aiswarya.pawar at gmail.com
• [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] calculation of density for martini coarse-grained   mohammad agha
      • [gmx-users] calculation of density for martini coarse-grained   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] Eigenvalue values from PCA (a general question)   Tsjerk Wassenaar
      • [gmx-users] Eigenvalue values from PCA (a general question)   R.S.K.Vijayan
• [gmx-users] free energy and UB term   lq z
  • [gmx-users] free energy and UB term   Mark Abraham
• [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] Re: Eigenvalue values from PCA (a general question)   Tsjerk Wassenaar
• [gmx-users] good reference for PCA in gromacs   Sanku M
  • [gmx-users] good reference for PCA in gromacs   Mark Abraham
• [gmx-users] compatible gromacs   aiswarya pawar
  • [gmx-users] compatible gromacs   Mark Abraham
    • [gmx-users] compatible gromacs   aiswarya pawar
• [gmx-users] Re: Eigenvalue values from PCA (a general question)   Niesen, Michiel
  • [gmx-users] Re: Eigenvalue values from PCA (a general question)   Tsjerk Wassenaar
• [gmx-users] Regarding free energy calculation   bipin singh
  • [gmx-users] Regarding free energy calculation   Justin A. Lemkul
    • [gmx-users] Regarding free energy calculation   David Mobley
      • [gmx-users] Regarding free energy calculation   bipin singh
• [gmx-users] tip3p water in gromacs_4.5.4   shahid nayeem
  • [gmx-users] tip3p water in gromacs_4.5.4   Tomek Wlodarski
• [gmx-users] Voronoi tessellation   Ramya Parthasarathi
  • [gmx-users] Voronoi tessellation   Justin A. Lemkul
    • [gmx-users] Voronoi tessellation   Ramya Parthasarathi
• [gmx-users] About plumed gromacs umbrella pulling   vidhya sankar
• [gmx-users] pressure coupling   mohammad agha
  • [gmx-users] pressure coupling   Mark Abraham
    • [gmx-users] pressure coupling   mohammad agha
      • [gmx-users] pressure coupling   Mark Abraham
      • [gmx-users] pressure coupling   mohammad agha
• [gmx-users] energy_terms   balaji nagarajan
  • [gmx-users] energy_terms   Mark Abraham
    • [gmx-users] energy_terms   balaji nagarajan
      • [gmx-users] energy_terms   Mark Abraham
      • [gmx-users] energy_terms   Mark Abraham
• [gmx-users] Coulomb Energies   Saba Ferdous
  • [gmx-users] Coulomb Energies   afsaneh maleki
    • [gmx-users] Coulomb Energies   Justin A. Lemkul
• [gmx-users] Test mail   priya thiyagarajan
  • [gmx-users] Test mail   victor doss
• [gmx-users] Coulomb Energy   Saba Ferdous
  • [gmx-users] Coulomb Energy   Mark Abraham
• [gmx-users] Information about boxX,boxY e boxZ   Alex Jemulin
  • [gmx-users] Information about boxX,boxY e boxZ   Mark Abraham
• [gmx-users] LINCS error   aiswarya pawar
  • [gmx-users] LINCS error   Mark Abraham
    • [gmx-users] LINCS error   aiswarya pawar
      • [gmx-users] LINCS error   Justin A. Lemkul
  • [gmx-users] Re: LINCS error   aiswarya pawar
• [gmx-users] Invitation to connect on LinkedIn   ram prasad via LinkedIn
• [gmx-users] maxh not causing termination   Ben Reynwar
  • [gmx-users] maxh not causing termination   Mark Abraham
• [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] About restraint for umbrella sampling   vidhya sankar
• [gmx-users] Reg: Parallel run   Rohit Farmer
  • [gmx-users] Reg: Parallel run   Justin A. Lemkul
• [gmx-users] regarding rtp file   priya thiyagarajan
  • [gmx-users] regarding rtp file   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] 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] EM curve question   Mark Abraham
• [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] Normal Mode Analysis starting from an optimized geometry and known partial charges   Thomas Evangelidis
    • [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges   Mark Abraham
• [gmx-users] Re: LINCS error   Mark Abraham
  • [gmx-users] Re: LINCS error   aiswarya.pawar at gmail.com
• [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] a doubt about pbc nojump or mol or whole   Tsjerk Wassenaar
• [gmx-users] [Fwd: h-bonds constraints]   Gavin Melaugh
  • [gmx-users] [Fwd: h-bonds constraints]   Justin A. Lemkul
• [gmx-users] About conformation choice for Umbrella sampling   vidhya sankar
  • [gmx-users] About conformation choice for Umbrella sampling   Justin A. Lemkul
• [gmx-users] umbrella sampling with replica exchange   Sanku M
• [gmx-users] pressure profiles   Ramya Parthasarathi
  • [gmx-users] pressure profiles   Dallas Warren
    • [gmx-users] pressure profiles   Ramya Parthasarathi
• [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] 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] 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] 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] discrepancy between ED motions and the MD motion   Tsjerk Wassenaar
    • [gmx-users] discrepancy between ED motions and the MD motion   R.S.K.Vijayan
• [gmx-users] about umbrella sampling   vidhya sankar
  • [gmx-users] about umbrella sampling   Justin A. Lemkul
• [gmx-users] EM curve question   parto haghighi
  • [gmx-users] EM curve question   Justin A. Lemkul
• [gmx-users] About Choice PDB   vidhya sankar
  • [gmx-users] About Choice PDB   Justin A. Lemkul
• [gmx-users] energy_terms   balaji nagarajan
  • [gmx-users] energy_terms   Justin A. Lemkul
• [gmx-users] g_angle calculation   SebastianWaltz
  • [gmx-users] g_angle calculation   Bogdan Costescu
• [gmx-users] Gromacs is aborting without error during nvt equilibration   Bodmer, Nicholas (bodmernk)
• [gmx-users] regarding top file   priya thiyagarajan
  • [gmx-users] regarding top file   Mark Abraham
• [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] 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] Reg: Langevine Thermostat   Mark Abraham
• [gmx-users] calculation of concentration   mohammad agha
  • [gmx-users] calculation of concentration   Tsjerk Wassenaar
• [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] Temperature de-coupling in Langevin Dynamics   Mark Abraham
    • [gmx-users] Temperature de-coupling in Langevin Dynamics   Inon Sharony
      • [gmx-users] Temperature de-coupling in Langevin Dynamics   David van der Spoel
• [gmx-users] micelle clustering   mohammad agha
  • [gmx-users] micelle clustering   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] Fw: calculation charges copmatible with GROMOS   Su Nh
    • [gmx-users] Fw: calculation charges copmatible with GROMOS   Justin A. Lemkul
• [gmx-users] (no subject)   banafsheh mehrazma
• [gmx-users] how to obtain error bar for plotting?   leila karami
  • [gmx-users] how to obtain error bar for plotting?   Mark Abraham
• [gmx-users] Fw: modifying the mutated DNA parameters   banafsheh mehrazma
  • [gmx-users] Fw: modifying the mutated DNA parameters   Mark Abraham
  • [gmx-users] Fw: modifying the mutated DNA parameters   banafsheh mehrazma
    • [gmx-users] Fw: modifying the mutated DNA parameters   Mark Abraham
      • [gmx-users] Fw: modifying the mutated DNA parameters   banafsheh mehrazma
• [gmx-users] how to obtain error bar for plotting?   leila karami
• [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] oligosaccharide oplsaa .itp   Ashalatha Sreshty
  • [gmx-users] oligosaccharide oplsaa .itp   Mark Abraham
• [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] how to use gromacs 4.5.5's temple?   Mark Abraham
• [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] 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] Atomtype not found - grompp - charmm27 and charmm22   Justin A. Lemkul
• [gmx-users] trjconv and g_clustsize   mohammad agha
  • [gmx-users] trjconv and g_clustsize   Mark Abraham
    • [gmx-users] trjconv and g_clustsize   mohammad agha
      • [gmx-users] trjconv -nojump   mohammad agha
• [gmx-users] No default Angle types and Improper Dih. types   Lara Bunte
  • [gmx-users] No default Angle types and Improper Dih. types   Mark Abraham
• [gmx-users] average pressure using g_energy   Efrat Exlrod
  • [gmx-users] average pressure using g_energy   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] Problem with umbrella sampling and g_wham   Eric LeGresley
• [gmx-users] (no subject)   Nidhi Katyal
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] exploding system   lina
  • [gmx-users] exploding system   Mark Abraham
• [gmx-users] TI results   parto haghighi
  • [gmx-users] TI results   Justin A. Lemkul
• [gmx-users] problem with access to Gromacs after installation   Sylwia Chmielewska
  • [gmx-users] problem with access to Gromacs after installation   Mark Abraham
• [gmx-users] Intel composer vs. Intel Studio   Sudip Roy
  • [gmx-users] Intel composer vs. Intel Studio   Mark Abraham
    • [gmx-users] Intel composer vs. Intel Studio   Peter C. Lai
• [gmx-users] SPC density   Theodora García
  • [gmx-users] SPC density   David van der Spoel
    • [gmx-users] SPC density   Theodora García
      • [gmx-users] SPC density   Theodora García
• [gmx-users] Modify charge groups   parto haghighi
  • [gmx-users] Modify charge groups   Justin A. Lemkul
• [gmx-users] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np'   David Perel
  • [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] how to obtain error bar for plotting?   leila karami
• [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] -pbc nojump   Tsjerk Wassenaar
• [gmx-users] Ligand-Ligand interaction   Hovakim Grabski
  • [gmx-users] Ligand-Ligand interaction   Justin A. Lemkul
• [gmx-users] -pbc nojump   Tsjerk Wassenaar
  • [gmx-users] -pbc nojump   mohammad agha
• [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 obtain error bar for plotting?   Tsjerk Wassenaar
• [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] 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] shell molecular dynamics   Mark Abraham
• [gmx-users] g_analyze -ee   leila karami
  • [gmx-users] g_analyze -ee   Mark Abraham
• [gmx-users] Re: Generating Pairs with a Buckingham Potential   Olivia Waring
  • [gmx-users] Re: Generating Pairs with a Buckingham Potential   Mark Abraham
• [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] trjconv in martini   mohammad agha
  • [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
      • 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] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5   Rashek Kazi
  • [gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5   Mark Abraham
• [gmx-users] where are GB parameters stored?   David Mobley
  • [gmx-users] where are GB parameters stored?   Justin A. Lemkul
• [gmx-users] Warning: g_sas Vdwradii.dat   afsaneh maleki
• [gmx-users] Configurations stored in REMD trajectories   César Ávila
  • [gmx-users] Configurations stored in REMD trajectories   Mark Abraham
    • [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   Justin A. Lemkul
      • [gmx-users] Re: Folding rate   KS Rotondi
      • [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] Re: Folding rate   KS Rotondi
• [gmx-users] About restraints   vidhya sankar
• [gmx-users] g_sas vdwradii.dat   afsaneh maleki
  • [gmx-users] g_sas vdwradii.dat   Mark Abraham
• [gmx-users] g_analyze -ee   leila karami
• [gmx-users] After installation help   Willian Pereira Felix
• [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

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...