December 2012 Archives by author

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Starting: Sat Dec 1 07:18:56 CET 2012
Ending: Mon Dec 31 23:54:56 CET 2012
Messages: 669

[gmx-users] conformational change Shine A
[gmx-users] change in conformation Shine A
[gmx-users] oplsaa force field Shine A
[gmx-users] (no subject) Shine A
[gmx-users] segmentation fault Shine A
[gmx-users] amber forcefield Shine A
[gmx-users] structure building and manipulating software Amir Abbasi
[gmx-users] Installing 4.6 beta1 Mark Abraham
[gmx-users] Energy estimations of the protein-ligand complexes Mark Abraham
[gmx-users] strange lincs warning with version 4.6 Mark Abraham
[gmx-users] strange lincs warning with version 4.6 Mark Abraham
[gmx-users] GROMACS 4.6-beta2 released Mark Abraham
[gmx-users] GROMACS 4.6-beta2 released Mark Abraham
[gmx-users] Fwd: [gmx-developers] cmake bug when install GMX 4.6 beta2 Mark Abraham
[gmx-users] Installation Error Mark Abraham
[gmx-users] Error during compilation of Gromacs-4.5.5 Mark Abraham
[gmx-users] GPU compatibility Mark Abraham
[gmx-users] What is the purpose of the [ pairs ] section? Mark Abraham
[gmx-users] What is the purpose of the [ pairs ] section? Mark Abraham
[gmx-users] Error with MARTINI depending by the box size Mark Abraham
[gmx-users] Error with MARTINI depending by the box size Mark Abraham
[gmx-users] Error with MARTINI depending by the box size Mark Abraham
[gmx-users] Error with MARTINI depending by the box size Mark Abraham
[gmx-users] Is there any tool in gromacs for calculating intermolecular interactions and intramolecular interactions indepedently? Mark Abraham
[gmx-users] Atom index (13154) in position_restraints out of bounds Mark Abraham
[gmx-users] force autocorrelation Mark Abraham
[gmx-users] glibc error Mark Abraham
[gmx-users] Re: force autocorrelation Mark Abraham
[gmx-users] I want to stop my run Mark Abraham
[gmx-users] g_sas : Total surface area Mark Abraham
[gmx-users] Re: I want to stop my run Mark Abraham
[gmx-users] Re: force autocorrelation Mark Abraham
[gmx-users] REMD simulation Mark Abraham
[gmx-users] particle decomposition with distance restraints Mark Abraham
[gmx-users] trjconv -split Mark Abraham
[gmx-users] particle decomposition with distance restraints Mark Abraham
[gmx-users] Question about 'mdrun -nosum' Mark Abraham
[gmx-users] GPU running problem with GMX-4.6 beta2 Mark Abraham
[gmx-users] increase of temperature or pressure Mark Abraham
[gmx-users] GROMACS 4.6 beta 3 is out! Mark Abraham
[gmx-users] Re: about -return of mdrun Mark Abraham
[gmx-users] Continuing a simulation Mark Abraham
[gmx-users] does error estimate given by g_energy considering auto-correlation? Mark Abraham
[gmx-users] problems installing 4.5.5 on mac Mark Abraham
[gmx-users] g_dih calculation doubt Mark Abraham
[gmx-users] Dangling bond at terminal end of RNA rosetta model Mark Abraham
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC Mark Abraham
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC Mark Abraham
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC Mark Abraham
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC Mark Abraham
[gmx-users] Build on OSX with 4.6beta1 Albert
[gmx-users] Build on OSX with 4.6beta1 Albert
[gmx-users] failed with intel compiler Albert
[gmx-users] amber to gromacs error Albert
[gmx-users] GPU running problem with GMX-4.6 beta2 Albert
[gmx-users] GPU running problem with GMX-4.6 beta2 Albert
[gmx-users] GPU running problem with GMX-4.6 beta2 Albert
[gmx-users] GPU running problem with GMX-4.6 beta2 Albert
[gmx-users] GPU running problem with GMX-4.6 beta2 Albert
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Albert
[gmx-users] voltage for membrane? Albert
[gmx-users] how to convert CGenFF into .itp file? Albert
[gmx-users] how to convert CGenFF into .itp file? Albert
[gmx-users] how to convert CGenFF into .itp file? Albert
[gmx-users] how to convert CGenFF into .itp file? Albert
[gmx-users] Can i construct a solid wall in gromacs? Ali Alizadeh
[gmx-users] Re: Can i construct a solid wall in gromacs? Ali Alizadeh
[gmx-users] I want to stop my run Ali Alizadeh
R: [gmx-users] Metadynamics with Esential Dynamics Sampling Spitaleri Andrea
[gmx-users] area per lipid Shima Arasteh
[gmx-users] Protein-POPC-water Shima Arasteh
[gmx-users] Poteintial energy of my system Shima Arasteh
[gmx-users] Re: Poteintial energy of my system Shima Arasteh
[gmx-users] Re: Poteintial energy of my system Shima Arasteh
[gmx-users] Re: Poteintial energy of my system Shima Arasteh
[gmx-users] Re: Poteintial energy of my system Shima Arasteh
[gmx-users] Energy minimization Shima Arasteh
[gmx-users] Energy minimization Shima Arasteh
Fw: [gmx-users] Energy minimization Shima Arasteh
[gmx-users] Energy minimization Shima Arasteh
[gmx-users] Energy minimization Shima Arasteh
[gmx-users] protein membrane system Shima Arasteh
[gmx-users] protein membrane system Shima Arasteh
[gmx-users] protein membrane system Shima Arasteh
[gmx-users] Delete some molecules from gro file Shima Arasteh
[gmx-users] Delete some molecules from gro file Shima Arasteh
[gmx-users] water can not be settled Shima Arasteh
[gmx-users] water can not be settled Shima Arasteh
[gmx-users] Index file Shima Arasteh
[gmx-users] Index file Shima Arasteh
[gmx-users] Index file Shima Arasteh
[gmx-users] Index file Shima Arasteh
[gmx-users] Index file Shima Arasteh
[gmx-users] Re: Pulling ion - US Leandro Bortot
[gmx-users] conformational change Leandro Bortot
[gmx-users] Re: Simulation of 2D lattice model Leandro Bortot
[gmx-users] Re: gmx-users Digest, Vol 104, Issue 7 Carlo Camilloni
[gmx-users] Re: Build on OSX with 4.6beta1 Carlo Camilloni
[gmx-users] Index file Luis Felipe Pineda de Castro
[gmx-users] What is the purpose of the [ pairs ] section? Javier Cerezo
[gmx-users] Re: Can i construct a solid wall in gromacs? Dr. Vitaly Chaban
[gmx-users] Re: I want to stop my run Dr. Vitaly Chaban
[gmx-users] Re: Langevin Dynamics Dr. Vitaly Chaban
[gmx-users] Re: Langevin Dynamics Dr. Vitaly Chaban
[gmx-users] Is there any tool in gromacs for calculating intermolecular interactions and intramolecular interactions indepedently? Wu Chaofu
[gmx-users] about -return of mdrun Wu Chaofu
[gmx-users] g_tune_pme for multiple nodes Chandan Choudhury
[gmx-users] g_tune_pme for multiple nodes Chandan Choudhury
[gmx-users] g_tune_pme for multiple nodes Chandan Choudhury
[gmx-users] Index file Chandan Choudhury
[gmx-users] Index file Chandan Choudhury
[gmx-users] Scientific notation in .itp files Bogdan Costescu
[gmx-users] Re: What is the purpose of the [ pairs ] section? Bogdan Costescu
[gmx-users] Installation Error BHARATI DUTTA
[gmx-users] Error during compilation of Gromacs-4.5.5 BHARATI DUTTA
[gmx-users] Question about dihedral angle notation Andrew DeYoung
[gmx-users] Specifying no temperature coupling in contrast to grompp output Andrew DeYoung
[gmx-users] Scientific notation in .itp files Andrew DeYoung
[gmx-users] What is the purpose of the [ pairs ] section? Andrew DeYoung
[gmx-users] Re: What is the purpose of the [ pairs ] section? Andrew DeYoung
[gmx-users] Re: What is the purpose of the [ pairs ] section? Andrew DeYoung
[gmx-users] Re: What is the purpose of the [ pairs ] section? Andrew DeYoung
[gmx-users] Coordinates problem Marcelo Depolo
[gmx-users] Fatal Error with AMBER03 Marcelo Depolo
[gmx-users] Invalid line in coordinate file Shine Devaraj
[gmx-users] pbs not returning gromacs files John Doe
[gmx-users] Printing thermo data John Doe
[gmx-users] Box Pressure on individual box walls John Doe
[gmx-users] conformational change Julio Dominguez
[gmx-users] conformational change Julio Dominguez
[gmx-users] RE: gmx-users Digest, Vol 104, Issue 114 Julio Dominguez
[gmx-users] merge .gro, .top files Vedat Durmaz
[gmx-users] GPU warnings Thomas Evangelidis
[gmx-users] pca-based MD Thomas Evangelidis
[gmx-users] (no subject) ANINDITA GAYEN
[gmx-users] (no subject) ANINDITA GAYEN
[gmx-users] after genbox Nur Syafiqah Abdul Ghani
[gmx-users] add more solvent? Nur Syafiqah Abdul Ghani
[gmx-users] System killed after genbox Nur Syafiqah Abdul Ghani
[gmx-users] Hbonds between Adenine and Thymine Hovakim Grabski
[gmx-users] Solvating Podophyllotoxin in ethanol Hovakim Grabski
[gmx-users] intermolecular rdfs for a bulky cation Jeevapani Ha
Fw: [gmx-users] intermolecular rdfs for a bulky cation Jeevapani Ha
[gmx-users] Restart a run with different files Davit Hakobyan
[gmx-users] gold-protein simulation stop by error in equilibrum step Martin Hoefling
[gmx-users] voltage for membrane? Martin Hoefling
[gmx-users] editconf not centering, and it is cutting off my molecule Xu Dong Huang
[gmx-users] editconf not centering, and it is cutting off my molecule Xu Dong Huang
[gmx-users] editconf not centering, and it is cutting off my molecule Xu Dong Huang
[gmx-users] virtual site generation for backbone hydrogen Jochen Hub
[gmx-users] virtual site generation for backbone hydrogen Jochen Hub
[gmx-users] exact average distances with g_mdmat IsaureCB
[gmx-users] time-dependent electric field Norbert Jeszenői
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Joakim Jämbeck
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Joakim Jämbeck
[gmx-users] Re: force autocorrelation Keith
[gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions Ariana Torres Knoop
[gmx-users] GPU compatibility Cara Kreck
[gmx-users] Mutation-induced binding affinity change using BAR Oliver Kuhn
[gmx-users] g_tune_pme for multiple nodes Carsten Kutzner
[gmx-users] g_tune_pme for multiple nodes Carsten Kutzner
[gmx-users] Essential dynamics (ED) sampling using make_edi Carsten Kutzner
[gmx-users] voltage for membrane? Carsten Kutzner
[gmx-users] voltage for membrane? Peter Lai
[gmx-users] voltage for membrane? Peter Lai
[gmx-users] barium ion simulation Peter C. Lai
[gmx-users] area per lipid Peter C. Lai
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Peter C. Lai
[gmx-users] gold-S simulation Peter C. Lai
[gmx-users] Energy minimization Peter C. Lai
[gmx-users] Energy minimization Peter C. Lai
[gmx-users] SDS micelle simulation in TFE solvent Peter C. Lai
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Peter C. Lai
[gmx-users] Energy minimization Peter C. Lai
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Peter C. Lai
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Peter C. Lai
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Peter C. Lai
[gmx-users] how to convert CGenFF into .itp file? Peter C. Lai
[gmx-users] how to convert CGenFF into .itp file? Peter C. Lai
[gmx-users] Is vacuum simulation NVT? Jong Wha Lee
[gmx-users] Re: Re: Is vacuum simulation NVT? Jong Wha Lee
[gmx-users] regarding the free energy calculation of justin tutorial... Justin Lemkul
[gmx-users] About Packing of Lipids Justin Lemkul
[gmx-users] Hbonds between Adenine and Thymine Justin Lemkul
[gmx-users] Question about dihedral angle notation Justin Lemkul
[gmx-users] help Justin Lemkul
[gmx-users] Interaction energy between two molecules. Justin Lemkul
[gmx-users] Build on OSX with 4.6beta1 Justin Lemkul
[gmx-users] Build on OSX with 4.6beta1 Justin Lemkul
[gmx-users] metal_ligand complex Justin Lemkul
[gmx-users] Can i construct a solid wall in gromacs? Justin Lemkul
[gmx-users] metal_ligand complex Justin Lemkul
[gmx-users] g_rms alignment question Justin Lemkul
[gmx-users] Coordinates problem Justin Lemkul
[gmx-users] system is not well equilibrated -Reg Justin Lemkul
[gmx-users] results of md Justin Lemkul
[gmx-users] results of md Justin Lemkul
[gmx-users] force field Justin Lemkul
[gmx-users] Green fluorescent protein's chromophore Justin Lemkul
[gmx-users] Asymmetry in homo dimer simulation Justin Lemkul
[gmx-users] Asymmetry in homo dimer simulation Justin Lemkul
[gmx-users] Green fluorescent protein's chromophore Justin Lemkul
[gmx-users] Asymmetry in homo dimer simulation Justin Lemkul
[gmx-users] Green fluorescent protein's chromophore Justin Lemkul
[gmx-users] Green fluorescent protein's chromophore Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] force field Justin Lemkul
[gmx-users] Asymmetry in homo dimer simulation Justin Lemkul
[gmx-users] Asymmetry in homo dimer simulation Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] How to merge Self-made ammonia .top with tip4p Justin Lemkul
[gmx-users] oplsff- need of gro and itp file -reg Justin Lemkul
[gmx-users] gold-protein simulation stop by error in equilibrum step Justin Lemkul
[gmx-users] add more solvent? Justin Lemkul
[gmx-users] GROMACS 4.6-beta2 released Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Specifying no temperature coupling in contrast to grompp output Justin Lemkul
[gmx-users] Scientific notation in .itp files Justin Lemkul
[gmx-users] Pulling ion - US Justin Lemkul
[gmx-users] Center of mass drift in interfacial systems. Justin Lemkul
[gmx-users] Pulling ion - US Justin Lemkul
[gmx-users] Re: What is the purpose of the [ pairs ] section? Justin Lemkul
[gmx-users] Re: What is the purpose of the [ pairs ] section? Justin Lemkul
[gmx-users] Error with MARTINI depending by the box size Justin Lemkul
[gmx-users] Error with MARTINI depending by the box size Justin Lemkul
[gmx-users] Error with MARTINI depending by the box size Justin Lemkul
[gmx-users] gen-vel=no Justin Lemkul
[gmx-users] Atom index (13154) in position_restraints out of bounds Justin Lemkul
[gmx-users] Is vacuum simulation NVT? Justin Lemkul
[gmx-users] Umbrella sampling - chain A does not get pulled Justin Lemkul
[gmx-users] DNA simulation Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Protein-POPC-water Justin Lemkul
[gmx-users] Re: What is the purpose of the [ pairs ] section? Justin Lemkul
[gmx-users] g_x2top help Justin Lemkul
[gmx-users] apply force to the protein Justin Lemkul
[gmx-users] Solvating Podophyllotoxin in ethanol Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] g_x2top help Justin Lemkul
[gmx-users] pbs not returning gromacs files Justin Lemkul
[gmx-users] gen-vel=no Justin Lemkul
[gmx-users] g_msd additional information Justin Lemkul
[gmx-users] Re: Poteintial energy of my system Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Re: Poteintial energy of my system Justin Lemkul
[gmx-users] g_sas : Total surface area Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Umbrella sampling - chain A does not get pulled Justin Lemkul
[gmx-users] Umbrella sampling - chain A does not get pulled Justin Lemkul
[gmx-users] how to build xtc file from many same crystal structures which are different conformational states. Justin Lemkul
[gmx-users] Invalid line in coordinate file Justin Lemkul
[gmx-users] Average values on the plot - Justin Tutorial Justin Lemkul
[gmx-users] conformational change Justin Lemkul
[gmx-users] Re: Langevin Dynamics Justin Lemkul
[gmx-users] Fatal Error with AMBER03 Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Printing thermo data Justin Lemkul
[gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields Justin Lemkul
[gmx-users] gold-S simulation Justin Lemkul
[gmx-users] Input vdwradii.dat file when using genbox Justin Lemkul
[gmx-users] oplsaa force field Justin Lemkul
[gmx-users] error while running mdrun Justin Lemkul
[gmx-users] error when running NVT equilibrium Justin Lemkul
[gmx-users] mdp file warnings Justin Lemkul
[gmx-users] mdp file warnings Justin Lemkul
[gmx-users] error when running NVT equilibrium Justin Lemkul
[gmx-users] error "No such moleculetype W" Justin Lemkul
[gmx-users] error "No such moleculetype W" Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Actual box size Justin Lemkul
[gmx-users] GPU running problem with GMX-4.6 beta2 Justin Lemkul
[gmx-users] Re: Actual box size Justin Lemkul
[gmx-users] Re: Actual box size Justin Lemkul
[gmx-users] Re: gold-S simulation Justin Lemkul
[gmx-users] question of improper dihedral of opls aa Justin Lemkul
[gmx-users] Error in energy minimization Justin Lemkul
[gmx-users] error while running mdrun Justin Lemkul
[gmx-users] MARTINI MD-CG Justin Lemkul
[gmx-users] Cutoff influence on performance Justin Lemkul
[gmx-users] What do res_cog, whole_res_cog, and part_res_cog mean in g_select? Justin Lemkul
[gmx-users] Re: Actual box size Justin Lemkul
[gmx-users] Pre-equilibrated CHARMM lipid bilayers Justin Lemkul
[gmx-users] Re: Actual box size Justin Lemkul
[gmx-users] g_sans Justin Lemkul
[gmx-users] System killed after genbox Justin Lemkul
[gmx-users] gold-S simulation Justin Lemkul
[gmx-users] Mutation-induced binding affinity change using BAR Justin Lemkul
[gmx-users] Where to stop with TM protein PMF calculations Justin Lemkul
[gmx-users] Where to stop with TM protein PMF calculations Justin Lemkul
[gmx-users] g_hbond index Justin Lemkul
[gmx-users] g_hbond index Justin Lemkul
[gmx-users] How to convert coarse-grained to fine-grained Justin Lemkul
[gmx-users] Re: High density after NPT Justin Lemkul
[gmx-users] g_sans Justin Lemkul
[gmx-users] Re: High density after NPT Justin Lemkul
[gmx-users] RE: Energy Minimization/ NpT settling problem Justin Lemkul
[gmx-users] Restart a run with different files Justin Lemkul
[gmx-users] about -return of mdrun Justin Lemkul
[gmx-users] exact average distances with g_mdmat Justin Lemkul
[gmx-users] Regarding coupling constant Justin Lemkul
[gmx-users] Re: Continuing a simulation plus another error Justin Lemkul
[gmx-users] Re: Continuing a simulation plus another error Justin Lemkul
[gmx-users] Rerun same trajectory - Pulling Justin Lemkul
[gmx-users] Update atom number after "cat" 2 file.gro Justin Lemkul
[gmx-users] Update atom number after "cat" 2 file.gro Justin Lemkul
[gmx-users] merge .gro, .top files Justin Lemkul
[gmx-users] protein membrane system Justin Lemkul
[gmx-users] Rerun same trajectory - Pulling Justin Lemkul
[gmx-users] Rerun same trajectory - Pulling Justin Lemkul
[gmx-users] Rerun same trajectory - Pulling Justin Lemkul
[gmx-users] protein membrane system Justin Lemkul
[gmx-users] Re: about -return of mdrun Justin Lemkul
[gmx-users] About topology for cyclic petide Justin Lemkul
[gmx-users] g_dih calculation doubt Justin Lemkul
[gmx-users] Dangling bond at terminal end of RNA rosetta model Justin Lemkul
[gmx-users] merge .gro, .top files Justin Lemkul
[gmx-users] amber forcefield Justin Lemkul
[gmx-users] question about define groups Justin Lemkul
[gmx-users] Delete some molecules from gro file Justin Lemkul
[gmx-users] GMXRC execution problem on centos Justin Lemkul
[gmx-users] water can not be settled Justin Lemkul
[gmx-users] PMF Transmembrane proteins Justin Lemkul
[gmx-users] PMF Transmembrane proteins Justin Lemkul
[gmx-users] Index file Justin Lemkul
[gmx-users] Index file Justin Lemkul
[gmx-users] Index file Justin Lemkul
[gmx-users] Index file Justin Lemkul
[gmx-users] editconf not centering, and it is cutting off my molecule Justin Lemkul
[gmx-users] editconf not centering, and it is cutting off my molecule Justin Lemkul
[gmx-users] editconf not centering, and it is cutting off my molecule Justin Lemkul
[gmx-users] Center of mass drift in interfacial systems. Anders Lervik
[gmx-users] particle decomposition with distance restraints Da-Wei Li
[gmx-users] particle decomposition with distance restraints Da-Wei Li
[gmx-users] particle decomposition with distance restraints Da-Wei Li
[gmx-users] Question about 'mdrun -nosum' Da-Wei Li
[gmx-users] Invitation to connect on LinkedIn Gideon Lapidoth via LinkedIn
[gmx-users] Join my network on LinkedIn Tuba KILINC via LinkedIn
[gmx-users] virtual sites with CHARMM lipids Bastien Loubet
[gmx-users] Dimer jumping during simulation Kavyashree M
[gmx-users] Re: Dimer jumping during simulation Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Kavyashree M
[gmx-users] g_sas : Total surface area Kavyashree M
[gmx-users] Re: g_sas : Total surface area Kavyashree M
[gmx-users] Re: g_sas : Total surface area Kavyashree M
[gmx-users] g_sas : Total surface area Kavyashree M
[gmx-users] g_sas : Total surface area Kavyashree M
[gmx-users] g_sas : Total surface area Kavyashree M
[gmx-users] g_hbond index Kavyashree M
[gmx-users] g_hbond index Kavyashree M
[gmx-users] g_hbond index Kavyashree M
[gmx-users] g_dih calculation doubt Kavyashree M
[gmx-users] g_dih calculation doubt Kavyashree M
[gmx-users] Asymmetry in homo dimer simulation Erik Marklund
[gmx-users] merge .gro, .top files Erik Marklund
[gmx-users] using g_analyze for calculating distance autocorrelation functions Erik Marklund
[gmx-users] gen-vel=no Bahar Mehrpuyan
[gmx-users] gen-vel=no Bahar Mehrpuyan
[gmx-users] Umbrella sampling - chain A does not get pulled Davide Mercadante
[gmx-users] Umbrella sampling - chain A does not get pulled Davide Mercadante
[gmx-users] Dihedral angle restraints Antonia Mey
[gmx-users] extract dihedrals from ALAD.pdb Antonia Mey
[gmx-users] How to merge Self-made ammonia .top with tip4p Kenji Mochizuki
[gmx-users] How to merge Self-made ammonia .top with tip4p Kenji Mochizuki
[gmx-users] g_analyze -oneacf Humphrey Morhenn
[gmx-users] Interaction energy between two molecules. Mortuza Munna
[gmx-users] PME vs Shift: Cut offs Juliette N.
[gmx-users] Where to stop with TM protein PMF calculations Nash, Anthony
[gmx-users] Where to stop with TM protein PMF calculations Nash, Anthony
[gmx-users] PMF Transmembrane proteins Nash, Anthony
[gmx-users] PMF Transmembrane proteins Nash, Anthony
[gmx-users] PMF Transmembrane proteins Nash, Anthony
[gmx-users] Pulling ion - US Steven Neumann
[gmx-users] Pulling ion - US Steven Neumann
[gmx-users] Pulling ion - US Steven Neumann
[gmx-users] Re: Pulling ion - US Steven Neumann
[gmx-users] Average values on the plot - Justin Tutorial Steven Neumann
[gmx-users] Average values on the plot - Justin Tutorial Steven Neumann
[gmx-users] Rerun same trajectory - Pulling Steven Neumann
[gmx-users] Gibbs free energy Steven Neumann
[gmx-users] Rerun same trajectory - Pulling Steven Neumann
[gmx-users] Gibbs free energy Steven Neumann
[gmx-users] Rerun same trajectory - Pulling Steven Neumann
[gmx-users] Rerun same trajectory - Pulling Steven Neumann
[gmx-users] Rerun same trajectory - Pulling Steven Neumann
[gmx-users] Rerun same trajectory - Pulling Steven Neumann
[gmx-users] Input vdwradii.dat file when using genbox Kieu Thu Nguyen
[gmx-users] Input vdwradii.dat file when using genbox Kieu Thu Nguyen
[gmx-users] Input vdwradii.dat file when using genbox Kieu Thu Nguyen
[gmx-users] error when running NVT equilibrium Kieu Thu Nguyen
[gmx-users] error when running NVT equilibrium Kieu Thu Nguyen
[gmx-users] error "No such moleculetype W" Kieu Thu Nguyen
[gmx-users] error "No such moleculetype W" Kieu Thu Nguyen
[gmx-users] error "No such moleculetype W" Kieu Thu Nguyen
[gmx-users] Error in energy minimization Kieu Thu Nguyen
[gmx-users] Error in energy minimization Kieu Thu Nguyen
[gmx-users] merge .gro, .top files Kieu Thu Nguyen
[gmx-users] merge .gro, .top files Kieu Thu Nguyen
[gmx-users] MARTINI MD-CG Kieu Thu Nguyen
[gmx-users] MARTINI MD-CG Kieu Thu Nguyen
[gmx-users] How to convert coarse-grained to fine-grained Kieu Thu Nguyen
[gmx-users] How to convert coarse-grained to fine-grained Kieu Thu Nguyen
[gmx-users] How to convert coarse-grained to fine-grained Kieu Thu Nguyen
[gmx-users] How to convert coarse-grained to fine-grained Kieu Thu Nguyen
[gmx-users] Update atom number after "cat" 2 file.gro Kieu Thu Nguyen
[gmx-users] Update atom number after "cat" 2 file.gro Kieu Thu Nguyen
[gmx-users] Update atom number after "cat" 2 file.gro Kieu Thu Nguyen
[gmx-users] merge .gro, .top files Kieu Thu Nguyen
[gmx-users] Convert .psf to .top Kieu Thu Nguyen
[gmx-users] Convert .psf to .top Kieu Thu Nguyen
[gmx-users] merge .gro, .top files Kieu Thu Nguyen
[gmx-users] Using g_membed with MD-CG Kieu Thu Nguyen
[gmx-users] Using g_membed with MD-CG Kieu Thu Nguyen
[gmx-users] Fatal Error with AMBER03 Eduardo Oliveira
[gmx-users] mdp file warnings Eduardo Oliveira
[gmx-users] mdp file warnings Eduardo Oliveira
[gmx-users] mdp file warnings Eduardo Oliveira
[gmx-users] Error with MARTINI depending by the box size XAvier Periole
[gmx-users] Dangling bond at terminal end of RNA rosetta model Gert Peters
[gmx-users] strange lincs warning with version 4.6 Thomas Piggot
[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs Payman Pirzadeh
[gmx-users] Build on OSX with 4.6beta1 Szilárd Páll
[gmx-users] Build on OSX with 4.6beta1 Szilárd Páll
[gmx-users] strange lincs warning with version 4.6 Szilárd Páll
[gmx-users] Re: Build on OSX with 4.6beta1 Szilárd Páll
[gmx-users] GPU warnings Szilárd Páll
[gmx-users] GPU warnings Szilárd Páll
[gmx-users] gromacs 4.6 on NVIDIA K10 Szilárd Páll
[gmx-users] GPU running problem with GMX-4.6 beta2 Szilárd Páll
[gmx-users] GPU running problem with GMX-4.6 beta2 Szilárd Páll
[gmx-users] GPU running problem with GMX-4.6 beta2 Szilárd Páll
[gmx-users] GPU running problem with GMX-4.6 beta2 Szilárd Páll
[gmx-users] virtual site in solvation free energy Qin Qiao
[gmx-users] Topolbuild configuration Bruce D. Ray
[gmx-users] gen-vel=no Venkat Reddy
[gmx-users] doubt regarding make_ndx Venkat Reddy
[gmx-users] g_membed *** glibc detected *** Ricardo
[gmx-users] Extending REMD simulations problem Kenny Bravo Rodriguez
[gmx-users] REMD simulation Kenny Bravo Rodriguez
[gmx-users] g_x2top help Milinda Samaraweera
[gmx-users] error while running mdrun Christopher Samuel
[gmx-users] Issue building template file for Gromacs 4.6-beta1 Hubert Santuz
[gmx-users] help about opls-aa for thiophene Thomas Schlesier
[gmx-users] Re: help about opls-aa for thiophene Thomas Schlesier
[gmx-users] Re: Pulling ion - US Thomas Schlesier
[gmx-users] Question about 'mdrun -nosum' Thomas Schlesier
[gmx-users] Installing 4.6 beta1 Roland Schulz
[gmx-users] strange lincs warning with version 4.6 Roland Schulz
[gmx-users] strange lincs warning with version 4.6 Roland Schulz
[gmx-users] Issue building template file for Gromacs 4.6-beta1 Roland Schulz
[gmx-users] GROMACS 4.6-beta2 released Roland Schulz
[gmx-users] failed with intel compiler Roland Schulz
[gmx-users] g_sans Roland Schulz
[gmx-users] Topolbuild configuration SeokYun123
[gmx-users] amber to gromacs error Yun Shi
[gmx-users] Atom index (13154) in position_restraints out of bounds Yun Shi
[gmx-users] What do res_cog, whole_res_cog, and part_res_cog mean in g_select? Yun Shi
[gmx-users] voltage for membrane? Yun Shi
[gmx-users] Rotational correlation time Yun Shi
[gmx-users] Effects of -P and -fitfn in g_rotacf Yun Shi
[gmx-users] Atom triplets in g_rotacf Yun Shi
[gmx-users] Is vacuum simulation NVT? Michael Shirts
[gmx-users] Re: Re: Is vacuum simulation NVT? Michael Shirts
[gmx-users] Protein at given pH Alexey Shvetsov
[gmx-users] g_sans Alexey Shvetsov
[gmx-users] g_sans Alexey Shvetsov
[gmx-users] g_sans Alexey Shvetsov
[gmx-users] GMXRC execution problem on centos Ayush Singhal
[gmx-users] SDS micelle simulation in TFE solvent Archana Sonawani
[gmx-users] Box Pressure on individual box walls David van der Spoel
[gmx-users] how to convert CGenFF into .itp file? David van der Spoel
[gmx-users] how to convert CGenFF into .itp file? David van der Spoel
[gmx-users] Energy estimations of the protein-ligand complexes James Starlight
[gmx-users] Energy estimations of the protein-ligand complexes James Starlight
[gmx-users] Green fluorescent protein's chromophore James Starlight
[gmx-users] Green fluorescent protein's chromophore James Starlight
[gmx-users] Green fluorescent protein's chromophore James Starlight
[gmx-users] Green fluorescent protein's chromophore James Starlight
[gmx-users] Green fluorescent protein's chromophore James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Analysis of solvent dynamics James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Essential dynamics (ED) sampling using make_edi James Starlight
[gmx-users] Re: Re: Is vacuum simulation NVT? James Starlight
[gmx-users] pca-based MD James Starlight
[gmx-users] Energy estimations in the principal components analysis James Starlight
[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields James Starlight
[gmx-users] Pre-equilibrated CHARMM lipid bilayers James Starlight
[gmx-users] Pre-equilibrated CHARMM lipid bilayers James Starlight
[gmx-users] Pre-equilibrated CHARMM lipid bilayers James Starlight
[gmx-users] Pre-equilibrated CHARMM lipid bilayers James Starlight
[gmx-users] Pre-equilibrated CHARMM lipid bilayers James Starlight
[gmx-users] Pre-equilibrated CHARMM lipid bilayers James Starlight
[gmx-users] Reduction of system dimensions James Starlight
[gmx-users] Reduction of system dimensions James Starlight
[gmx-users] Metadynamics with Esential Dynamics Sampling James Starlight
[gmx-users] Metadynamics with Esential Dynamics Sampling James Starlight
[gmx-users] Metadynamics with Esential Dynamics Sampling James Starlight
[gmx-users] Reduction of system dimensions James Starlight
[gmx-users] Simulation of 2D lattice model James Starlight
[gmx-users] Re: Simulation of 2D lattice model James Starlight
[gmx-users] Re: Simulation of 2D lattice model James Starlight
[gmx-users] g_sans XUEMING TANG
[gmx-users] g_sans XUEMING TANG
[gmx-users] g_sans XUEMING TANG
[gmx-users] 9-oder cosine series of dihedral angle Tom
[gmx-users] help about opls-aa for thiophene Tom
[gmx-users] Re: gmx-users Digest, Vol 104, Issue 24 Tom
[gmx-users] question of improper dihedral of opls aa Tom
[gmx-users] GPU warnings Mirco Wahab
[gmx-users] trjconv -split Wall, Michael E
[gmx-users] apply force to the protein Congyue Wang
[gmx-users] GROMACS 4.6-beta2 released Yorquant Wang
[gmx-users] GROMACS 4.6-beta2 released Yorquant Wang
[gmx-users] g_rms alignment question Tsjerk Wassenaar
[gmx-users] after genbox Tsjerk Wassenaar
[gmx-users] Error with MARTINI depending by the box size Tsjerk Wassenaar
[gmx-users] conformational change Tsjerk Wassenaar
[gmx-users] merge .gro, .top files Tsjerk Wassenaar
[gmx-users] Reduction of system dimensions Tsjerk Wassenaar
[gmx-users] How to convert coarse-grained to fine-grained Tsjerk Wassenaar
[gmx-users] merge .gro, .top files Tsjerk Wassenaar
[gmx-users] merge .gro, .top files Tsjerk Wassenaar
[gmx-users] Using g_membed with MD-CG Tsjerk Wassenaar
[gmx-users] g_rms alignment question Jia Xu
[gmx-users] results of md mohammad agha
[gmx-users] results of md mohammad agha
[gmx-users] free energy mohammad agha
[gmx-users] equilibrium state mohammad agha
[gmx-users] Gibbs free energy mohammad agha
[gmx-users] Gibbs free energy mohammad agha
[gmx-users] Gibbs free energy mohammad agha
[gmx-users] DNA simulation delara aghaie
[gmx-users] pseudo-2d Ewald‏ akn
[gmx-users] error while running mdrun ananyachatterjee
[gmx-users] Missing interactions error during alchemical free energy calculation hyunjink at andrew.cmu.edu
[gmx-users] g_densmap: adsorbed species and output format anouri
[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us benjfitz
[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us benjfitz
[gmx-users] barium ion simulation ram bio
[gmx-users] g_msd additional information dakoenig
[gmx-users] Virtual sites LJ/mass dakoenig
[gmx-users] regarding the free energy calculation of justin tutorial... rama david
[gmx-users] About g_enemat problem rama david
[gmx-users] Regarding the measuring potential Ene of peptide .. rama david
[gmx-users] Fwd: Regarding the measuring potential Ene of peptide .. rama david
[gmx-users] Re: Can i construct a solid wall in gromacs? rajat desikan
[gmx-users] Energy Minimization/ NpT settling problem emmanuelle
[gmx-users] RE: Energy Minimization/ NpT settling problem emmanuelle
[gmx-users] Re: Potential energy from a previous configuration mismatch escajarro
[gmx-users] order parameter of small molecule manoj gadhwal
[gmx-users] glibc error vahid garshasbi
[gmx-users] adsorption vahid garshasbi
[gmx-users] problems installing 4.5.5 on mac maria goranovic
[gmx-users] problems installing 4.5.5 on mac maria goranovic
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC maria goranovic
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC maria goranovic
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC maria goranovic
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC maria goranovic
[gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC maria goranovic
[gmx-users] Green fluorescent protein's chromophore bharat gupta
[gmx-users] structure building and manipulating software kota jaya
[gmx-users] metal_complex as ligand tarak karmakar
[gmx-users] metal_ligand complex tarak karmakar
[gmx-users] metal_ligand complex tarak karmakar
[gmx-users] Langevin Dynamics tarak karmakar
[gmx-users] Re: Langevin Dynamics tarak karmakar
[gmx-users] force autocorrelation khuws
[gmx-users] Re: force autocorrelation khuws
[gmx-users] does error estimate given by g_energy considering auto-correlation? zifeng li
[gmx-users] adsorption ms
[gmx-users] Continuing a simulation Ankita naithani
[gmx-users] Re: Continuing a simulation plus another error Ankita naithani
[gmx-users] Re: Continuing a simulation plus another error Ankita naithani
[gmx-users] force field cuong nguyen
[gmx-users] force field cuong nguyen
[gmx-users] force field cuong nguyen
[gmx-users] Error with MARTINI depending by the box size francesco oteri
[gmx-users] Error with MARTINI depending by the box size francesco oteri
[gmx-users] Error with MARTINI depending by the box size francesco oteri
[gmx-users] Error with MARTINI depending by the box size francesco oteri
[gmx-users] Error with MARTINI depending by the box size francesco oteri
[gmx-users] g_sas : Total surface area francesco oteri
[gmx-users] gold-S simulation francesco oteri
[gmx-users] gold-S simulation francesco oteri
[gmx-users] Re: gold-S simulation francesco oteri
[gmx-users] Convert .psf to .top francesco oteri
[gmx-users] Pre-equilibrated CHARMM lipid bilayers pcl
[gmx-users] Energy Minimization/ NpT settling problem pcl
[gmx-users] Regarding coupling constant sreelakshmi ramesh
[gmx-users] umbrella simulation sreelakshmi ramesh
[gmx-users] gold-protein simulation stop by error in equilibrum step fatemeh ramezani
[gmx-users] gold-S simulation fatemeh ramezani
[gmx-users] gold-S simulation fatemeh ramezani
[gmx-users] gold-S simulation fatemeh ramezani
[gmx-users] Re: gmx-users Digest, Vol 104, Issue 73 fatemeh ramezani
[gmx-users] Re: gmx-users Digest, Vol 104, Issue 83 fatemeh ramezani
[gmx-users] system is not well equilibrated -Reg venkatesh s
[gmx-users] oplsff- need of gro and itp file -reg venkatesh s
[gmx-users] About Packing of Lipids vidhya sankar
[gmx-users] About construction of Cyclic peptide vidhya sankar
[gmx-users] About topology for cyclic petide vidhya sankar
[gmx-users] Issue building template file for Gromacs 4.6-beta1 hubert santuz
[gmx-users] Installing 4.6 beta1 sebastian
[gmx-users] strange lincs warning with version 4.6 sebastian
[gmx-users] strange lincs warning with version 4.6 sebastian
[gmx-users] strange lincs warning with version 4.6 sebastian
[gmx-users] gromacs 4.6 on NVIDIA K10 sebastian
[gmx-users] Re: add more solvent? shika
[gmx-users] Re: Poteintial energy of my system shika
[gmx-users] External electric field (Static or Oscillating) Ashutosh singh
[gmx-users] Essential dynamics (ED) sampling using make_edi bipin singh
[gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations mircial at sjtu.edu.cn
[gmx-users] Re: about -return of mdrun xiaowu759
[gmx-users] Re: about -return of mdrun xiaowu759
[gmx-users] question about define groups yeqing1211
[gmx-users] increase of temperature or pressure Ahmet yıldırım
[gmx-users] how to build xtc file from many same crystal structures which are different conformational states. xi zhao
[gmx-users] Actual box size zugunder
[gmx-users] Re: Actual box size zugunder
[gmx-users] Re: Actual box size zugunder
[gmx-users] Cutoff influence on performance zugunder
[gmx-users] Re: Actual box size zugunder
[gmx-users] Re: Actual box size zugunder
[gmx-users] Re: Actual box size zugunder
[gmx-users] High density after NPT zugunder
[gmx-users] Re: High density after NPT zugunder
[gmx-users] Re: High density after NPT zugunder
[gmx-users] help 申昊
[gmx-users] using g_analyze for calculating distance autocorrelation functions 申昊
[gmx-users] Re: gmx-users Digest, Vol 104, Issue 94 申昊
[gmx-users] Re: using g_analyze for calculating distance autocorrelation functions(Hao Shen) 申昊

Last message date: Mon Dec 31 23:54:56 CET 2012
Archived on: Thu Nov 14 12:13:43 CET 2013

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