April 2012 Archives by author

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Starting: Sun Apr 1 01:06:15 CEST 2012
Ending: Mon Apr 30 22:30:59 CEST 2012
Messages: 1009

[gmx-users] oscillational period problem in Martini force field Du Jiangfeng (BIOCH)
[gmx-users] Re: hkl harker sections Mark Abraham
[gmx-users] g_tune_pme error in blue gene Mark Abraham
[gmx-users] g_tune_pme error in blue gene Mark Abraham
[gmx-users] ifp file in Gromacs? Mark Abraham
[gmx-users] 2 chain protein itp file Mark Abraham
[gmx-users] Possible error in the gromacs calculation Mark Abraham
[gmx-users] Possible error in the gromacs calculation Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] pdb2gmx error Mark Abraham
[gmx-users] pdb2gmx error Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] mdrun -rerun in parallel? Mark Abraham
[gmx-users] Adding Born Radii for implicit solvent MD Mark Abraham
[gmx-users] Problems with simulation on multi-nodes cluster Mark Abraham
[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom Mark Abraham
[gmx-users] how to get a minimized structure pdb Mark Abraham
[gmx-users] Is the PME domain decomposition flexible in some hidden way? Mark Abraham
[gmx-users] Re: Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom Mark Abraham
[gmx-users] Parallel Computation of g_rdf Mark Abraham
[gmx-users] the -extend function of the tpbconv command Mark Abraham
[gmx-users] do_dssp Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] Further discussion: the -extend function of the tpbconv command Mark Abraham
[gmx-users] on a on-line command for Mark Abraham
[gmx-users] Re: do_dssp Mark Abraham
[gmx-users] Re: do_dssp Mark Abraham
[gmx-users] Re: do_dssp Mark Abraham
[gmx-users] how to change the timestamp of a xtc file Mark Abraham
[gmx-users] Re: do_dssp Mark Abraham
[gmx-users] something about tpr file Mark Abraham
[gmx-users] how to change the timestamp of a xtc file Mark Abraham
[gmx-users] Monitoring of Salt bridges during simulation Run Mark Abraham
[gmx-users] further discussion on the mdrun -append function Mark Abraham
[gmx-users] Re: job failed Mark Abraham
[gmx-users] Different results from identical tpr after MD Mark Abraham
[gmx-users] the g_rms function after we trjcat the trajectory files before and after extension Mark Abraham
[gmx-users] Atom N not found.... Mark Abraham
[gmx-users] Atom N not found.... Mark Abraham
[gmx-users] MD after equilibration phase Mark Abraham
[gmx-users] MD after equilibration phase Mark Abraham
[gmx-users] MPI installation Mark Abraham
[gmx-users] MPI installation Mark Abraham
[gmx-users] Box generation for monoclinic crystal - regd Mark Abraham
[gmx-users] Re: Simulation in the high temperature conditions Mark Abraham
[gmx-users] Re: Simulation in the high temperature conditions Mark Abraham
[gmx-users] .itp file for "Fe" atom.. Mark Abraham
[gmx-users] Rerun error - the file has been replaced or its content has been changed Mark Abraham
[gmx-users] Rerun error - the file has been replaced or its content has been changed Mark Abraham
[gmx-users] on g_rms analysis Mark Abraham
[gmx-users] protein folding / pbc Mark Abraham
[gmx-users] Box generation for monoclinic crystal - regd Mark Abraham
[gmx-users] multiple dihedral function types - regd Mark Abraham
[gmx-users] Can gromacs handle reflective boundary condition ? Mark Abraham
[gmx-users] regarding micelle and its analysis Mark Abraham
[gmx-users] Van der waals types Mark Abraham
[gmx-users] Van der waals types Mark Abraham
[gmx-users] Van der waals types Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] GROMACS (w. OpenMPI) fails to run with -np larger than 10 Mark Abraham
[gmx-users] Parallel run on multiple nodes Mark Abraham
[gmx-users] Re: GROMACS (w. OpenMPI) fails to run with -np larger than 10 Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] mdrun segmentation fault Mark Abraham
[gmx-users] Question on checkpoint files and restarts/continuity Mark Abraham
[gmx-users] mdrun -rerun Mark Abraham
[gmx-users] Tabulated potential segmentation fault Mark Abraham
[gmx-users] distance restraints fails Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] Box Size in MD Mark Abraham
[gmx-users] progressive imbalance in REMD Mark Abraham
[gmx-users] File editing - only one layer of water around a molecule Mark Abraham
[gmx-users] g_select tutorial Mark Abraham
[gmx-users] How can I install Gromacs on Window XP? Mark Abraham
[gmx-users] progressive imbalance in REMD Mark Abraham
[gmx-users] Adding GROMOS force field to pdb2gmx Mark Abraham
[gmx-users] DD load balancing is limited by minimum cell size in dimension Z Mark Abraham
[gmx-users] Charmm27.ff with FEP Mark Abraham
[gmx-users] Tabulated potential segmentation fault Mark Abraham
[gmx-users] installation issues Mark Abraham
[gmx-users] Re: temperature Mark Abraham
[gmx-users] Re: Questions Mark Abraham
[gmx-users] Protein ligand molecular dynamics simulation Mark Abraham
[gmx-users] Re: Extending a simulation Mark Abraham
[gmx-users] Methods for accelerated MD simulation for Protein-Mg-GTP system in gromacs Mark Abraham
[gmx-users] Error- Atom not found in residue seq nr while adding atom Mark Abraham
[gmx-users] polarizable ff and free energy calculation Mark Abraham
[gmx-users] polarizable ff and free energy calculation Mark Abraham
[gmx-users] Re: Simulation in the high temperature conditions Mark Abraham
[gmx-users] Extending run using tpbconv and mdrun Mark Abraham
[gmx-users] Extending run using tpbconv and mdrun Mark Abraham
[gmx-users] Re: Extending run using tpbconv and mdrun Mark Abraham
[gmx-users] Re: : Extending run append Mark Abraham
[gmx-users] Heme group with CHARMM27 FF Mark Abraham
[gmx-users] Heme group with CHARMM27 FF Mark Abraham
[gmx-users] Re: : Extending run append Mark Abraham
[gmx-users] Heme group with CHARMM27 FF Mark Abraham
[gmx-users] Heme group with CHARMM27 FF Mark Abraham
[gmx-users] How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Mark Abraham
[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Mark Abraham
[gmx-users] using AMBER force field by GROMACS Mark Abraham
[gmx-users] Charm forcefield error..Atomtype CR not found .. Mark Abraham
[gmx-users] Type of unit cell Mark Abraham
[gmx-users] Type of unit cell Mark Abraham
[gmx-users] Fwd: help Mark Abraham
[gmx-users] gromacs 4.5.5 on Cygwin Mark Abraham
[gmx-users] PDB2GMX error in charmm27 Forcefield Mark Abraham
[gmx-users] Heme group with CHARMM27 FF Mark Abraham
[gmx-users] why it is so slow in Blue gene? Mark Abraham
[gmx-users] Fwd: Error: coordinate file does not match with the topology file Mark Abraham
[gmx-users] How to increase the ratio of cell size to constrain length per error message Mark Abraham
[gmx-users] Can I equilibrate with Parinello-Rahman? Mark Abraham
[gmx-users] Regarding errors Mark Abraham
[gmx-users] Regarding errors Mark Abraham
[gmx-users] How to use -tablep mdrun option? Mark Abraham
[gmx-users] REMD - low temperature ranges Mark Abraham
[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF Mark Abraham
[gmx-users] How to use -tablep mdrun option? Mark Abraham
[gmx-users] SWM4_DP water on graphite surface Mark Abraham
[gmx-users] SWM4_DP water on graphite surface Mark Abraham
[gmx-users] blue gene running error Mark Abraham
[gmx-users] blue gene running error Mark Abraham
[gmx-users] disulfide bonds Mark Abraham
[gmx-users] Make an index file Mark Abraham
[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun Mark Abraham
[gmx-users] TRR file with nstxout= 0 Mark Abraham
[gmx-users] Regading error Mark Abraham
[gmx-users] Acpype doubts Alan
[gmx-users] another g_tune_pme problem Albert
[gmx-users] g_cluster for concoord output? Albert
[gmx-users] jobs failed Albert
[gmx-users] Re: job failed Albert
[gmx-users] Re: job failed Albert
[gmx-users] where can we obtain the latest Amber ff12SB FF? Albert
[gmx-users] why it is so slow in Blue gene? Albert
[gmx-users] Re: why it is so slow in Blue gene Albert
[gmx-users] why it is so slow in Blue gene? Albert
[gmx-users] a question about energygrps Albert
[gmx-users] a question about energygrps Albert
[gmx-users] a question about energygrps Albert
[gmx-users] how to run g_tune_pme in cluster? Albert
[gmx-users] how to run g_tune_pme in cluster? Albert
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Albert
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Albert
[gmx-users] how to run g_tune_pme in cluster? Albert
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Albert
[gmx-users] blue gene running error Albert
[gmx-users] blue gene running error Albert
[gmx-users] blue gene running error Albert
[gmx-users] Simulation with nbutanol Juliana Angeiras
[gmx-users] Another do_dssp problem Clement Angkawidjaja
[gmx-users] Residue 'FOR' not found in residue topology database Shima Arasteh
[gmx-users] Gromos87 Shima Arasteh
[gmx-users] Gromos87 Shima Arasteh
[gmx-users] Define a new residue in oplsaa Shima Arasteh
[gmx-users] Define a new residue in oplsaa Shima Arasteh
[gmx-users] GROMOS87 and CHARMM27 Shima Arasteh
[gmx-users] GROMOS87 and CHARMM27 Shima Arasteh
[gmx-users] Type of unit cell Shima Arasteh
[gmx-users] Type of unit cell Shima Arasteh
[gmx-users] Error: No default angle/bond types Shima Arasteh
[gmx-users] fatal error: The solvent group non-Protein is not continuous Shima Arasteh
[gmx-users] .top file for POPC membrane Shima Arasteh
[gmx-users] .top file for POPC membrane Shima Arasteh
[gmx-users] Fatal error in popc simulation: Atomtype LC3 not found Shima Arasteh
[gmx-users] Make an index file Shima Arasteh
[gmx-users] Make an index file Shima Arasteh
[gmx-users] Make an index file Shima Arasteh
[gmx-users] Make an index file Shima Arasteh
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder J B
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder J B
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder J B
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder J B
[gmx-users] Van der waals types Chrisostomos Batistakis
[gmx-users] Van der waals types Chrisostomos Batistakis
[gmx-users] Van der waals types Chrisostomos Batistakis
[gmx-users] 2 chain protein itp file Acoot Brett
[gmx-users] Possible error in the gromacs calculation Acoot Brett
[gmx-users] Possible error in the gromacs calculation Acoot Brett
[gmx-users] on Umbrella Sampling Acoot Brett
[gmx-users] on Umbrella Sampling Acoot Brett
[gmx-users] on Umbrella Sampling Acoot Brett
[gmx-users] a question related to force field on terminal residues Acoot Brett
[gmx-users] pdb2gmx error Acoot Brett
[gmx-users] pdb2gmx error Acoot Brett
[gmx-users] pdb2gmx error Acoot Brett
[gmx-users] pdb2gmx error Acoot Brett
[gmx-users] a question related to the extending of md Acoot Brett
[gmx-users] on the Umbrella Sampling on-line tutorial Acoot Brett
[gmx-users] the mdrun -reprod in gromacs 4.5.5 Acoot Brett
[gmx-users] on the Umbrella Sampling on-line tutorial Acoot Brett
[gmx-users] the mdrun "-v" Acoot Brett
[gmx-users] on the Umbrella Sampling tutorial Acoot Brett
[gmx-users] the -extend function of the tpbconv command Acoot Brett
[gmx-users] on the Umbrella Sampling tutorial Acoot Brett
[gmx-users] the -extend function of the tpbconv command Acoot Brett
[gmx-users] which xtc file should be used for the trjconv command Acoot Brett
[gmx-users] Further discussion: the -extend function of the tpbconv command Acoot Brett
[gmx-users] on a on-line command for Acoot Brett
[gmx-users] on the MD extension command Acoot Brett
[gmx-users] the different protonation state of HIS Acoot Brett
[gmx-users] the different protonation state of HIS Acoot Brett
[gmx-users] Different results from identical tpr after MD Acoot Brett
[gmx-users] Different results from identical tpr after MD Acoot Brett
[gmx-users] Different results from identical tpr after MD Acoot Brett
[gmx-users] on the attachment symbol of some e-mail from our GROMACS users Acoot Brett
[gmx-users] further discussion on the mdrun -append function Acoot Brett
[gmx-users] further discussion on the mdrun -append function Acoot Brett
[gmx-users] the g_rms function after we trjcat the trajectory files before and after extension Acoot Brett
[gmx-users] Further question on protonation state of histiding Acoot Brett
[gmx-users] on PDB2gmx Acoot Brett
[gmx-users] how pdb2gmx calculate the total charge of a protein Acoot Brett
[gmx-users] how pdb2gmx calculate the total charge of a protein Acoot Brett
[gmx-users] on the .rtp file Acoot Brett
[gmx-users] on PDB2gmx Acoot Brett
[gmx-users] on the trr file of the production MD Acoot Brett
[gmx-users] on g_rms analysis Acoot Brett
[gmx-users] on 2 different mini.mdp file Acoot Brett
[gmx-users] on the "tc-grps = Protein Non-Protein ; two coupling groups" in the on-line tutorial Acoot Brett
[gmx-users] the value of nsteps in the mdp file in the on-line tutorial Acoot Brett
[gmx-users] on the NPT equilibration of the on-line tutorial of lysozyme Acoot Brett
[gmx-users] a question related to NMR Acoot Brett
[gmx-users] a question related to production MD Acoot Brett
[gmx-users] using AMBER force field by GROMACS Acoot Brett
[gmx-users] calculation of the mean B factor of a PDB file Acoot Brett
[gmx-users] Shape of box Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] Box Size in MD Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] g_select tutorial Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] New Gromacs Release Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] File editing - only one layer of water around a molecule Lara Bunte
[gmx-users] couple-moltype question Fabian Casteblanco
[gmx-users] FEP Fabian Casteblanco
[gmx-users] Error- Atom not found in residue seq nr while adding atom Javier Cerezo
[gmx-users] Error- Atom not found in residue seq nr while adding atom Javier Cerezo
[gmx-users] make_ndx: atomname selection Javier Cerezo
[gmx-users] Re: jobs failed Dr. Vitaly V. Chaban
[gmx-users] Re: why it is so slow in Blue gene Dr. Vitaly V. Chaban
[gmx-users] g_dist explanation Shilpi Chaurasia
R: Re: [gmx-users] g_dist explanation Shilpi Chaurasia
[gmx-users] MPI installation TH Chew
[gmx-users] g_nmeig & eigenfrequencies Yongchul Chung
[gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5 Yongchul Chung
[gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5 Yongchul Chung
[gmx-users] Re: double precision energy minimization show zero pressure in gromacs 4.5.5 Yongchul Chung
[gmx-users] Software inconsistency error: One or more interactions were multiple assigned in the domain decomposition Bogdan Costescu
[gmx-users] Extending run using tpbconv and mdrun D_Roy
[gmx-users] Re: Extending run using tpbconv and mdrun D_Roy
[gmx-users] Re: Extending run using tpbconv and mdrun D_Roy
[gmx-users] Re: Extending run using tpbconv and mdrun D_Roy
[gmx-users] pdb2gmx error Bishwajit Das
[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom Andrew DeYoung
[gmx-users] Re: Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom Andrew DeYoung
[gmx-users] Converting a new-version .tpr file to an old-version .tpr file Andrew DeYoung
[gmx-users] Pseudo 2-D Ewald Summation and Slab Geometry Andrew DeYoung
[gmx-users] Classical Ewald summation Andrew DeYoung
[gmx-users] ewald_rtol Andrew DeYoung
[gmx-users] What is epsilon_r? Andrew DeYoung
[gmx-users] Re: What is epsilon_r? Andrew DeYoung
[gmx-users] Re: What is epsilon_r? Andrew DeYoung
[gmx-users] Re: What is epsilon_r? Andrew DeYoung
[gmx-users] Inconsistent shifts in periodic molecules Andrew DeYoung
[gmx-users] Units of density in the g_spatial output Andrew DeYoung
[gmx-users] How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Andrew DeYoung
[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Andrew DeYoung
[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Andrew DeYoung
[gmx-users] Radial distribution function (RDF) in cylindrical coordinates Andrew DeYoung
[gmx-users] -com switch in g_rdf Andrew DeYoung
[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun Andrew DeYoung
[gmx-users] Re: Question about starting Gromacs 4.5.4 parallel runs using mpirun Andrew DeYoung
[gmx-users] Ion conductivity: current-current (auto)correlation function Andrew DeYoung
[gmx-users] Atom types for phosphate group in OPLS-AA force field Delmotte, Antoine
[gmx-users] Atom types for phosphate group in OPLS-AA force field Delmotte, Antoine
[gmx-users] Atom types for phosphate group in OPLS-AA force field Delmotte, Antoine
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] (no subject) Nilesh Dhumal
[gmx-users] grompp error Nilesh Dhumal
[gmx-users] Re: questions about Principal Component Analysis Thomas Evangelidis
[gmx-users] Re: questions about Principal Component Analysis Thomas Evangelidis
[gmx-users] how to optimize the orientation of the protein in a dodecahedron Thomas Evangelidis
[gmx-users] how to optimize the orientation of the protein in a dodecahedron Thomas Evangelidis
[gmx-users] minimum distance between periodic images does not aggree with box dimensions Thomas Evangelidis
[gmx-users] Writing out individual coordinates Rodrigo Faccioli
[gmx-users] Re: Gromacs on "HPC workstations" ? Nicola Fantini
[gmx-users] Pull code: separating molecules. distance and direction Eudes Fileti
[gmx-users] Re: Pull code: separating molecules. distance and direction (SOLVED) Eudes Fileti
[gmx-users] Silly little question about PMF - g_wham Eudes Fileti
[gmx-users] How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Dommert Florian
[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz? Dommert Florian
[gmx-users] writing ff parameters as a text file Dommert Florian
[gmx-users] Ion conductivity: current-current (auto)correlation function Dommert Florian
[gmx-users] Is the PME domain decomposition flexible in some hidden way? Paolo Franz
[gmx-users] Is the PME domain decomposition flexible in some hidden way? Paolo Franz
[gmx-users] disulfide bonds Hagit G
[gmx-users] disulfide bonds Hagit G
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Velocities in trjconv 4.5.5 Ignacio Fernández Galván
[gmx-users] Velocities in trjconv 4.5.5 Ignacio Fernández Galván
[gmx-users] Velocities in trjconv 4.5.5 Ignacio Fernández Galván
[gmx-users] Thole Potential Sai Janani Ganesan
[gmx-users] free energy calculation and g_bar error Chunxia Gao
[gmx-users] charges R.Perez Garcia
[gmx-users] charges R.Perez Garcia
[gmx-users] Best Force Field for a Membrane Protein Anirban Ghosh
[gmx-users] Best Force Field for a Membrane Protein Anirban Ghosh
[gmx-users] GPCR MD Tutorial Using GROMACS Anirban Ghosh
[gmx-users] GPCR MD Tutorial Using GROMACS Anirban Ghosh
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Regarding errors Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Anirban Ghosh
[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun Anirban Ghosh
[gmx-users] Regarding error Anirban Ghosh
[gmx-users] Is GPU GTX 560 compatible with GROMACS? Gaurav Goel
[gmx-users] Is GPU GTX 560 compatible with GROMACS? Gaurav Goel
[gmx-users] Adding GROMOS force field to pdb2gmx Marc Gordon
[gmx-users] Hypericin dimer affinity Hovakim Grabski
[gmx-users] Umbrella Sampling Hypericin Dimer Hovakim Grabski
[gmx-users] Zn Coordination Thomas Grant
[gmx-users] GROMACS (w. OpenMPI) fails to run with -np larger than 10 Seyyed Mohtadin Hashemi
[gmx-users] SWM4_DP water on graphite surface Ho, Tuan A.
[gmx-users] SWM4_DP water on graphite surface Ho, Tuan A.
[gmx-users] SWM4_DP water on graphite surface Ho, Tuan A.
[gmx-users] lipid.itp for AMBER-GAFF Henry Hocking
[gmx-users] extra factor in PMF Martin Hoefling
[gmx-users] Structures and topologies of cholesterol-containing membranes Jochen Hub
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder Jochen Hub
[gmx-users] (no subject) Suhaila Haji Mohd Hussin
[gmx-users] Re: Gromacs-CPMD: QMMM Jacob Jantzi
[gmx-users] Heme group with CHARMM27 FF Sundar Jubilant
[gmx-users] Heme group with CHARMM27 FF Sundar Jubilant
[gmx-users] Heme group with CHARMM27 FF Sundar Jubilant
[gmx-users] Heme group with CHARMM27 FF Sundar Jubilant
[gmx-users] Heme group with CHARMM27 FF Sundar Jubilant
[gmx-users] Gromacs on "HPC workstations" ? Jonathan KHAO
[gmx-users] Fatal error: Bond atom type names can't be single digits Sangita Kachhap
[gmx-users] g_wham problem with negative COM differences Anni Kauko
[gmx-users] g_wham problem with negative COM differences Anni Kauko
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 115 Anni Kauko
[gmx-users] g_wham problem with negative COM differences Anni Kauko
[gmx-users] error in starting/completing minimization Rashek Kazi
[gmx-users] Force field for graphene sheet: deformation at the boundaries Kathleen Kirchner
[gmx-users] Problem with g_dipoles and SPCE water Tom Kirchner
[gmx-users] Problem with g_dipoles and SPCE water Tom Kirchner
[gmx-users] Problem with g_dipoles and SPCE water Tom Kirchner
[gmx-users] Using polarizable ff for ions in conjunction with free energy calculation Tom Kirchner
[gmx-users] polarizable ff and free energy calculation Tom Kirchner
[gmx-users] polarizable ff and free energy calculation Tom Kirchner
[gmx-users] do_dssp Bernhard Knapp
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 30 Bernhard Knapp
[gmx-users] Acpype doubts Thales Kronenberger
[gmx-users] doubt about OpenMM Thales Kronenberger
[gmx-users] protein and DMPC in Charmm36 ff Krzysztof Kuczera
[gmx-users] REMD - low temperature ranges Krzysztof Kuczera
[gmx-users] another g_tune_pme problem Carsten Kutzner
[gmx-users] Error: 4095 characters, fgets2 has size 4095 Carsten Kutzner
[gmx-users] how to run g_tune_pme in cluster? Carsten Kutzner
[gmx-users] how to run g_tune_pme in cluster? Carsten Kutzner
[gmx-users] on PDB2gmx Peter Lai
[gmx-users] grompp error Peter C. Lai
[gmx-users] Monitoring of Salt bridges during simulation Run Peter C. Lai
[gmx-users] how to change the timestamp of a xtc file Peter C. Lai
[gmx-users] how to change the timestamp of a xtc file Peter C. Lai
[gmx-users] the different protonation state of HIS Peter C. Lai
[gmx-users] the different protonation state of HIS Peter C. Lai
[gmx-users] Different results from identical tpr after MD Peter C. Lai
[gmx-users] jobs failed Peter C. Lai
[gmx-users] Re: job failed Peter C. Lai
[gmx-users] Help: Anyone worked with "Wall"? Peter C. Lai
[gmx-users] further discussion on the mdrun -append function Peter C. Lai
[gmx-users] further discussion on the mdrun -append function Peter C. Lai
[gmx-users] further discussion on the mdrun -append function Peter C. Lai
[gmx-users] the g_rms function after we trjcat the trajectory files before and after extension Peter C. Lai
[gmx-users] MD after equilibration phase Peter C. Lai
[gmx-users] Charmm36_lipids with gromacs Peter C. Lai
[gmx-users] on PDB2gmx Peter C. Lai
[gmx-users] how pdb2gmx calculate the total charge of a protein Peter C. Lai
[gmx-users] Atom MNZ1 in residue LYS 107 was not found Peter C. Lai
[gmx-users] GROMOS87 and CHARMM27 Peter C. Lai
[gmx-users] GROMOS87 and CHARMM27 Peter C. Lai
[gmx-users] Best Force Field for a Membrane Protein Peter C. Lai
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Peter C. Lai
Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF Peter C. Lai
Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun Peter C. Lai
Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun Peter C. Lai
[gmx-users] Make an index file Peter C. Lai
[gmx-users] sigma and epsilon. Peter C. Lai
[gmx-users] Tabulated potential segmentation fault Laura Leay
[gmx-users] Tabulated potential segmentation fault Laura Leay
[gmx-users] on Umbrella Sampling Justin A. Lemkul
[gmx-users] on Umbrella Sampling Justin A. Lemkul
[gmx-users] on Umbrella Sampling Justin A. Lemkul
[gmx-users] on Umbrella Sampling Justin A. Lemkul
[gmx-users] on Umbrella Sampling Justin A. Lemkul
[gmx-users] Editing of the existing system Justin A. Lemkul
[gmx-users] a question related to force field on terminal residues Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] Re: Carbohydrate simulation: problem with the terminal atoms Justin A. Lemkul
[gmx-users] ions error Justin A. Lemkul
[gmx-users] ions error Justin A. Lemkul
[gmx-users] on the Umbrella Sampling on-line tutorial Justin A. Lemkul
[gmx-users] on the Umbrella Sampling tutorial Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] the -extend function of the tpbconv command Justin A. Lemkul
[gmx-users] on the Umbrella Sampling tutorial Justin A. Lemkul
[gmx-users] Bad box in protein.gro Justin A. Lemkul
AW: [gmx-users] Shape of box Justin A. Lemkul
[gmx-users] do_dssp Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] do_dssp Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] Atom N not found.... Justin A. Lemkul
[gmx-users] the different protonation state of HIS Justin A. Lemkul
[gmx-users] Zn Coordination Justin A. Lemkul
[gmx-users] g_hbond Justin A. Lemkul
[gmx-users] Different results from identical tpr after MD Justin A. Lemkul
[gmx-users] Different results from identical tpr after MD Justin A. Lemkul
[gmx-users] Different results from identical tpr after MD Justin A. Lemkul
[gmx-users] Re: job failed Justin A. Lemkul
[gmx-users] Different results from identical tpr after MD Justin A. Lemkul
[gmx-users] Further question on protonation state of histiding Justin A. Lemkul
[gmx-users] Atom N not found.... Justin A. Lemkul
[gmx-users] MD after equilibration phase Justin A. Lemkul
[gmx-users] MD after equilibration phase Justin A. Lemkul
[gmx-users] SS bond forcing Justin A. Lemkul
[gmx-users] Charmm36_lipids with gromacs Justin A. Lemkul
[gmx-users] MD after equilibration phase Justin A. Lemkul
[gmx-users] on PDB2gmx Justin A. Lemkul
[gmx-users] Re: Protein charge Justin A. Lemkul
[gmx-users] Error message in reading AMBER's mdcrd files? Justin A. Lemkul
[gmx-users] Error message in reading AMBER's mdcrd files? Justin A. Lemkul
[gmx-users] mdrun -rerun Justin A. Lemkul
[gmx-users] regarding rmsd and gyrate Justin A. Lemkul
[gmx-users] SS bond forcing Justin A. Lemkul
[gmx-users] regarding g_sas and rdf Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] Re: on the trr file of the production MD Justin A. Lemkul
[gmx-users] SS bond forcing Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] SS bond forcing Justin A. Lemkul
[gmx-users] lipid.itp for AMBER-GAFF Justin A. Lemkul
[gmx-users] SS bond forcing Justin A. Lemkul
[gmx-users] on 2 different mini.mdp file Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] g_wham problem with negative COM differences Justin A. Lemkul
[gmx-users] NPT simulation with parinello-rahman pressure coupling Justin A. Lemkul
[gmx-users] tau_t and tau_p values Justin A. Lemkul
[gmx-users] tau_t and tau_p values Justin A. Lemkul
[gmx-users] Re: Re: NPT simulation with parinello-rahman pressure coupling Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] on the "tc-grps = Protein Non-Protein ; two coupling groups" in the on-line tutorial Justin A. Lemkul
[gmx-users] the value of nsteps in the mdp file in the on-line tutorial Justin A. Lemkul
[gmx-users] Converting a new-version .tpr file to an old-version .tpr file Justin A. Lemkul
[gmx-users] %exist of hydrogen bonds + No -map specified! Justin A. Lemkul
[gmx-users] segmentation fault Justin A. Lemkul
[gmx-users] Gromos87 Justin A. Lemkul
[gmx-users] simulations in vacuum in parallel Justin A. Lemkul
[gmx-users] Gromos87 Justin A. Lemkul
[gmx-users] on the NPT equilibration of the on-line tutorial of lysozyme Justin A. Lemkul
[gmx-users] -rcon parameter in mdrun - what values have sense? Justin A. Lemkul
[gmx-users] Simulation of the pure lipid bilayer Justin A. Lemkul
[gmx-users] a question related to NMR Justin A. Lemkul
[gmx-users] Simulation of the pure lipid bilayer Justin A. Lemkul
[gmx-users] g_wham problem with negative COM differences Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] a question related to production MD Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] Justin protein-ligand complex... Justin A. Lemkul
[gmx-users] Justin protein-ligand complex... Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] Classical Ewald summation Justin A. Lemkul
[gmx-users] Define a new residue in oplsaa Justin A. Lemkul
[gmx-users] Define a new residue in oplsaa Justin A. Lemkul
[gmx-users] protein and DMPC in Charmm36 ff Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] how to install DSSP in linux with Gromacs 4.0.7 Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] Re: Simulation in the high temperature conditions Justin A. Lemkul
[gmx-users] Protein ligand molecular dynamics simulation Justin A. Lemkul
[gmx-users] Re: Re: NPT simulation for mutation study Justin A. Lemkul
[gmx-users] GROMOS87 and CHARMM27 Justin A. Lemkul
[gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul) Justin A. Lemkul
[gmx-users] ewald_rtol Justin A. Lemkul
[gmx-users] What is epsilon_r? Justin A. Lemkul
[gmx-users] Fe atom problems....in simulation Justin A. Lemkul
[gmx-users] Re: Questions Justin A. Lemkul
[gmx-users] Re: Questions Justin A. Lemkul
[gmx-users] Extending a simulation Justin A. Lemkul
[gmx-users] Fatal error: Bond atom type names can't be single digits Justin A. Lemkul
[gmx-users] Re: Extending a simulation Justin A. Lemkul
[gmx-users] Error- Atom not found in residue seq nr while adding atom Justin A. Lemkul
[gmx-users] g_wham problem with negative COM differences Justin A. Lemkul
[gmx-users] Re: Questions WHAM Justin A. Lemkul
[gmx-users] Re: g_wham problem with negative COM differences Justin A. Lemkul
[gmx-users] Re:WHAM question Justin A. Lemkul
[gmx-users] Re: Extending a simulation Justin A. Lemkul
[gmx-users] Silly little question about PMF - g_wham Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] Writing out individual coordinates Justin A. Lemkul
[gmx-users] Re: Data Analysis Justin A. Lemkul
[gmx-users] Re: Data Analysis Justin A. Lemkul
[gmx-users] Error: No default angle/bond types Justin A. Lemkul
[gmx-users] fatal error: The solvent group non-Protein is not continuous Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] Radial distribution function (RDF) in cylindrical coordinates Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] .top file for POPC membrane Justin A. Lemkul
[gmx-users] g_dist explanation Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] writing ff parameters as a text file Justin A. Lemkul
[gmx-users] About hydrogen bond .. Justin A. Lemkul
[gmx-users] Need help with tabulated non-bonding potential tablep file Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] Extending umbrella sampling window Justin A. Lemkul
[gmx-users] error in starting/completing minimization Justin A. Lemkul
[gmx-users] -com switch in g_rdf Justin A. Lemkul
[gmx-users] Simulation with nbutanol Justin A. Lemkul
[gmx-users] Hypericin dimer affinity Justin A. Lemkul
[gmx-users] PBC treatment: need an explanation Justin A. Lemkul
[gmx-users] why it is so slow in Blue gene? Justin A. Lemkul
[gmx-users] Fatal error in popc simulation: Atomtype LC3 not found Justin A. Lemkul
[gmx-users] Fatal error Justin A. Lemkul
[gmx-users] a question about energygrps Justin A. Lemkul
[gmx-users] a question about energygrps Justin A. Lemkul
[gmx-users] a question about energygrps Justin A. Lemkul
[gmx-users] Error in MD simulation Justin A. Lemkul
[gmx-users] How to choose two atoms at the same time, using g_select selection.dat Justin A. Lemkul
[gmx-users] Atom types for phosphate group in OPLS-AA force field Justin A. Lemkul
[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs Justin A. Lemkul
[gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5 Justin A. Lemkul
[gmx-users] Atom types for phosphate group in OPLS-AA force field Justin A. Lemkul
[gmx-users] Atom types for phosphate group in OPLS-AA force field Justin A. Lemkul
[gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5 Justin A. Lemkul
[gmx-users] Position Restraints Justin A. Lemkul
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Justin A. Lemkul
[gmx-users] Position Restraints Justin A. Lemkul
[gmx-users] help about "Inconsistent DD boundary staggering limits" Justin A. Lemkul
[gmx-users] help about "Inconsistent DD boundary staggering limits" Justin A. Lemkul
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Justin A. Lemkul
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Justin A. Lemkul
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Justin A. Lemkul
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Justin A. Lemkul
[gmx-users] TRR file with nstxout= 0 Justin A. Lemkul
[gmx-users] TRR file with nstxout= 0 Justin A. Lemkul
[gmx-users] TRR file with nstxout= 0 Justin A. Lemkul
[gmx-users] calculation of the mean B factor of a PDB file Justin A. Lemkul
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder Justin A. Lemkul
[gmx-users] Making Disulfide Bonds Justin A. Lemkul
[gmx-users] Making Disulfide Bonds Justin A. Lemkul
[gmx-users] Make an index file Justin A. Lemkul
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder Justin A. Lemkul
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] File editing - only one layer of water around a molecule Justin A. Lemkul
[gmx-users] Umbrella Sampling Hypericin Dimer Justin A. Lemkul
[gmx-users] New Gromacs Release Justin A. Lemkul
[gmx-users] distance restraints fails Qinghua Liao
[gmx-users] simulations in vacuum in parallel Qinghua Liao
[gmx-users] FINAL CHANCE: GROMACS survey closing May 1! Erik Lindahl
[gmx-users] why it is so slow in Blue gene? Hannes Loeffler
[gmx-users] Need help with pabulated non-bonding potential tablep file Marcelo Lopez
[gmx-users] Need help with tabulated non-bonding potential tablep file Marcelo Lopez
[gmx-users] Tabulated non-bonding potential tablep file problem Marcelo Lopez
[gmx-users] Tabulated non-bonding potential tablep file problem Marcelo Lopez
[gmx-users] Need help with tabulated non-bonding potential tablep file Marcelo Lopez
[gmx-users] How to use -tablep mdrun option? Marcelo Lopez
[gmx-users] How to use -tablep mdrun option? Marcelo Lopez
[gmx-users] single X double precision Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] single X double precision Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] Charmm27.ff with FEP Sanku M
[gmx-users] PBC treatment: need an explanation Anna Marabotti
[gmx-users] em fatal error! Erik Marklund
[gmx-users] em fatal error! Erik Marklund
[gmx-users] the mdrun "-v" Erik Marklund
[gmx-users] Clustering Erik Marklund
[gmx-users] Clustering Erik Marklund
[gmx-users] how to install DSSP in linux with Gromacs 4.0.7 Erik Marklund
[gmx-users] Extending run using tpbconv and mdrun Erik Marklund
[gmx-users] Re: Extending run using tpbconv and mdrun Erik Marklund
[gmx-users] Re: : Extending run append Erik Marklund
[gmx-users] Type of unit cell Erik Marklund
[gmx-users] Chemical potential of protein Erik Marklund
[gmx-users] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it Erik Marklund
[gmx-users] how to optimize the orientation of the protein in a dodecahedron Erik Marklund
[gmx-users] Velocities in trjconv 4.5.5 Alex Marshall
[gmx-users] Gromos87 Marzinek, Jan
[gmx-users] Gromos87 Marzinek, Jan
[gmx-users] g_dist explanation Marzinek, Jan
[gmx-users] g_dist explanation Marzinek, Jan
[gmx-users] isothermal compressibility Shyno Mathew
[gmx-users] NPT simulation with parinello-rahman pressure coupling Shyno Mathew
[gmx-users] tau_t and tau_p values Shyno Mathew
[gmx-users] Re: Re: NPT simulation with parinello-rahman pressure coupling Shyno Mathew
[gmx-users] NPT simulation for mutation study Shyno Mathew
[gmx-users] Re: Re: NPT simulation for mutation study Shyno Mathew
[gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul) Shyno Mathew
[gmx-users] Extending a simulation Shyno Mathew
[gmx-users] Re: Extending a simulation Shyno Mathew
[gmx-users] Re: Extending a simulation Shyno Mathew
[gmx-users] Different results from identical tpr after MD Robert McGibbon
[gmx-users] DD load balancing is limited by minimum cell size in dimension Z Gavin Melaugh
[gmx-users] extra factor in PMF Gavin Melaugh
[gmx-users] wham histograms Gavin Melaugh
[gmx-users] Position Restraints Dariush Mohammadyani
[gmx-users] Position Restraints Dariush Mohammadyani
[gmx-users] File editing - only one layer of water around a molecule Teemu Murtola
[gmx-users] How to choose two atoms at the same time, using g_select selection.dat Teemu Murtola
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] mdrun -rerun in parallel? Juliette N.
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] mdrun -rerun Juliette N.
[gmx-users] Methanesulfinamide Stability and Synthesis Nancy
[gmx-users] t-Butyl sulfinamide Stability Nancy
[gmx-users] Rerun error - the file has been replaced or its content has been changed Steven Neumann
[gmx-users] Rerun error - the file has been replaced or its content has been changed Steven Neumann
[gmx-users] Error: 4095 characters, fgets2 has size 4095 Steven Neumann
[gmx-users] Error: 4095 characters, fgets2 has size 4095 Steven Neumann
[gmx-users] Error: 4095 characters, fgets2 has size 4095 Steven Neumann
[gmx-users] Umbrella from checkpoint file Steven Neumann
[gmx-users] Atom MNZ1 in residue LYS 107 was not found Steven Neumann
[gmx-users] Atom MNZ1 in residue LYS 107 was not found Steven Neumann
[gmx-users] Extending umbrella sampling window Steven Neumann
[gmx-users] Extending umbrella sampling window Steven Neumann
[gmx-users] Chemical potential of protein Steven Neumann
[gmx-users] Chemical potential of protein Steven Neumann
[gmx-users] Extract pullF from trajectory Steven Neumann
[gmx-users] Extract pullF from trajectory Steven Neumann
[gmx-users] TRR file with nstxout= 0 Steven Neumann
[gmx-users] TRR file with nstxout= 0 Steven Neumann
[gmx-users] TRR file with nstxout= 0 Steven Neumann
[gmx-users] TRR file with nstxout= 0 Steven Neumann
[gmx-users] TRR file with nstxout= 0 Steven Neumann
[gmx-users] Umbrella - NPT equilibration Steven Neumann
[gmx-users] ions error Eduardo Oliveira
[gmx-users] grompp error Eduardo Oliveira
[gmx-users] grompp error Eduardo Oliveira
[gmx-users] grompp error Eduardo Oliveira
[gmx-users] how pdb2gmx calculate the total charge of a protein Francesco Oteri
[gmx-users] progressive imbalance in REMD Francesco Oteri
[gmx-users] Making Disulfide Bonds Francesco Oteri
[gmx-users] How to increase the ratio of cell size to constrain length per error message PAVAN PAYGHAN
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 189 PAVAN PAYGHAN
[gmx-users] martini coarse-grained XAvier Periole
[gmx-users] wham histograms XAvier Periole
[gmx-users] Best Force Field for a Membrane Protein Thomas Piggot
[gmx-users] Re: GPU support on GROMACS Szilárd Páll
[gmx-users] Re: GROMACS (w. OpenMPI) fails to run with -np larger than 10 Szilárd Páll
[gmx-users] single X double precision Szilárd Páll
[gmx-users] single X double precision Szilárd Páll
[gmx-users] Gromacs 4.6 with CUDA 4.2 Szilárd Páll
[gmx-users] Free Energy calcualtions Sai Kumar Ramadugu
AW: [gmx-users] the mdrun "-v" Rausch, Felix
AW: [gmx-users] Shape of box Rausch, Felix
AW: [gmx-users] Residue 'FOR' not found in residue topology database Rausch, Felix
AW: [gmx-users] Gromos87 Rausch, Felix
[gmx-users] Biasing a dipole vector direction relative to the moment of inertia tensor eigenvectors Andrew Ritchie
[gmx-users] Re: temperature Roy
[gmx-users] Re: temperature Roy
[gmx-users] .itp file for "Fe" atom.. Kamalesh Roy
[gmx-users] Fe atom problems....in simulation Kamalesh Roy
[gmx-users] Fe atom problems....in simulation Kamalesh Roy
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL) Bala S
[gmx-users] Re: g_wham problem with negative COM differences Thomas Schlesier
[gmx-users] g_wham problem with negative COM differences Thomas Schlesier
[gmx-users] Re: g_wham problem with negative COM differences Thomas Schlesier
[gmx-users] extra factor in PMF Thomas Schlesier
[gmx-users] g_dist explanation Thomas Schlesier
[gmx-users] -com switch in g_rdf Thomas Schlesier
[gmx-users] Extract pullF from trajectory Thomas Schlesier
[gmx-users] How to set the VMD_PLUGIN_PATH for gromacs analysis? Roland Schulz
[gmx-users] further discussion on the mdrun -append function Roland Schulz
[gmx-users] Question on checkpoint files and restarts/continuity J. Nathan Scott
[gmx-users] Gromacs 4.6 with CUDA 4.2 SebastianWaltz
[gmx-users] To know Anik Sen
[gmx-users] protein folding / pbc Shi, Huilin
[gmx-users] protein folding / pbc Shi, Huilin
[gmx-users] how to g_select bound water molecules Yun Shi
[gmx-users] Re: how to g_select bound water molecules Yun Shi
[gmx-users] Re: how to g_select bound water molecules Yun Shi
[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF Ricardo O. S. Soares
[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF Ricardo O. S. Soares
[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF Ricardo O. S. Soares
[gmx-users] NBFIX to gromacs Ricardo O. S. Soares
[gmx-users] Velocity autocorrelation David van der Spoel
[gmx-users] Velocity autocorrelation David van der Spoel
[gmx-users] charges David van der Spoel
[gmx-users] charges David van der Spoel
[gmx-users] Velocity autocorrelation David van der Spoel
[gmx-users] Does electric field be screened by the water ? David van der Spoel
[gmx-users] Does electric field be screened by the water ? David van der Spoel
[gmx-users] Problem with g_dipoles and SPCE water David van der Spoel
[gmx-users] Problem with g_dipoles and SPCE water David van der Spoel
[gmx-users] Problem with g_dipoles and SPCE water David van der Spoel
[gmx-users] Error: 4095 characters, fgets2 has size 4095 David van der Spoel
[gmx-users] Error: 4095 characters, fgets2 has size 4095 David van der Spoel
[gmx-users] progressive imbalance in REMD David van der Spoel
[gmx-users] NPT simulation for mutation study David van der Spoel
[gmx-users] Re: What is epsilon_r? David van der Spoel
[gmx-users] Re: What is epsilon_r? David van der Spoel
[gmx-users] PDB2GMX error in charmm27 Forcefield David van der Spoel
Fwd: [gmx-users] Editing of the existing system James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Problems with simulation on multi-nodes cluster James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Monitoring of Salt bridges during simulation Run James Starlight
[gmx-users] Monitoring of Salt bridges during simulation Run James Starlight
[gmx-users] MD after equilibration phase James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Simulation of the pure lipid bilayer James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Re: Simulation in the high temperature conditions James Starlight
[gmx-users] Making Disulfide Bonds James Starlight
[gmx-users] Making Disulfide Bonds James Starlight
[gmx-users] Making Disulfide Bonds James Starlight
[gmx-users] Making Disulfide Bonds James Starlight
[gmx-users] SS bond forcing Pierre THEVENET
[gmx-users] SS bond forcing Pierre THEVENET
[gmx-users] SS bond forcing Pierre THEVENET
[gmx-users] SS bond forcing Pierre THEVENET
[gmx-users] Residue 'FOR' not found in residue topology database Lucio Ricardo Montero Valenzuela
[gmx-users] Gromacs using openmpi [mdrun_mpi] Dharmendra Verma
[gmx-users] Position restraint of crystal waters NG HUI WEN
[gmx-users] Particle Insertion with Buckingham Potential Tina Wang
[gmx-users] Does electric field be screened by the water ? Xianwei Wang
[gmx-users] Does electric field be screened by the water ? Xianwei Wang
[gmx-users] Does electric field be screened by the water ? Xianwei Wang
[gmx-users] Software inconsistency error: One or more interactions were multiple assigned in the domain decomposition Olivia Waring
[gmx-users] a question related to the extending of md Dallas Warren
[gmx-users] a question related to the extending of md Dallas Warren
[gmx-users] Re: how to g_select bound water molecules Dallas Warren
[gmx-users] regarding micelle and its analysis Dallas Warren
[gmx-users] afm simulation Dallas Warren
[gmx-users] Error in using gromacs for MD simulation Dallas Warren
[gmx-users] Error in using gromacs for MD simulation Dallas Warren
[gmx-users] RE: ask about SDF Dallas Warren
[gmx-users] em fatal error! Tsjerk Wassenaar
[gmx-users] g_cluster for concoord output? Tsjerk Wassenaar
[gmx-users] Re: questions about Principal Component Analysis Tsjerk Wassenaar
[gmx-users] something about tpr file Tsjerk Wassenaar
[gmx-users] volume in ensemble Tsjerk Wassenaar
[gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file? Tsjerk Wassenaar
[gmx-users] Box generation for monoclinic crystal - regd Tsjerk Wassenaar
[gmx-users] martini coarse-grained Tsjerk Wassenaar
[gmx-users] Re: Simulation in the high temperature conditions Tsjerk Wassenaar
[gmx-users] Re: Simulation in the high temperature conditions Tsjerk Wassenaar
[gmx-users] Re: Simulation in the high temperature conditions Tsjerk Wassenaar
[gmx-users] the value of nsteps in the mdp file in the on-line tutorial Tsjerk Wassenaar
[gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file? Tsjerk Wassenaar
[gmx-users] What is an acceptable cosine content values? Tsjerk Wassenaar
[gmx-users] What is an acceptable cosine content values? Tsjerk Wassenaar
[gmx-users] Writing out individual coordinates Tsjerk Wassenaar
[gmx-users] PBC treatment: need an explanation Tsjerk Wassenaar
[gmx-users] how to optimize the orientation of the protein in a dodecahedron Tsjerk Wassenaar
[gmx-users] how to optimize the orientation of the protein in a dodecahedron Tsjerk Wassenaar
[gmx-users] ifp file in Gromacs? Eric Will
[gmx-users] protein and DMPC in Charmm36 ff Tomek Wlodarski
[gmx-users] REMD - low temperature ranges Tomek Wlodarski
[gmx-users] REMD - low temperature ranges Tomek Wlodarski
[gmx-users] Potential bug? Different results from different versions of gromacs with cos_acceleration Zhe Wu
[gmx-users] RE: Potential bug? Different results from different versions of gromacs with cos_acceleration Zhe Wu
[gmx-users] Parallel run on multiple nodes Huaichen(Bobby) Zhang
[gmx-users] Help: Anyone worked with "Wall"? Huaichen(Bobby) Zhang
[gmx-users] help about "Inconsistent DD boundary staggering limits" Desheng Zheng
[gmx-users] help about "Inconsistent DD boundary staggering limits" Desheng Zheng
[gmx-users] Parallel Computation of g_rdf Size Zheng
[gmx-users] Different results from identical tpr after MD Matthew Zwier
[gmx-users] protein folding / pbc Matthew Zwier
[gmx-users] Methods for accelerated MD simulation for Protein-Mg-GTP system in gromacs Matthew Zwier
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 146 Matthew Zwier
[gmx-users] Error message in reading AMBER's mdcrd files? a a
[gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file? a a
[gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file? a a
[gmx-users] What is an acceptable cosine content values? a a
[gmx-users] What is an acceptable cosine content values? a a
[gmx-users] Domain Decomposition cemilyigit at arcor.de
[gmx-users] epsilon_r vs. gb_epsilon_solvent bo.shuang
[gmx-users] Polymer crystal simulations-regd ramesh cheerla
[gmx-users] Monoclinic crystal simulations- gromacs - Regd ramesh cheerla
[gmx-users] Box generation for monoclinic crystal - regd ramesh cheerla
[gmx-users] multiple dihedral function types - regd ramesh cheerla
[gmx-users] Box generation for monoclinic crystal - regd ramesh cheerla
[gmx-users] Box generation for monoclinic crystal - regd ramesh cheerla
[gmx-users] multiple dihedral function types - regd ramesh cheerla
[gmx-users] Box generation for monoclinic crystal - regd ramesh cheerla
[gmx-users] Sigma and Epsilon chip
[gmx-users] sigma and epsilon. chip
[gmx-users] em fatal error! rama david
[gmx-users] Atom N not found.... rama david
[gmx-users] Atom N not found.... rama david
[gmx-users] Atom N not found.... rama david
[gmx-users] Atom N not found.... rama david
[gmx-users] Atom N not found.... rama david
[gmx-users] regarding rmsd and gyrate rama david
[gmx-users] regarding micelle and its analysis rama david
[gmx-users] How to fit ligand in specific site in protein in simulation rama david
[gmx-users] regarding micelle and its analysis - index group rama david
[gmx-users] How to fit ligand in specific site in protein in simulation rama david
[gmx-users] regarding micelle index group rama david
[gmx-users] Justin protein-ligand complex... rama david
[gmx-users] Justin protein-ligand complex... rama david
[gmx-users] Charm forcefield error..Atomtype CR not found .. rama david
[gmx-users] Charm forcefield error..Atomtype CR not found .. rama david
[gmx-users] Fwd: help rama david
[gmx-users] About hydrogen bond .. rama david
[gmx-users] Simulation of the pure lipid bilayer rajat desikan
[gmx-users] Is GPU GTX 560 compatible with GROMACS? shouliang dong
[gmx-users] volume in ensemble dina dusti
[gmx-users] volume in ensemble dina dusti
[gmx-users] martini coarse-grained dina dusti
[gmx-users] martini coarse-grained dina dusti
[gmx-users] martini coarse-grained dina dusti
[gmx-users] Clustering dina dusti
[gmx-users] Clustering dina dusti
[gmx-users] Clustering dina dusti
[gmx-users] the radius of gyration dina dusti
[gmx-users] Re: Williams wmiranda at estudiantes.fbio.uh.cu
[gmx-users] Charmm36_lipids with gromacs ffavela
[gmx-users] SS bond forcing pithevenet at free.fr
[gmx-users] SS bond forcing pithevenet at free.fr
[gmx-users] Domain Decomposition grita
[gmx-users] Protein charge grita
[gmx-users] Re: do_dssp bharat gupta
[gmx-users] Re: do_dssp bharat gupta
[gmx-users] Re: do_dssp bharat gupta
[gmx-users] Re: do_dssp bharat gupta
[gmx-users] Monitoring of Salt bridges during simulation Run bharat gupta
[gmx-users] MPI installation bharat gupta
[gmx-users] Re: Protein charge gutierrezangel
[gmx-users] Re: Parallel run on multiple nodes haadah
[gmx-users] Re: GROMACS (w. OpenMPI) fails to run with -np larger than 10 haadah
[gmx-users] g_rdf -surf -rdf res_com: details needed jneeraj
[gmx-users] %exist of hydrogen bonds + No -map specified! leila karami
[gmx-users] Re: Carbohydrate simulation: problem with the terminal atoms khuchtumur
[gmx-users] Re: sangeeta kundu
[gmx-users] Regading error pragna lakshmi
[gmx-users] em fatal error! lina
[gmx-users] how to change the timestamp of a xtc file lina
[gmx-users] how to change the timestamp of a xtc file lina
[gmx-users] which xtc file should be used for the trjconv command lina
[gmx-users] something about tpr file lina
[gmx-users] how to change the timestamp of a xtc file lina
[gmx-users] the different protonation state of HIS lina
[gmx-users] Protein ligand molecular dynamics simulation lina
[gmx-users] Fwd: help vineetha mandlik
[gmx-users] Error in using gromacs for MD simulation vineetha mandlik
[gmx-users] how to get a minimized structure pdb balaji nagarajan
[gmx-users] how to get a minimized structure pdb balaji nagarajan
[gmx-users] Bad box in protein.gro sai nitin
[gmx-users] How to fit ligand in specific site in protein in simulation sai nitin
[gmx-users] How to fit ligand in specific site in protein in simulation sai nitin
[gmx-users] How to fit ligand in specific site in protein in simulation sai nitin
[gmx-users] Protein ligand molecular dynamics simulation sai nitin
[gmx-users] Protein ligand molecular dynamics simulation sai nitin
[gmx-users] PDB2GMX error in charmm27 Forcefield sai nitin
[gmx-users] em fatal error! ankita oindrila
[gmx-users] File editing - only one layer of water around a molecule francesco oteri
[gmx-users] File editing - only one layer of water around a molecule francesco oteri
[gmx-users] progressive imbalance in REMD francesco oteri
[gmx-users] Fe atom problems....in simulation francesco oteri
[gmx-users] Best Force Field for a Membrane Protein francesco oteri
[gmx-users] problem with hemiltonian replica exchange restarting francesco oteri
[gmx-users] Velocities in trjconv 4.5.5 francesco oteri
[gmx-users] Making Disulfide Bonds francesco oteri
[gmx-users] afm simulation swati patel
[gmx-users] simulation in vaccum swati patel
[gmx-users] Error- Atom not found in residue seq nr while adding atom aiswarya pawar
[gmx-users] Error- Atom not found in residue seq nr while adding atom aiswarya pawar
[gmx-users] Adding Born Radii for implicit solvent MD german.erlenkamp at pharmazie.uni-halle.de
[gmx-users] Adding Born Radii for implicit solvent MD german.erlenkamp at pharmazie.uni-halle.de
[gmx-users] add nonbonded parameter for interaction between CNT and waters niaz poorgholami
[gmx-users] Re: hkl harker sections lloyd riggs
[gmx-users] Re:Data Analysis lloyd riggs
[gmx-users] Re: pre-wham lloyd riggs
[gmx-users] Re: pre-wham lloyd riggs
[gmx-users] Re: Questions lloyd riggs
[gmx-users] Re: Questions lloyd riggs
[gmx-users] Re: Questions lloyd riggs
[gmx-users] Re: Questions WHAM lloyd riggs
[gmx-users] Re: Questions WHAM lloyd riggs
[gmx-users] Re:WHAM question lloyd riggs
[gmx-users] Re:WHAM question lloyd riggs
[gmx-users] Re: : Extending run append lloyd riggs
[gmx-users] Re: : Extending run append lloyd riggs
[gmx-users] Re: Data Analysis lloyd riggs
[gmx-users] Re: Data Analysis lloyd riggs
[gmx-users] Re: Data Analysis lloyd riggs
[gmx-users] Oscillating electric field with a frequency of 14 Ghz. roberto
[gmx-users] Oscillating electric field with a frequency of 14 Ghz. roberto
[gmx-users] Methods for accelerated MD simulation for Protein-Mg-GTP system in gromacs neeru sharma
[gmx-users] Flooding approach and parameters for protein system neeru sharma
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 146 neeru sharma
[gmx-users] PLUMED plugin in gromacs for protein system neeru sharma
[gmx-users] Different results from identical tpr after MD bipin singh
[gmx-users] Different results from identical tpr after MD bipin singh
[gmx-users] Different results from identical tpr after MD bipin singh
[gmx-users] Different results from identical tpr after MD bipin singh
[gmx-users] MD after equilibration phase bipin singh
[gmx-users] MD after equilibration phase bipin singh
[gmx-users] MD after equilibration phase bipin singh
[gmx-users] MD after equilibration phase bipin singh
[gmx-users] installation issues anupam sinha
[gmx-users] sampling the side chain conformations by MD simulations mircial at sjtu.edu.cn
[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs mircial at sjtu.edu.cn
[gmx-users] PLUMED plugin in gromacs for protein system andrea spitaleri
[gmx-users] Can gromacs handle reflective boundary condition ? stjohn55
[gmx-users] writing ff parameters as a text file Bala subramanian
[gmx-users] gromacs 4.5.5 on Cygwin vijaya subramanian
[gmx-users] gromacs 4.5.5 on Cygwin vijaya subramanian
[gmx-users] gromacs 4.5.4 on cygwin cmake vijaya subramanian
[gmx-users] palusoori at gmail.com seera suryanarayana
[gmx-users] Fatal error seera suryanarayana
[gmx-users] Regarding errors seera suryanarayana
[gmx-users] Regarding errors seera suryanarayana
[gmx-users] Regarding errors seera suryanarayana
[gmx-users] Regarding error seera suryanarayana
[gmx-users] Regarding errors seera suryanarayana
[gmx-users] Regading error seera suryanarayana
[gmx-users] regarding rmsd and gyrate priya thiyagarajan
[gmx-users] regarding g_sas and rdf priya thiyagarajan
[gmx-users] regarding micelle and its analysis priya thiyagarajan
[gmx-users] mdrun segmentation fault priya thiyagarajan
[gmx-users] segmentation fault priya thiyagarajan
[gmx-users] regarding micelle and its analysis - index group priya thiyagarajan
[gmx-users] regarding micelle index group priya thiyagarajan
[gmx-users] micelle analysis priya thiyagarajan
[gmx-users] How to compile the template.c when GMX is builded with cmake chris.neale at utoronto.ca
[gmx-users] on the Umbrella Sampling on-line tutorial chris.neale at utoronto.ca
[gmx-users] further discussion on the mdrun -append function chris.neale at utoronto.ca
[gmx-users] Different results from identical tpr after MD chris.neale at utoronto.ca
[gmx-users] Error in MD simulation vinee2here
[gmx-users] Writing out individual coordinates patrick wintrode
[gmx-users] How to choose two atoms at the same time, using g_select selection.dat mu xiaojia
[gmx-users] How to choose two atoms at the same time, using g_select selection.dat mu xiaojia
[gmx-users] Explicit silvent together with implicit solvent model li yan
[gmx-users] Explicit solvent together with implicit solvent li yan
[gmx-users] Explicit solvent together with implicit solvent li yan
[gmx-users] How to fit ligand in specific site in protein in simulation Андрей Гончар
[gmx-users] How to fit ligand in specific site in protein in simulation Андрей Гончар
[gmx-users] -rcon parameter in mdrun - what values have sense? Иимяа Фаамиилиияа
[gmx-users] how to install DSSP in linux with Gromacs 4.0.7 李麗花
[gmx-users] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it 李麗花

Last message date: Mon Apr 30 22:30:59 CEST 2012
Archived on: Thu Nov 14 12:12:40 CET 2013

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