August 2011 Archives by thread

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Starting: Mon Aug 1 01:42:28 CEST 2011
Ending: Wed Aug 31 23:20:19 CEST 2011
Messages: 798

• [gmx-users] OPLSAA parameters   Elisabeth
  • [gmx-users] OPLSAA parameters   Justin A. Lemkul
    • [gmx-users] OPLSAA parameters   Elisabeth
• Re: Re: [gmx-users] OPLSAA parameters   wibke.sudholt at cloudbroker.com
• [gmx-users] protein ligand   Ragothaman Yennamalli
  • [gmx-users] protein ligand   Mark Abraham
• [gmx-users] Re: PRODRG tools   René Pool
• [gmx-users] large error bars in PMF   Rebeca García Fandiño
  • [gmx-users] large error bars in PMF   Justin A. Lemkul
• [gmx-users] atom types   Gavin Melaugh
  • [gmx-users] atom types   Justin A. Lemkul
    • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Justin A. Lemkul
      • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Justin A. Lemkul
      • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Mark Abraham
      • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Mark Abraham
      • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Justin A. Lemkul
      • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Mark Abraham
      • [gmx-users] atom types   Gavin Melaugh
      • [gmx-users] atom types   Justin A. Lemkul
      • [gmx-users] atom types   Mark Abraham
      • [gmx-users] to clear up the confusion regarding fudge LJ and QQ   Gavin Melaugh
• [gmx-users] g_disre problems   Francisco Gomes Neto
  • [gmx-users] g_disre problems   Justin A. Lemkul
• [gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water   Andrew DeYoung
  • [gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water   Justin A. Lemkul
• [gmx-users] dispersion corrections in an anisotropic system   Zuzana Benkova
  • [gmx-users] dispersion corrections in an anisotropic system   Justin A. Lemkul
• Re: [gmx-users] dispersion corrections in an anisotropic system   wibke.sudholt at cloudbroker.com
• [gmx-users] umbrella sampling using replica exchange   Sanku M
  • [gmx-users] umbrella sampling using replica exchange   Justin A. Lemkul
• [gmx-users] Total Kinetic Energy And Rotational And Translational Kinetic Energy   Size Zheng
• [gmx-users] "VdW radii" of carbons in an unified-atom system   Kyeong Hyunho
• [gmx-users] Regarding generating topology file.   Ravi Kumar Venkatraman
  • [gmx-users] Regarding generating topology file.   Mark Abraham
  • [gmx-users] Regarding generating topology file.   Bruce D. Ray
• [gmx-users] Re: a question about order parameter of POPC   Justin A. Lemkul
• [gmx-users] pair types in FEP calculations   Marcelino Arciniega Castro
  • [gmx-users] pair types in FEP calculations   Justin A. Lemkul
  • [gmx-users] pair types in FEP calculations   Mark Abraham
• [gmx-users] center of box protein   nahren manuel
  • [gmx-users] center of box protein   Justin A. Lemkul
• [gmx-users] malloc on mac   Sara baretller
  • [gmx-users] malloc on mac   Justin A. Lemkul
    • [gmx-users] malloc on mac   Sara baretller
      • [gmx-users] malloc on mac   Justin A. Lemkul
      • [gmx-users] malloc on mac   Sara baretller
      • [gmx-users] malloc on mac   Tsjerk Wassenaar
• [gmx-users] Heat of Vaporization   Elisabeth
• [gmx-users] (no subject)   Sara baretller
  • [gmx-users] Re: coarse grain hydrogen bonding   Justin A. Lemkul
• [gmx-users] Re: Heat of Vaporization   Dr. Vitaly V. Chaban
• [gmx-users] Jarzynski and PMF   Sai Kumar Ramadugu
• [gmx-users] spatial distribution function in a binary solvent mixture   dbiswal at ucalgary.ca
• [gmx-users] bug in demux.pl   Swarnendu Tripathi
  • [gmx-users] bug in demux.pl   Mark Abraham
    • [gmx-users] bug in demux.pl   Swarnendu Tripathi
• Re: [gmx-users] bug in demux.pl   wibke.sudholt at cloudbroker.com
• [gmx-users] cannot open file   Justin A. Lemkul
• [gmx-users] spatial distribution function in a binary solvent mixture   chris.neale at utoronto.ca
  • [gmx-users] spatial distribution function in a binary solvent mixture   dbiswal at ucalgary.ca
• [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
  • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Justin A. Lemkul
    • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Justin A. Lemkul
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Justin A. Lemkul
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Justin A. Lemkul
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Justin A. Lemkul
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Justin A. Lemkul
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Mark Abraham
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Mark Abraham
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Sanku M
      • [gmx-users] Problem with temperature and stochastic dynamics in FEP   Mark Abraham
• [gmx-users] spatial distribution function in a binary solvent mixture   chris.neale at utoronto.ca
• [gmx-users] Force-field checking options   mcgrath
  • [gmx-users] Force-field checking options   Justin A. Lemkul
• [gmx-users] Problem of Kinetic Energy   Size Zheng
  • [gmx-users] Problem of Kinetic Energy   Mark Abraham
• [gmx-users] Force-field checking options   mcgrath
  • [gmx-users] Force-field checking options   Mark Abraham
    • [gmx-users] Force-field checking options   Mark Abraham
• [gmx-users] Force-field checking options   mcgrath
  • [gmx-users] Force-field checking options   Justin A. Lemkul
    • [gmx-users] Force-field checking options   Mark Abraham
• [gmx-users] bug in editconf for making a box ? combined two residues into one   maria goranovic
  • [gmx-users] bug in editconf for making a box ? combined two residues into one   lina
  • [gmx-users] bug in editconf for making a box ? combined two residues into one   Justin A. Lemkul
    • [gmx-users] bug in editconf for making a box ? combined two residues into one   maria goranovic
      • [gmx-users] bug in editconf for making a box ? combined two residues into one   Justin A. Lemkul
      • [gmx-users] bug in editconf for making a box ? combined two residues into one   Justin A. Lemkul
      • [gmx-users] bug in editconf for making a box ? combined two residues into one   Tsjerk Wassenaar
• [gmx-users] Re: Problem of Kinetic Energy   Size Zheng
• [gmx-users] Re: Heat of Vaporization   Dr. Vitaly V. Chaban
  • [gmx-users] Re: Heat of Vaporization   Elisabeth
    • [gmx-users] Re: Heat of Vaporization   Dr. Vitaly V. Chaban
• [gmx-users] Problem of Kinetic Energy   Size Zheng
  • [gmx-users] Problem of Kinetic Energy   Mark Abraham
• [gmx-users] Invitation to connect on LinkedIn   Marco Miele via LinkedIn
• [gmx-users] deprotonated Cys in Zn ion binding site   Tomek Wlodarski
• [gmx-users] Force-field checking options   mcgrath
• Re: Re: [gmx-users] Force-field checking options   wibke.sudholt at cloudbroker.com
• [gmx-users] setting vdw cutoff with specific force-filed?   Yun Shi
  • [gmx-users] setting vdw cutoff with specific force-filed?   Justin A. Lemkul
    • [gmx-users] setting vdw cutoff with specific force-filed?   Mark Abraham
• [gmx-users] Gromacs on GPU: GTX or Tesla?   Efrat Exlrod
  • [gmx-users] RE: Gromacs on GPU: GTX or Tesla?   Jagdish S. Varma
    • [gmx-users] RE: Gromacs on GPU: GTX or Tesla?   Szilárd Páll
• [gmx-users] Regarding Segmentation fault during mdrun_d   Ravi Kumar Venkatraman
  • [gmx-users] Regarding Segmentation fault during mdrun_d   lina
  • [gmx-users] Regarding Segmentation fault during mdrun_d   Mark Abraham
• [gmx-users] g_dipoles - averaging   Kukol, Andreas
  • [gmx-users] g_dipoles - averaging   Dommert Florian
    • [gmx-users] g_dipoles - averaging   Kukol, Andreas
      • [gmx-users] g_dipoles - averaging   Dommert Florian
• [gmx-users] the density does not stablize   xiaowu759
  • [gmx-users] the density does not stablize   Mark Abraham
• [gmx-users] Fwd: Regarding segmentation fault   Mark Abraham
• [gmx-users] g_membed stops after only one iteration   maria goranovic
• [gmx-users] Hydrogen atoms type   Amir Abbasi
  • [gmx-users] Hydrogen atoms type   Justin A. Lemkul
• [gmx-users] add Argon to a force field?   Amir Abbasi
  • [gmx-users] add Argon to a force field?   Justin A. Lemkul
• [gmx-users] PRODRG topology   Marzinek, Jan
  • [gmx-users] PRODRG topology   Justin A. Lemkul
• [gmx-users] setting vdw cutoff with specific force-filed?   Yun Shi
  • [gmx-users] setting vdw cutoff with specific force-filed?   Justin A. Lemkul
• [gmx-users] angular velocities in gromacs?   Tom
  • [gmx-users] angular velocities in gromacs?   Mark Abraham
  • [gmx-users] angular velocities in gromacs?   Matthew Zwier
• [gmx-users] Re: setting vdw cutoff with specific force-filed?   Yun Shi
• [gmx-users] How to exclude the interactions between molecule A and B in Gromacs?   DeChang Li
  • [gmx-users] How to exclude the interactions between molecule A and B in Gromacs?   Mark Abraham
• [gmx-users] How to run solvation dynamics for some organic molecules   Ravi Kumar Venkatraman
  • [gmx-users] How to run solvation dynamics for some organic molecules   Justin A. Lemkul
  • [gmx-users] How to run solvation dynamics for some organic molecules   lina
    • [gmx-users] How to run solvation dynamics for some organic molecules   Matthias Schmidt
      • [gmx-users] How to run solvation dynamics for some organic molecules   Justin A. Lemkul
• [gmx-users] Dihedral Question   Fabian Casteblanco
  • [gmx-users] Dihedral Question   Justin A. Lemkul
  • [gmx-users] Re: Dihedral Question   Fabian Casteblanco
• [gmx-users] Charge groups in Charmm for lipids   Michael McGovern
  • [gmx-users] Charge groups in Charmm for lipids   Thomas Piggot
    • [gmx-users] Charge groups in Charmm for lipids   Michael McGovern
    • [gmx-users] Charge groups in Charmm for lipids   Peter C. Lai
      • [gmx-users] Charge groups in Charmm for lipids   Thomas Piggot
      • [gmx-users] Charge groups in Charmm for lipids   Thomas Piggot
• [gmx-users] couldn't find topology match for atom type opls_102   Amir Abbasi
  • [gmx-users] couldn't find topology match for atom type opls_102   Justin A. Lemkul
• [gmx-users] couldn't find topology match for atom type opls_102   Justin A. Lemkul
  • [gmx-users] couldn't find topology match for atom type opls_102   Amir Abbasi
• [gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute   Pradip Biswas
  • [gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute   César Ávila
• [gmx-users] charge assignment for the anomeric carbon in 53a6 ff   Yun Shi
  • [gmx-users] charge assignment for the anomeric carbon in 53a6 ff   Justin A. Lemkul
• [gmx-users] Gromacs 4.0.7 on Blue Gene/P   Rongliang Wu
• [gmx-users] RE: Gromacs on GPU: GTX or Tesla?   Efrat Exlrod
• [gmx-users] SWM4-NDP or SWM4-DP water model is needed.   zhongjin
  • [gmx-users] SWM4-NDP or SWM4-DP water model is needed.   Justin A. Lemkul
• [gmx-users] charge assignment for the anomeric carbon in 53a6 ff   Yun Shi
  • [gmx-users] charge assignment for the anomeric carbon in 53a6 ff   Justin A. Lemkul
• [gmx-users] charge assignment for the anomeric carbon in 53a6 ff   Yun Shi
  • [gmx-users] charge assignment for the anomeric carbon in 53a6 ff   Justin A. Lemkul
• [gmx-users] Adding_topology_aminoacid   shahid nayeem
  • [gmx-users] Adding_topology_aminoacid   Kukol, Andreas
• [gmx-users] -dt option in g_velacc   Jinan Niu
  • [gmx-users] -dt option in g_velacc   Mark Abraham
• [gmx-users] Re: Carbon Nanotubes with Cisplatin Inside it   Justin A. Lemkul
• [gmx-users] Re: Essential Dynamic analysis   Justin A. Lemkul
  • [gmx-users] Re: Essential Dynamic analysis   Tsjerk Wassenaar
• [gmx-users] Regarding PCA and FEL   bipin singh
• [gmx-users] Conversion of the GLYCAM dihedral parameters   sa
• [gmx-users] Restart a simulation from a power source failure   Luís Pereira
  • [gmx-users] Restart a simulation from a power source failure   Justin A. Lemkul
    • [gmx-users] Restart a simulation from a power source failure   Luís Pereira
      • [gmx-users] Restart a simulation from a power source failure   Justin A. Lemkul
• [gmx-users] (no subject)   Janowicz, Adrianna C.
  • [gmx-users] (no subject)   Justin A. Lemkul
  • [gmx-users] Re:   Janowicz, Adrianna C.
    • [gmx-users] Re:   Mark Abraham
• [gmx-users] Free energy calculation   Fabian Casteblanco
  • [gmx-users] Free energy calculation   Justin A. Lemkul
  • [gmx-users] Re: Free energy calculation   Fabian Casteblanco
• [gmx-users] Regarding PCA and Free energy landscape   bipin singh
• [gmx-users] .mdp file   manoj damale
  • [gmx-users] .mdp file   Mark Abraham
    • [gmx-users] .mdp file   datta sarma
• [gmx-users] Contribution of delta bonding energy in the delta free energy   afsaneh maleki
  • [gmx-users] Contribution of delta bonding energy in the delta free energy   Mark Abraham
    • [gmx-users] Contribution of delta bonding energy in the delta free energy   afsaneh maleki
      • [gmx-users] Contribution of delta bonding energy in the delta free energy   Justin A. Lemkul
• [gmx-users] Obtain in a readable format the pairtypes values generated by grompp   intra\sa175950
  • [gmx-users] Obtain in a readable format the pairtypes values generated by grompp   Mark Abraham
• [gmx-users] git release-4-5-patches behind proxy   César Ávila
• [gmx-users] RE: gmx-users Digest, Vol 88, Issue 46   intra\sa175950
• [gmx-users] LINCS with amber99SB ?   Yun Shi
  • [gmx-users] LINCS with amber99SB ?   Justin A. Lemkul
• [gmx-users] TR: Obtain in a readable format the pairtypes values generated by grompp   intra\sa175950
• [gmx-users] git release-4-5-patches behind proxy   Roland Schulz
• [gmx-users] Force evaluation in umbrella pulling with nonzero pull_rate   Lin, Dejun
• [gmx-users] Gromacs compilation   Anthony Cruz Balberdi
  • [gmx-users] Gromacs compilation   Mark Abraham
• [gmx-users] Invitation to connect on LinkedIn   MING LI via LinkedIn
• [gmx-users] Invitation to connect on LinkedIn   MING LI via LinkedIn
• [gmx-users] secondary structure propensities of residues   César Ávila
  • [gmx-users] secondary structure propensities of residues   Mark Abraham
    • [gmx-users] secondary structure propensities of residues   César Ávila
      • [gmx-users] secondary structure propensities of residues   Mark Abraham
• [gmx-users] Re: LINCS with amber99SB ?   Yun Shi
  • [gmx-users] Re: LINCS with amber99SB ?   Justin A. Lemkul
• [gmx-users] VMD_PLUGIN_PATH   PAUL NEWMAN
  • [gmx-users] VMD_PLUGIN_PATH   Mark Abraham
• [gmx-users] Regarding PCA and Gibbs Free energy landscape   bipin singh
• [gmx-users] Regarding Equilibration   Ravi Kumar Venkatraman
  • [gmx-users] Regarding Equilibration   Justin A. Lemkul
• [gmx-users] (no subject)   Nilesh Dhumal
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
  • [gmx-users] strange vdw energy from rerun with GBSA model.   Mark Abraham
    • [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Mark Abraham
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Mark Abraham
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Justin A. Lemkul
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Justin A. Lemkul
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Mark Abraham
      • [gmx-users] strange vdw energy from rerun with GBSA model.   Da-Wei Li
• [gmx-users] Re: RTILs   Dr. Vitaly V. Chaban
• [gmx-users] Constraints not working in pull code (sometimes, sometimes not)   Krapnik
  • [gmx-users] Constraints not working in pull code (sometimes, sometimes not)   Justin A. Lemkul
    • [gmx-users] append files in Gromacs 3.3   Rebeca García Fandiño
      • [gmx-users] append files in Gromacs 3.3   Justin A. Lemkul
      • [gmx-users] append files in Gromacs 3.3   Rebeca García Fandiño
  • [gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)   Krapnik
  • [gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)   Krapnik
• [gmx-users] Constraints not working in pull code (sometimes, sometimes not)   chris.neale at utoronto.ca
• [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package   Micholas Smith
• [gmx-users] running at higher temperatures   Ragothaman Yennamalli
  • [gmx-users] running at higher temperatures   Kukol, Andreas
• [gmx-users] Viscosity calculations   Rini Gupta
• [gmx-users] Recommended parameters for NVE simulation of SPCE water   Michael Shirts
  • [gmx-users] Recommended parameters for NVE simulation of SPCE water   Michael Shirts
• [gmx-users] Kinetic energy of a single molecule   Size Zheng
  • [gmx-users] Kinetic energy of a single molecule   Justin A. Lemkul
• [gmx-users] To modify PRODRG-generated .itp file?   Yun Shi
  • [gmx-users] To modify PRODRG-generated .itp file?   Justin A. Lemkul
• [gmx-users] Selenomethionine in pdb file   R.Vidya Rajendran (10PHD013)
  • [gmx-users] Selenomethionine in pdb file   Mark Abraham
• [gmx-users] У вас новое сообщение на Badoo! Посмотреть его сейчас...   Badoo
• [gmx-users] Arginine_Hydrochloride topology   shahid nayeem
  • [gmx-users] Arginine_Hydrochloride topology   Mark Abraham
    • [gmx-users] Arginine_Hydrochloride topology   shahid nayeem
      • [gmx-users] Arginine_Hydrochloride topology   Justin A. Lemkul
      • [gmx-users] Arginine_Hydrochloride topology   shahid nayeem
      • [gmx-users] Arginine_Hydrochloride topology   Justin A. Lemkul
• [gmx-users] Topology for a new ligand   Kavyashree M
  • [gmx-users] Topology for a new ligand   Justin A. Lemkul
    • [gmx-users] Topology for a new ligand   Kavyashree M
      • [gmx-users] Topology for a new ligand   Justin A. Lemkul
      • [gmx-users] Topology for a new ligand   Mark Abraham
• [gmx-users] pmf_calculation   Justin A. Lemkul
  • [gmx-users] pmf_calculation   shahid nayeem
    • [gmx-users] pmf_calculation   Justin A. Lemkul
      • [gmx-users] pmf_calculation   shahid nayeem
      • [gmx-users] pmf_calculation   Justin A. Lemkul
• [gmx-users] Re: A very good morning Sir   Justin A. Lemkul
• [gmx-users] Constraints not working in pull code (sometimes, sometimes not)   chris.neale at utoronto.ca
• [gmx-users] Re: VMD_PLUGIN_PATH   PAUL NEWMAN
  • [gmx-users] Re: VMD_PLUGIN_PATH   Mark Abraham
• [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package   Micholas Smith
  • [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package   Justin A. Lemkul
  • [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package   Андрей Гончар
• [gmx-users] How to install FFTW 3.2.2   afsaneh maleki
  • [gmx-users] How to install FFTW 3.2.2   Justin A. Lemkul
• [gmx-users] Regarding parametrisation   Ravi Kumar Venkatraman
  • [gmx-users] Regarding parametrisation   Justin A. Lemkul
• [gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field   intra\sa175950
  • [gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field   Mark Abraham
• [gmx-users] Re: -dt option in g_velacc   Jinan Niu
  • [gmx-users] Re: -dt option in g_velacc   Mark Abraham
• [gmx-users] RE: gmx-users Digest, Vol 88, Issue 65   intra\sa175950
• [gmx-users] how to calculate the conc in the genion   lina
  • [gmx-users] how to calculate the conc in the genion   Mark Abraham
    • [gmx-users] how to calculate the conc in the genion   lina
      • [gmx-users] how to calculate the conc in the genion   Tsjerk Wassenaar
      • [gmx-users] how to calculate the conc in the genion   lina
      • [gmx-users] how to calculate the conc in the genion   lina
      • [gmx-users] how to calculate the conc in the genion   Mark Abraham
      • [gmx-users] how to calculate the conc in the genion   lina
      • [gmx-users] how to calculate the conc in the genion   Justin A. Lemkul
      • [gmx-users] how to calculate the conc in the genion   Tsjerk Wassenaar
• [gmx-users] How to install gromacs 4.5.1   afsaneh maleki
  • [gmx-users] How to install gromacs 4.5.1   Mark Abraham
    • [gmx-users] How to install gromacs 4.5.1   lina
• [gmx-users] vsites with NAC and opls   chris.neale at utoronto.ca
• [gmx-users] PCA and Free energy landscape   bipin singh
• [gmx-users] reg genion   vidhya sankar
  • [gmx-users] reg genion   Justin A. Lemkul
• [gmx-users] compile template.c   Park, Jae Hyun nmn
• [gmx-users] compile template.c   Park, Jae Hyun nmn
  • [gmx-users] compile template.c   Mark Abraham
• [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package   Micholas Smith
• [gmx-users] Re: non-neutralized system   Justin A. Lemkul
• [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'   Sebastian Breuers
  • [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'   Mark Abraham
  • [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'   lina
    • [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'   Sebastian Breuers
      • [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'   Da-Wei Li
• [gmx-users] Regarding g_sham   bipin singh
• [gmx-users] correction for minimum image distance violation   Kavyashree M
  • [gmx-users] correction for minimum image distance violation   Justin A. Lemkul
    • [gmx-users] correction for minimum image distance violation   Kavyashree M
      • [gmx-users] correction for minimum image distance violation   Mark Abraham
• [gmx-users] SWM4-NDP WATER MODEL AND IONS   zhongjin
  • [gmx-users] SWM4-NDP WATER MODEL AND IONS   D.G. Sprous, PhD
• [gmx-users] validation of ligand parameters   Yun Shi
• [gmx-users] possible bug in structure factor calculation in g_rdf?   Sanku M
• [gmx-users] How to suppress the screen info & how to overwrite files?   Hiroshi Fujisaki
  • [gmx-users] How to suppress the screen info & how to overwrite files?   Justin A. Lemkul
    • [gmx-users] How to suppress the screen info & how to overwrite files?   Hiroshi Fujisaki
      • [gmx-users] How to suppress the screen info & how to overwrite files?   Da-Wei Li
    • [gmx-users] How to suppress the screen info & how to overwrite files?   Bogdan Costescu
• [gmx-users] Regarding mdrunfor small organic molecules   Ravi Kumar Venkatraman
  • [gmx-users] Regarding mdrunfor small organic molecules   Justin A. Lemkul
  • [gmx-users] Re: Regarding mdrunfor small organic molecules   Ravi Kumar Venkatraman
• [gmx-users] Dear Lemkul   Ravi Kumar Venkatraman
  • [gmx-users] Regarding mdrunfor small organic molecules   Justin A. Lemkul
  • [gmx-users] Dear Lemkul   Tsjerk Wassenaar
• [gmx-users] Viscosity units   Rini Gupta
• [gmx-users] how to simulate a line charge   Amit Choubey
  • [gmx-users] how to simulate a line charge   Justin A. Lemkul
    • [gmx-users] how to simulate a line charge   Amit Choubey
      • [gmx-users] how to simulate a line charge   Justin A. Lemkul
      • [gmx-users] how to simulate a line charge   Amit Choubey
      • [gmx-users] how to simulate a line charge   Justin A. Lemkul
      • [gmx-users] how to simulate a line charge   Amit Choubey
      • [gmx-users] how to simulate a line charge   Amit Choubey
      • [gmx-users] how to simulate a line charge   Justin A. Lemkul
      • [gmx-users] how to simulate a line charge   Amit Choubey
      • [gmx-users] how to simulate a line charge   Justin A. Lemkul
      • [gmx-users] how to simulate a line charge   Amit Choubey
      • [gmx-users] how to simulate a line charge   Justin A. Lemkul
  • [gmx-users] how to simulate a line charge   Bogdan Costescu
    • [gmx-users] how to simulate a line charge   Amit Choubey
• [gmx-users] Regarding g_sham   bipin singh
  • [gmx-users] Regarding g_sham   lina
    • [gmx-users] Regarding g_sham   bipin singh
• [gmx-users] do_dssp   afsaneh maleki
  • [gmx-users] do_dssp   Justin A. Lemkul
• [gmx-users] aldehida   hamed amini
  • [gmx-users] aldehida   Justin A. Lemkul
• [gmx-users] aldehida   Justin A. Lemkul
• [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program   H.Ghorbanfekr
  • [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program   Justin A. Lemkul
    • [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program   H.Ghorbanfekr
• [gmx-users] Compute Intensive benchmarks for Gromacs   rajat phull
• [gmx-users] negative dihedral cp (during cgenff conversion)   Peter C. Lai
  • [gmx-users] negative dihedral cp (during cgenff conversion)   Mark Abraham
• [gmx-users] Liquid/Liquid   Maria Hamilton
  • [gmx-users] Liquid/Liquid   Justin A. Lemkul
• [gmx-users] RMS force is very large for shell MD   zhongjin
• [gmx-users] regarding genbox   Ravi Kumar Venkatraman
  • [gmx-users] regarding genbox   Justin A. Lemkul
    • [gmx-users] regarding genbox   Mark Abraham
• [gmx-users] (no subject)   Gavin Melaugh
• [gmx-users] bond constraints   Gavin Melaugh
  • [gmx-users] bond constraints   Justin A. Lemkul
• [gmx-users] (no subject)   Nilesh Dhumal
• [gmx-users] Gromacs tool   Dina Kreter
  • [gmx-users] Gromacs tool   Justin A. Lemkul
• [gmx-users] berendsen P coupling and fluctuation properties   Elisabeth
  • [gmx-users] berendsen P coupling and fluctuation properties   Mark Abraham
    • [gmx-users] berendsen P coupling and fluctuation properties   Elisabeth
      • [gmx-users] berendsen P coupling and fluctuation properties   Justin A. Lemkul
      • [gmx-users] berendsen P coupling and fluctuation properties   Elisabeth
      • [gmx-users] berendsen P coupling and fluctuation properties   Justin A. Lemkul
• [gmx-users] Velocity autocorrelation function   Nilesh Dhumal
  • [gmx-users] Velocity autocorrelation function   Elton Carvalho
    • [gmx-users] Velocity autocorrelation function   Dommert Florian
• [gmx-users] Hamiltonian replica exchange ?   Sanku M
• [gmx-users] g_covar   גדעון לפידות
  • [gmx-users] g_covar   Tsjerk Wassenaar
  • [gmx-users] g_covar   Yuri Garmay
    • [gmx-users] g_covar   Tsjerk Wassenaar
      • [gmx-users] g_covar   Yuri Garmay
      • [gmx-users] g_covar   Tsjerk Wassenaar
      • [gmx-users] g_covar   Yuri Garmay
• [gmx-users] Re: g_covar   גדעון לפידות
  • [gmx-users] Re: g_covar   Yuri Garmay
  • [gmx-users] Re: g_covar   Tsjerk Wassenaar
• [gmx-users] CMAP Dihedrals and free energy perturbations   Wright, Louise
  • [gmx-users] CMAP Dihedrals and free energy perturbations   Mark Abraham
• [gmx-users] Box-size   Kavyashree M
  • [gmx-users] Box-size   Mark Abraham
• [gmx-users] Pull Simulation: Force spike on F vs X output and extension stall   Natalie Stephenson
  • [gmx-users] Pull Simulation: Force spike on F vs X output and extension stall   Justin A. Lemkul
• [gmx-users] Regarding orientation restraints   Nitin Agrawal
  • [gmx-users] Regarding orientation restraints   Justin A. Lemkul
    • [gmx-users] Regarding orientation restraints   Nitin Agrawal
• [gmx-users] HIS N Terminal - Charmm27 force field   Rodrigo Faccioli
  • [gmx-users] HIS N Terminal - Charmm27 force field   Justin A. Lemkul
• [gmx-users] Free_energy size selection   Fabian Casteblanco
• [gmx-users] reg pullf.xvg   vidhya sankar
  • [gmx-users] reg pullf.xvg   Justin A. Lemkul
• [gmx-users] Re: berendsen P coupling and fluctuation properties   Dr. Vitaly V. Chaban
• [gmx-users] Atomtype CR1 not found   rainy908
  • [gmx-users] Atomtype CR1 not found   Justin A. Lemkul
• [gmx-users] Hamiltonian replica exchange?   Sanku M
  • [gmx-users] Hamiltonian replica exchange?   Michael Shirts
• [gmx-users] converting cpt between single and double precision   Peter C. Lai
  • [gmx-users] converting cpt between single and double precision   Mark Abraham
    • [gmx-users] converting cpt between single and double precision   Peter C. Lai
      • [gmx-users] converting cpt between single and double precision   Mark Abraham
• [gmx-users] suggestion that mdrun should ensure npme < the number of processes   chris.neale at utoronto.ca
  • [gmx-users] suggestion that mdrun should ensure npme < the numberof processes   Carsten Kutzner
• [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Itamar Kass
  • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Matthew Zwier
    • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Itamar Kass (Med)
      • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Matthew Zwier
      • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Matthew Zwier
• [gmx-users] Box-size: please reply   Kavyashree M
  • [gmx-users] Box-size: please reply   Tsjerk Wassenaar
    • [gmx-users] Box-size: please reply   Kavyashree M
      • [gmx-users] Box-size: please reply   Kavyashree M
      • [gmx-users] Box-size: please reply   Mark Abraham
• [gmx-users] regarding xtc file   Ravi Kumar Venkatraman
  • [gmx-users] regarding xtc file   Mark Abraham
• [gmx-users] FEP charged molecule cuestion   Marcelino Arciniega Castro
  • [gmx-users] FEP charged molecule cuestion   David Mobley
• [gmx-users] reference structure of g_rms   Hsin-Lin Chiang
  • [gmx-users] reference structure of g_rms   Mark Abraham
• [gmx-users] cutoffs   Anja Kuhnhold
  • [gmx-users] cutoffs   Mark Abraham
• [gmx-users] reference structure of g_rms   Hsin-Lin Chiang
• [gmx-users] reference structure of g_rms   Hsin-Lin Chiang
  • [gmx-users] reference structure of g_rms   Tsjerk Wassenaar
• [gmx-users] Re: Recommended parameters for NVE simulation of SPCE water   Andrew DeYoung
• [gmx-users] Add ions in the MARTINI force field   Edroaldo Lummertz da Rocha
• [gmx-users] Velocity of atom   Nilesh Dhumal
  • [gmx-users] Velocity of atom   Justin A. Lemkul
• [gmx-users] reference structure of g_rms   Hsin-Lin Chiang
• [gmx-users] Regarding xtc   Ravi Kumar Venkatraman
  • [gmx-users] Regarding xtc   Justin A. Lemkul
• Re: Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water   wibke.sudholt at cloudbroker.com
• [gmx-users] Tutorial   Sara baretller
  • [gmx-users] Tutorial   Justin A. Lemkul
    • [gmx-users] Tutorial   Sara baretller
      • [gmx-users] Tutorial   Sara baretller
      • [gmx-users] Tutorial   Sara baretller
      • [gmx-users] Tutorial   Sara baretller
      • [gmx-users] Tutorial   Justin A. Lemkul
      • [gmx-users] Tutorial   Justin A. Lemkul
      • [gmx-users] Tutorial   Peter C. Lai
• [gmx-users] Force field for thiocyanate ions   Sanku M
  • [gmx-users] Force field for thiocyanate ions   Mark Abraham
• Re: Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.   wibke.sudholt at cloudbroker.com
• [gmx-users] GROMACS 4.5.4 keep crashing all the time.   chris.neale at utoronto.ca
  • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Justin A. Lemkul
    • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Itamar Kass
      • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Mark Abraham
      • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Itamar Kass
      • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Justin A. Lemkul
      • [gmx-users] GROMACS 4.5.4 keep crashing all the time.   Itamar Kass
• [gmx-users] Segmentation fault after mdrun for MD simulation   rainy908
  • [gmx-users] Segmentation fault after mdrun for MD simulation   Justin A. Lemkul
• [gmx-users] GROMACS 4.5.4 keep crashing all the time   chris.neale at utoronto.ca
  • [gmx-users] GROMACS 4.5.4 keep crashing all the time   Itamar Kass
• [gmx-users] GROMACS 4.5.4 keep crashing all the time   chris.neale at utoronto.ca
• [gmx-users] Not receiving replies   Kavyashree M
  • [gmx-users] Not receiving replies   Justin A. Lemkul
    • [gmx-users] Not receiving replies   Kavyashree M
      • [gmx-users] Not receiving replies   Mark Abraham
• [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure   KONG Xian
• [gmx-users] mdrun did not support large file offsets   Bert
  • [gmx-users] mdrun did not support large file offsets   Justin A. Lemkul
• [gmx-users] Segmentation fault after mdrun for MD simulation   rainy908
  • [gmx-users] Segmentation fault after mdrun for MD simulation   Mark Abraham
• [gmx-users] Using genbox to REMOVE solvent   Michael Daily
  • [gmx-users] Using genbox to REMOVE solvent   Mark Abraham
    • [gmx-users] Using genbox to REMOVE solvent   Michael Daily
      • [gmx-users] Using genbox to REMOVE solvent   Michael Daily
• [gmx-users] VSMP cluster performance changes with time   Anupam Nath Jha
  • [gmx-users] VSMP cluster performance changes with time   Mark Abraham
    • [gmx-users] VSMP cluster performance changes with time   Anupam Nath Jha
• [gmx-users] RE: mdrun did not support large file offsets   Bert
• [gmx-users] Slicing .gro file geometry   shikha nangia
  • [gmx-users] Slicing .gro file geometry   Mark Abraham
• [gmx-users] constraints on angle   Nilesh Dhumal
  • [gmx-users] constraints on angle   Tsjerk Wassenaar
  • [gmx-users] constraints on angle   Mark Abraham
    • [gmx-users] constraints on angle   Junior Nebeker
      • [gmx-users] constraints on angle   Mark Abraham
      • [gmx-users] constraints on angle   Junior Nebeker
      • [gmx-users] use of the mailing list   Mark Abraham
      • [gmx-users] use of the mailing list   Junior Nebeker
      • [gmx-users] use of the mailing list   Mark Abraham
      • [gmx-users] use of the mailing list   Amit Choubey
      • [gmx-users] use of the mailing list   Junior Nebeker
• [gmx-users] Tutorial   Sara baretller
  • [gmx-users] Tutorial   Sara baretller
    • [gmx-users] Tutorial   Sara baretller
      • [gmx-users] Tutorial   Justin A. Lemkul
• [gmx-users]Self-defined force-field problem, atomtype Nr not found   Ye Yang
  • [gmx-users]Self-defined force-field problem, atomtype Nr not found   Justin A. Lemkul
    • [gmx-users]Self-defined force-field problem, atomtype Nr not found   Ye Yang
      • [gmx-users]Self-defined force-field problem, atomtype Nr not found   Justin A. Lemkul
      • [gmx-users]Self-defined force-field problem, atomtype Nr not found   Ye Yang
• [gmx-users] extract subset from cpt?   Peter C. Lai
  • [gmx-users] extract subset from cpt?   Justin A. Lemkul
• [gmx-users]Self-defined force-field problem, atomtype Nr not found   Justin A. Lemkul
• [gmx-users] extract subset from cpt?   Roland Schulz
  • [gmx-users] extract subset from cpt?   Justin A. Lemkul
• [gmx-users] extract subset from cpt?   Roland Schulz
• [gmx-users] mdp params and forcefields   Алексей Раевский
  • [gmx-users] mdp params and forcefields   Justin A. Lemkul
• Re: Re: [gmx-users] constraints on angle   wibke.sudholt at cloudbroker.com
• [gmx-users] more than 100% CPU   Park, Jae Hyun nmn
  • [gmx-users] more than 100% CPU   Warren Gallin
    • [gmx-users] more than 100% CPU   Park, Jae Hyun nmn
      • [gmx-users] more than 100% CPU   Warren Gallin
    • [gmx-users] more than 100% CPU   felmerino at uchile.cl
• [gmx-users] GROMACS with GPU   Park, Jae Hyun nmn
  • [gmx-users] GROMACS with GPU   Szilárd Páll
    • [gmx-users] GROMACS with GPU   Jones de Andrade
• [gmx-users] more than 100% CPU   chris.neale at utoronto.ca
  • [gmx-users] more than 100% CPU   Szilárd Páll
    • [gmx-users] more than 100% CPU   Park, Jae Hyun nmn
• [gmx-users] Regarding g_sham:Please reply   bipin singh
  • [gmx-users] Regarding g_sham:Please reply   Mark Abraham
• [gmx-users] Прочитайте ваше сообщение или оно будет удалено!   Badoo
• [Fwd: Re: [gmx-users] VSMP cluster performance changes with time]   Anupam Nath Jha
  • [Fwd: Re: [gmx-users] VSMP cluster performance changes with time]   Mark Abraham
• [gmx-users] calculate residence time for a protein complex   aiswarya pawar
• [gmx-users] -ter option with pdb2gmx   Vijayaraj
  • [gmx-users] -ter option with pdb2gmx   Justin A. Lemkul
• [gmx-users] Possible bug in g_hbond with implicit solvent   Justin A. Lemkul
  • [gmx-users] Possible bug in g_hbond with implicit solvent   Mark Abraham
    • [gmx-users] Possible bug in g_hbond with implicit solvent   Justin A. Lemkul
      • [gmx-users] Possible bug in g_hbond with implicit solvent   Mark Abraham
• [gmx-users] -ter option with pdb2gmx   Vijayaraj
  • [gmx-users] -ter option with pdb2gmx   Mark Abraham
• [gmx-users] g_rdf   Nilesh Dhumal
  • [gmx-users] g_rdf   Justin A. Lemkul
• [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure   KONG Xian
  • [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure   Amit Choubey
  • [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure   Jianguo Li
• [gmx-users] parameters for CH1 -- S -- CH2 ?   Yun Shi
  • [gmx-users] parameters for CH1 -- S -- CH2 ?   Mark Abraham
• [gmx-users] h-bonds constraints   Dr. Vitaly V. Chaban
  • [gmx-users] h-bonds constraints   Bogdan Costescu
    • [gmx-users] h-bonds constraints   Dr. Vitaly V. Chaban
• [gmx-users] NPT - density off   Elisabeth
  • [gmx-users] NPT - density off   Mark Abraham
    • [gmx-users] NPT - density off   Elisabeth
      • [gmx-users] NPT - density off   Mark Abraham
• Re: [gmx-users] NPT - density off   wibke.sudholt at cloudbroker.com
• [gmx-users] increasing cut-off and PME grid spacing   Hsin-Lin Chiang
  • [gmx-users] increasing cut-off and PME grid spacing   Justin A. Lemkul
• [gmx-users] increasing cut-off and PME grid spacing   Hsin-Lin Chiang
• [gmx-users] increasing cut-off and PME grid spacing   Hsin-Lin Chiang
  • [gmx-users] increasing cut-off and PME grid spacing   Justin A. Lemkul
• [gmx-users] Warning and Notes in Grompp for minimization   meisam valizadeh kiamahalleh
  • [gmx-users] Warning and Notes in Grompp for minimization   Justin A. Lemkul
• [gmx-users] problem with g_density -center   Sanku M
  • [gmx-users] problem with g_density -center   Justin A. Lemkul
• [gmx-users] problem with g_density -center   chris.neale at utoronto.ca
• Re: [gmx-users] problem with g_density -center   wibke.sudholt at cloudbroker.com
• [gmx-users] wibke.sudholt spam needs to stop   chris.neale at utoronto.ca
  • [gmx-users] Sorry for the autoreplies!   Wibke Sudholt
• [gmx-users] increasing cut-off and PME grid spacing   Hsin-Lin Chiang
  • [gmx-users] increasing cut-off and PME grid spacing   Justin A. Lemkul
• [gmx-users] increasing cut-off and PME grid spacing   Hsin-Lin Chiang
• [gmx-users] Re: Warning and Notes in Grompp for minimization   meisam valizadeh kiamahalleh
  • [gmx-users] Re: Warning and Notes in Grompp for minimization   Mark Abraham
• [gmx-users] Re: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure   Jianguo Li
• Re: [gmx-users] Re: Re：the mdp parameters for lo calpressure calculation using gromacs-4.0.2_localpressure   wibke.sudholt at cloudbroker.com
• [gmx-users] gmx-users Digest, Vol 88, Issue 131   meisam valizadeh kiamahalleh
  • [gmx-users] gmx-users Digest, Vol 88, Issue 131   Mark Abraham
• [gmx-users] calculate residence time for a protein complex   aiswarya pawar
  • [gmx-users] calculate residence time for a protein complex   Mark Abraham
• Antw: Re: [gmx-users] calculate residence time for a protein complex   Emanuel Peter
  • Antw: Re: [gmx-users] calculate residence time for a protein complex   aiswarya.pawar at gmail.com
  • Antw: Re: [gmx-users] calculate residence time for a protein complex   aiswarya.pawar at gmail.com
• [gmx-users] PS_PC system   Du Jiangfeng (BIOCH)
  • [gmx-users] PS_PC system   Justin A. Lemkul
• [gmx-users] Free Energy Integrator Selection   Fabian Casteblanco
  • [gmx-users] Free Energy Integrator Selection   Justin A. Lemkul
    • [gmx-users] Free Energy Integrator Selection   Marcelino Arciniega Castro
• [gmx-users] dihedral problem when converging Charmm FF into Gromacs format   Baofu Qiao
• [gmx-users] parallel job crash for large system   Dr. Vitaly V. Chaban
  • [gmx-users] Re: parallel job crash for large system   Dr. Vitaly V. Chaban
    • [gmx-users] Re: parallel job crash for large system   Mark Abraham
• [gmx-users] Re: parallel job crash for large system   chris.neale at utoronto.ca
• [gmx-users] g_hbond simple question   Yao Yao
  • [gmx-users] g_hbond simple question   Justin A. Lemkul
• [gmx-users] Re: parallel job crash for large system   Dr. Vitaly V. Chaban
  • [gmx-users] Re: parallel job crash for large system   Mark Abraham
  • [gmx-users] Re: parallel job crash for large system   Dr. Vitaly V. Chaban
• [gmx-users] Re: parallel job crash for large system   Dr. Vitaly V. Chaban
  • [gmx-users] Re: parallel job crash for large system   Dr. Vitaly V. Chaban
• [gmx-users] OPLS-AA Unknown Atomtype   Yao Yao
  • [gmx-users] OPLS-AA Unknown Atomtype   Justin A. Lemkul
• [gmx-users] Free Energy Integrator Selection   chris.neale at utoronto.ca
• [gmx-users] Re: pdb2gmx fatal error - atom not found   Justin A. Lemkul
• [gmx-users] 答复: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure   KONG Xian
• [gmx-users] (no subject)   Joschua Sterzenbach
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] Regarding xpm2ps   bipin singh
  • [gmx-users] Regarding xpm2ps   Justin A. Lemkul
    • [gmx-users] Regarding xpm2ps   bipin singh
      • [gmx-users] Regarding xpm2ps   Justin A. Lemkul
      • [gmx-users] Regarding xpm2ps   bipin singh
      • [gmx-users] Regarding xpm2ps   Justin A. Lemkul
      • [gmx-users] Regarding xpm2ps   bipin singh
      • [gmx-users] Regarding xpm2ps   Justin A. Lemkul
      • [gmx-users] Regarding xpm2ps   bipin singh
• [gmx-users] OPLS-AA Unknown Atomtype   Justin A. Lemkul
  • [gmx-users] OPLS-AA Unknown Atomtype   Yao Yao
    • [gmx-users] OPLS-AA Unknown Atomtype   Justin A. Lemkul
      • [gmx-users] OPLS-AA Unknown Atomtype   Yao Yao
      • [gmx-users] OPLS-AA Unknown Atomtype   Justin A. Lemkul
• [gmx-users] Viscosity units: Please Reply   Rini Gupta
• [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Kamesh Narasimhan
  • [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Jianguo Li
    • [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Kamesh Narasimhan
      • [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Jianguo Li
      • [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Kamesh Narasimhan
      • [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Oliver Grant
      • [gmx-users] error:You might need to add atom H to the hydrogen database of residue   Kamesh Narasimhan
• [gmx-users] Conversion of gromacs trajectory file   aiswarya.pawar at gmail.com
  • [gmx-users] Conversion of gromacs trajectory file   Justin A. Lemkul
• [gmx-users] Conversion of gromacs trajectory file   aiswarya.pawar at gmail.com
• [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
  • [gmx-users] Hydrogen existence time   Justin A. Lemkul
• [gmx-users] Convert drug Charmm topology to Gromacs   Steven Neumann
  • [gmx-users] Convert drug Charmm topology to Gromacs   Justin A. Lemkul
    • [gmx-users] Convert drug Charmm topology to Gromacs   Mark Abraham
  • [gmx-users] Convert drug Charmm topology to Gromacs   Jianguo Li
    • [gmx-users] Convert drug Charmm topology to Gromacs   Steven Neumann
      • [gmx-users] Convert drug Charmm topology to Gromacs   Justin A. Lemkul
• [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
  • [gmx-users] Hydrogen existence time   Justin A. Lemkul
• [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
  • [gmx-users] Hydrogen existence time   Justin A. Lemkul
• Antw: Re: [gmx-users] Hydrogen existence time   Emanuel Peter
  • Antw: Re: [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
• [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
  • [gmx-users] Hydrogen existence time   Mark Abraham
    • [gmx-users] Hydrogen existence time   aiswarya pawar
• Antw: Re: [gmx-users] Hydrogen existence time   Emanuel Peter
  • Antw: Re: [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
• Antw: Re: [gmx-users] Hydrogen existence time   aiswarya.pawar at gmail.com
• [gmx-users] gromacs: sound wave in liquid?   Juliette N.
  • [gmx-users] gromacs: sound wave in liquid?   Dommert Florian
  • [gmx-users] gromacs: sound wave in liquid?   Jussi Lehtola
• Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time   Emanuel Peter
• [gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule   Pablo Englebienne
  • [gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule   Mark Abraham
• [gmx-users] Convert drug Charmm topology to Gromacs   Fabian Casteblanco
  • [gmx-users] Convert drug Charmm topology to Gromacs   Alexandre Suman de Araujo
  • [gmx-users] Re: Convert drug Charmm topology to Gromacs   Fabian Casteblanco
    • [gmx-users] Re: Convert drug Charmm topology to Gromacs   Alexandre Suman de Araujo
      • [gmx-users] Re: Convert drug Charmm topology to Gromacs   Justin A. Lemkul
• [gmx-users] index file subgroups   Elisabeth
  • [gmx-users] index file subgroups   Justin A. Lemkul
• [gmx-users] gd_29 or gd_41 ?   Yun Shi
  • [gmx-users] Re: gd_29 or gd_41 ?   Yun Shi
    • [gmx-users] Re: gd_29 or gd_41 ?   Justin A. Lemkul
  • [gmx-users] gd_29 or gd_41 ?   Justin A. Lemkul
• [gmx-users] sugar dihedral parameters   Yun Shi
  • [gmx-users] sugar dihedral parameters   Justin A. Lemkul
• [gmx-users] surface area calculations for MARTINI   Michael Daily
• Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time   Emanuel Peter
  • Antw: Re: [gmx-users] Hydrogen existence time   aiswarya pawar
• Antw: Re: Re: Antw: Re: [gmx-users] Hydrogen existence time   Emanuel Peter
• [gmx-users] g_wham issue   shikha nangia
• [gmx-users] Obtaining protein structure   Steven Neumann
  • [gmx-users] Obtaining protein structure   Justin A. Lemkul
  • [gmx-users] Obtaining protein structure   Mark Abraham
    • [gmx-users] Obtaining protein structure   Steven Neumann
      • [gmx-users] Obtaining protein structure   Justin A. Lemkul
• [gmx-users] g_wham issue   chris.neale at utoronto.ca
• [gmx-users] sequence of mdrun commands   Yongchul Chung
  • [gmx-users] sequence of mdrun commands   Justin A. Lemkul
    • [gmx-users] sequence of mdrun commands   Tsjerk Wassenaar
      • [gmx-users] sequence of mdrun commands   Yongchul Chung
• [gmx-users] Hamiltonian REMD code uploaded in gromacs / user contributions / other software   Mu Yuguang (Dr)
• [gmx-users] reg g_sas   vidhya sankar
  • [gmx-users] reg g_sas   Justin A. Lemkul
• [gmx-users] postdoc positions in chemical physics   Dr. Vitaly V. Chaban
• [gmx-users] To Justin   vidhya sankar
  • [gmx-users] To Justin   Justin A. Lemkul
• [gmx-users] LJ-14 / LJ(SR)   Juliette N.
  • [gmx-users] LJ-14 / LJ(SR)   Justin A. Lemkul
    • [gmx-users] LJ-14 / LJ(SR)   Juliette N.
• [gmx-users] Error from residues added to rtp file   Delmotte, Antoine
  • [gmx-users] Error from residues added to rtp file   Thomas Piggot
    • [gmx-users] Error from residues added to rtp file   Delmotte, Antoine
      • [gmx-users] Error from residues added to rtp file   Mark Abraham
• [gmx-users] coordinated of center of mass   shikha nangia
  • [gmx-users] coordinated of center of mass   Tsjerk Wassenaar
• [gmx-users] Re: LJ   Dr. Vitaly V. Chaban
  • [gmx-users] Re: LJ   Dr. Vitaly V. Chaban
    • [gmx-users] Re: LJ   Juliette N.
      • [gmx-users] Re: LJ   Justin A. Lemkul
      • [gmx-users] Re: LJ   Juliette N.
      • [gmx-users] Re: LJ   Dr. Vitaly V. Chaban
      • [gmx-users] Re: LJ   Justin A. Lemkul
      • [gmx-users] Re: LJ   Dr. Vitaly V. Chaban
• [gmx-users] If the system net charge is zero, do I need to add ions?   "Dr. Ramón Garduño-Juárez"
  • [gmx-users] If the system net charge is zero, do I need to add ions?   Justin A. Lemkul
• [gmx-users] proper dihedral types in the topology   ZHANG Lu
• [gmx-users] termini modification   Vijayaraj
  • [gmx-users] termini modification   lina
    • [gmx-users] termini modification   Justin A. Lemkul
• [gmx-users] cannot inactivate fitting in g_rmsf - incomplete coordinates are written   Thomas Evangelidis
• [gmx-users] part number in extending simulation   Hsin-Lin Chiang
  • [gmx-users] part number in extending simulation   Dommert Florian
• [gmx-users] Free energy   pawan raghav
• [gmx-users] part number in extending simulation   Hsin-Lin Chiang
  • [gmx-users] part number in extending simulation   Dommert Florian
• [gmx-users] part number in extending simulation   Hsin-Lin Chiang
• [gmx-users] distance between mass center of two groups   Sajad Ahrari
  • [gmx-users] distance between mass center of two groups   Amit Choubey
  • [gmx-users] distance between mass center of two groups   Mark Abraham
• [gmx-users] amber DNA non-integer charge   Kamesh Narasimhan
  • [gmx-users] amber DNA non-integer charge   Justin A. Lemkul
    • [gmx-users] amber DNA non-integer charge   Kamesh Narasimhan
      • [gmx-users] amber DNA non-integer charge   Justin A. Lemkul
      • [gmx-users] amber DNA non-integer charge   Kamesh Narasimhan
• [gmx-users] Phd positions available   Giovanni Bussi
• [gmx-users] Error found on grompp - energy minimization   ITHAYARAJA
  • [gmx-users] Error found on grompp - energy minimization   Mark Abraham
• [gmx-users] Re: gromacs question topologie   Justin A. Lemkul
• [gmx-users] Re: Difficulty building a topology for a synthetic, branched PEG-peptide molecule [SOLVED]   Pablo Englebienne
• [gmx-users] simulation at higher temperatures   arun kumar
  • [gmx-users] simulation at higher temperatures   Justin A. Lemkul
• [gmx-users] g_lie   pawan raghav
• [gmx-users] MARTINI / all-atom mapping   Michael Daily
  • [gmx-users] MARTINI / all-atom mapping   XAvier Periole
    • [gmx-users] MARTINI / all-atom mapping   Michael Daily
      • [gmx-users] MARTINI / all-atom mapping   Justin A. Lemkul
      • [gmx-users] MARTINI / all-atom mapping   Thomas Piggot
      • [gmx-users] MARTINI / all-atom mapping   XAvier Periole
• [gmx-users] restarting a crashed job   Payman Pirzadeh
  • [gmx-users] restarting a crashed job   Mark Abraham
• [gmx-users] Jumping protein   Steven Neumann
  • [gmx-users] Jumping protein   Justin A. Lemkul
• [gmx-users] trjconv - Protein and jumping ligands   Steven Neumann
  • [gmx-users] trjconv - Protein and jumping ligands   Justin A. Lemkul
• [gmx-users] Please rectify free energy problem   pawan raghav
  • [gmx-users] Please rectify free energy problem   Mark Abraham
• [gmx-users] simulation at higher temperatures gmx-users Digest, Vol 88, Issue 167   arun kumar
  • [gmx-users] simulation at higher temperatures   Justin A. Lemkul
• [gmx-users] g_energy - what is COMPull En   Ilona Baldus
• [gmx-users] Buckingham interactions   xiaojing gong
  • [gmx-users] Buckingham interactions   Mark Abraham
• [gmx-users] Fatal error when position restraint the coordinates-reg   ITHAYARAJA
  • [gmx-users] Fatal error when position restraint the coordinates-reg   Mark Abraham
• [gmx-users] remove the atom clashes-reg   ITHAYARAJA
  • [gmx-users] remove the atom clashes-reg   Mark Abraham
• [gmx-users] g_hbond   Steven Neumann
  • [gmx-users] g_hbond   Justin A. Lemkul
    • [gmx-users] g_hbond   Steven Neumann
      • [gmx-users] g_hbond   Justin A. Lemkul
      • [gmx-users] g_hbond   Steven Neumann
      • [gmx-users] g_hbond   Justin A. Lemkul
      • [gmx-users] g_hbond   Steven Neumann
      • [gmx-users] g_hbond   Steven Neumann
      • [gmx-users] g_hbond   Justin A. Lemkul
      • [gmx-users] g_hbond   Justin A. Lemkul
      • [gmx-users] g_hbond   Steven Neumann
      • [gmx-users] g_hbond   Justin A. Lemkul
• [gmx-users] pdb2gmx of nucleic acids with ffamber03 force field   MARIA ICIAR FRADES ALZUETA
  • [gmx-users] pdb2gmx of nucleic acids with ffamber03 force field   Justin A. Lemkul
• [gmx-users] Free energy calculation question   Fabian Casteblanco
  • [gmx-users] Free energy calculation question   Justin A. Lemkul
  • [gmx-users] Re: Free energy calculation question   Fabian Casteblanco
    • [gmx-users] Re: Free energy calculation question   Justin A. Lemkul
  • [gmx-users] Re: Free energy calculation question   Fabian Casteblanco
    • [gmx-users] Re: Free energy calculation question   Justin A. Lemkul
  • [gmx-users] Re: Free energy calculation question   Fabian Casteblanco
• [gmx-users] doubt in deuterium order parameter   Parthasarathi, Ramya
• [gmx-users] order parameter   Parthasarathi, Ramya
• [gmx-users] which charge is used in gromacs program   GZ Zhang
  • [gmx-users] which charge is used in gromacs program   Justin A. Lemkul

Last message date: Wed Aug 31 23:20:19 CEST 2011
Archived on: Thu Nov 14 12:11:30 CET 2013

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