June 2012 Archives by author

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Starting: Fri Jun 1 11:16:45 CEST 2012
Ending: Sat Jun 30 23:31:13 CEST 2012
Messages: 901

[gmx-users] simulated annealing mdp Lord RaviRaj ..
[gmx-users] number of gauche <-> trans transitions with CHARMM36 and AMBER force fields ABEL Stephane 175950
[gmx-users] Problems with Dihedral transition times for dodecane ABEL Stephane 175950
[gmx-users] TIP3P or TIP4P Amir Abbasi
[gmx-users] Atomtype OW_tip4p not found Amir Abbasi
[gmx-users] Atomtype OW_tip4p not found Amir Abbasi
[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type? Mark Abraham
[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for Mark Abraham
[gmx-users] Atomtype 1 Mark Abraham
[gmx-users] how to rename oxygen oxt to be recognized by MOLMOL Mark Abraham
[gmx-users] Regarding error Mark Abraham
[gmx-users] Tabulated potentials for dihedrals - regd Mark Abraham
[gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form? Mark Abraham
[gmx-users] Electrostatic interactions and atoms with nul charge Mark Abraham
[gmx-users] Writing and compiling new analyses for gromacs Mark Abraham
[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12? Mark Abraham
[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12? Mark Abraham
[gmx-users] Electrostatic interactions and atoms with nul charge Mark Abraham
[gmx-users] What does this message mean? Mark Abraham
[gmx-users] chirality changes during the simulation Mark Abraham
[gmx-users] TIP3P or TIP4P Mark Abraham
[gmx-users] Re:What does this message mean? Mark Abraham
[gmx-users] tip5p tip, not good, energy can only get -39, not -45 Mark Abraham
[gmx-users] Tabulated potentials for dihedrals - regd Mark Abraham
[gmx-users] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option Mark Abraham
[gmx-users] Error in grompp steps of position restrained Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 98, Issue 42 Mark Abraham
[gmx-users] Error in grompp steps of position restrained Mark Abraham
[gmx-users] query on table potential Mark Abraham
[gmx-users] Pulling - ligand outside the box Mark Abraham
[gmx-users] md.log i/o error in futil.c +459 Mark Abraham
[gmx-users] eneconv with -dt flag Mark Abraham
[gmx-users] Re: energy conservation: shift vs shifted user potential Mark Abraham
[gmx-users] eneconv with -dt flag Mark Abraham
[gmx-users] Furthest distance between 2 atoms Mark Abraham
[gmx-users] parameters for bond types for GROMOS force field. Mark Abraham
[gmx-users] Re: Re: energy conservation: shift vs shifted user potential Mark Abraham
[gmx-users] floating point exception in .xtc file Mark Abraham
[gmx-users] Re: Fatal error: Atomtype O2 not found Mark Abraham
[gmx-users] Re: Fatal error: Atomtype O2 not found Mark Abraham
[gmx-users] Parallel MD performance Mark Abraham
[gmx-users] MD continuation Mark Abraham
[gmx-users] GPU Mark Abraham
[gmx-users] Question about documentation of -a switch in g_hbond Mark Abraham
[gmx-users] Re: md.log i/o error in futil.c +459 Mark Abraham
[gmx-users] LINCS warnings Mark Abraham
[gmx-users] Regarding minim.mdp file. Mark Abraham
[gmx-users] LINCS warnings Mark Abraham
[gmx-users] Rhamnose on 53a6 Mark Abraham
[gmx-users] parameters for bond types for GROMOS force field. Mark Abraham
[gmx-users] Regarding .mdp files. Mark Abraham
[gmx-users] Total energy of a group of atoms Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] analysing of the long trajectories Mark Abraham
[gmx-users] Re: Can Gromacs functions be called by some other codes? Mark Abraham
[gmx-users] dihedral restraint MD Mark Abraham
[gmx-users] GPU Mark Abraham
[gmx-users] question about pdb file Mark Abraham
[gmx-users] Re: Press Equilibration Mark Abraham
[gmx-users] Re: energy conservation: shift vs shifted user potential Mark Abraham
[gmx-users] error in grompp run Mark Abraham
[gmx-users] Errors in Minimization using grompp Mark Abraham
[gmx-users] Effect of vdwradii.dat Mark Abraham
[gmx-users] unable to access redmine Mark Abraham
[gmx-users] Re: Dihedral Constraints Mark Abraham
[gmx-users] g_lie reproducibility (g_lie is lying) Mark Abraham
[gmx-users] Re: Dihedral Constraints Mark Abraham
[gmx-users] Re: Dihedral Constraints Mark Abraham
[gmx-users] (3x3) Hessian matrix without minimization Mark Abraham
[gmx-users] Insertion protein in the membrane via G_membed Mark Abraham
[gmx-users] protein near the edges of simulation box Mark Abraham
[gmx-users] (3x3) Hessian matrix without minimization Mark Abraham
[gmx-users] multi-chain pdbs with mdrun? Mark Abraham
[gmx-users] current directory files Mark Abraham
[gmx-users] analysing of the long trajectories Mark Abraham
[gmx-users] simulating dimer proteins Mark Abraham
[gmx-users] RE: Re: g_lie reproducibility Mark Abraham
[gmx-users] current directory files Mark Abraham
[gmx-users] protein near the edges of simulation box Mark Abraham
[gmx-users] problem regarding installation of gromacs-4.5.5 Mark Abraham
[gmx-users] simulating dimer proteins Mark Abraham
[gmx-users] simulating dimer proteins Mark Abraham
[gmx-users] simulation time Mark Abraham
[gmx-users] the error in "bondfree.c" when installing gromacs 4.5.4 Mark Abraham
[gmx-users] Expanding existing biphastic Box Mark Abraham
[gmx-users] hello Mark Abraham
[gmx-users] Code precision is double message Mark Abraham
[gmx-users] Trjconv error Mark Abraham
[gmx-users] Trjconv error Mark Abraham
[gmx-users] REMD in explicit solvent Mark Abraham
[gmx-users] error in g_cluster "diagonalization" method Mark Abraham
[gmx-users] CMAP in Gromacs Vs. CHARMM Mark Abraham
[gmx-users] Insertion protein in the membrane via G_membed Mark Abraham
[gmx-users] to know about constraints Mark Abraham
[gmx-users] Insertion protein in the membrane via G_membed Mark Abraham
[gmx-users] Re: pair interaction energy decomposition analysis Mark Abraham
[gmx-users] Calculation of dihedral force constants Mark Abraham
[gmx-users] How Coulomb energy terms are calculated? Mark Abraham
[gmx-users] How do you properly use g_msd to calculate MSD of bilayer and account for monolayer motion? David Ackerman
[gmx-users] CECAM ScalaLife Workshop, Oct 03 - Oct 05, 2012 Rossen Apostolov
[gmx-users] Temperature in NVT file Shima Arasteh
[gmx-users] Temperature in NVT file Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] Protein near the edges of simulation box Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] Tutorial KALP-15 in DPPC Shima Arasteh
[gmx-users] Tutorial KALP-15 in DPPC Shima Arasteh
[gmx-users] Tutorial KALP-15 in DPPC Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] protein near the edges of simulation box Shima Arasteh
[gmx-users] Strange behaviour of bonds Shima Arasteh
[gmx-users] Strange behaviour of bonds Shima Arasteh
[gmx-users] Trjconv error Shima Arasteh
[gmx-users] Trjconv error Shima Arasteh
[gmx-users] Trjconv error Shima Arasteh
[gmx-users] Top file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] residuetype.dat Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] H-atoms in .hdb file Shima Arasteh
[gmx-users] pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Re: pdb2gmx error Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] popc36 + paper Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] error with grompp Shima Arasteh
[gmx-users] error with grompp Shima Arasteh
[gmx-users] atom type Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] atom type Shima Arasteh
[gmx-users] Berger lipid Shima Arasteh
[gmx-users] comparing simulations with diffrent forcefields Kowsar Bagherzadeh
[gmx-users] MD continuation Kowsar Bagherzadeh
[gmx-users] error in g_cluster "diagonalization" method Isaure Chauvot de Beauchêne
[gmx-users] Results of the GROMACS user survey & NVIDIA board winners Emanuel Birru
[gmx-users] Regarding error Emanuel Birru
[gmx-users] Regarding error. Emanuel Birru
[gmx-users] REMD in explicit solvent Esben Jannik Bjerrum
[gmx-users] how to run production MD for only a fragment of protein Acoot Brett
[gmx-users] Re : How GROMACS calculate the energy of hydrogen bond Acoot Brett
[gmx-users] Re : How GROMACS calculate the energy of hydrogen bond Acoot Brett
[gmx-users] how to rename oxygen oxt to be recognized by MOLMOL Acoot Brett
[gmx-users] vsite as interaction site for COM of benzene Broadbent, Richard
[gmx-users] tabulated potentials and soft core free energy - this should not work .... Michael Brunsteiner
[gmx-users] g_bar ... the right answer for the wrong reason? Michael Brunsteiner
[gmx-users] problem with git/4.6 Michael Brunsteiner
[gmx-users] problem with git/4.6 Michael Brunsteiner
[gmx-users] unit conversion of a force constant Lara Bunte
[gmx-users] Configurational bias Monte Carlo Lara Bunte
[gmx-users] pdb to xyz file format Lara Bunte
[gmx-users] Structure optimization failure Lara Bunte
[gmx-users] Structure optimization failure Lara Bunte
[gmx-users] Incomplete frame Turgay Cakmak
[gmx-users] Incomplete frame Turgay Cakmak
[gmx-users] trajectory analysis Turgay Cakmak
[gmx-users] trajectory analysis Turgay Cakmak
[gmx-users] hydrophobic contacts Turgay Cakmak
[gmx-users] dssp doubt Turgay Cakmak
[gmx-users] eneconv with -dt flag Turgay Cakmak
[gmx-users] eneconv with -dt flag Turgay Cakmak
[gmx-users] Electrostatic interaction energy Turgay Cakmak
[gmx-users] protein near the edges of simulation box Elton Carvalho
[gmx-users] protein near the edges of simulation box Elton Carvalho
[gmx-users] Regarding error. Javier Cerezo
[gmx-users] Regarding error. Javier Cerezo
[gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters Javier Cerezo
[gmx-users] mdrun -v output Javier Cerezo
[gmx-users] Re: bond autocorrelation function Dr. Vitaly V. G. Chaban
[gmx-users] Re: bond autocorrelation function Dr. Vitaly V. G. Chaban
[gmx-users] center an atomic group Dr. Vitaly V. G. Chaban
[gmx-users] center an atomic group Dr. Vitaly V. G. Chaban
[gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form? Wayne Chen
[gmx-users] pdb to xyz file format Chandan Choudhury
[gmx-users] analysing of the long trajectories Chandan Choudhury
[gmx-users] problem regarding installation of gromacs-4.5.5 Chandan Choudhury
[gmx-users] problem regarding installation of gromacs-4.5.5 Chandan Choudhury
[gmx-users] mdrun -v output Chandan Choudhury
[gmx-users] mdrun -v output Chandan Choudhury
[gmx-users] mdrun -v output Chandan Choudhury
[gmx-users] Calculation of dihedral force constants Covington, Cody Lance
[gmx-users] Re: Restarting mdrun Cuiying
[gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue Alex Cumberworth
[gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue Alex Cumberworth
[gmx-users] Solvation Free Energy calculation (g_bar) Daniel
[gmx-users] Re: Solvation Free Energy calculation (g_bar) Daniel
[gmx-users] Selecting atom indices of residues whose centers of mass match a position range Andrew DeYoung
[gmx-users] Question about documentation of -a switch in g_hbond Andrew DeYoung
[gmx-users] Re: Question about documentation of -a switch in g_hbond Andrew DeYoung
[gmx-users] Bonds and atom-pairs in g_hbond Andrew DeYoung
[gmx-users] RE: Bonds and atom-pairs in g_hbond Andrew DeYoung
[gmx-users] What does the -don switch calculate in g_hbond? Andrew DeYoung
[gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters Edward Deira
[gmx-users] PBC Nilesh Dhumal
[gmx-users] Effect of vdwradii.dat Anna Duncan
[gmx-users] g_lie reproducibility (g_lie is lying) Tom Dupree
[gmx-users] RE: Re: g_lie reproducibility Tom Dupree
[gmx-users] Question regarding genion Matthias Ernst
[gmx-users] pdb to xyz file format Matthias Ernst
[gmx-users] Distance of pull group is larger than half the box size Eudes Fileti
[gmx-users] multi-chain pdbs with mdrun? Samuel Flores
[gmx-users] Re: Preserving chain id/information when using editconf (gromacs 4.0.7) Samuel Flores
[gmx-users] Results of the GROMACS user survey & NVIDIA board winners Dommert Florian
[gmx-users] MD Training Dommert Florian
[gmx-users] g_msd and MSD analysis Dommert Florian
[gmx-users] Angle deformation of Triphosphate moiety with charge -4 ?.. Alberto Sergio Garay
[gmx-users] Steered MD Miguel Ángel Mompeán García
[gmx-users] Rhamnose on 53a6 Marc Gordon
[gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas) Gerrit Groenhof
[gmx-users] qmmm and "real-life" meaning of null Gerrit Groenhof
[gmx-users] Configurational bias Monte Carlo Benjamin Haley
[gmx-users] Trouble with packing lipids around a protein using InflateGRO Erica Hicks
[gmx-users] Energy Minimization - not getting correct lipid area Hicks, Erica
[gmx-users] Re: Energy Minimization - not getting correct lipid area Erica Hicks
[gmx-users] RE: Energy Minimization - not getting correct lipid area Erica Hicks
[gmx-users] RE: Energy Minimization - not getting correct lipid area Erica Hicks
[gmx-users] RE: Energy Minimization - not getting correct lipid area Erica Hicks
[gmx-users] RE: Energy Minimization - not getting correct lipid area Erica Hicks
[gmx-users] RE: Energy Minimization - not getting correct lipid area Erica Hicks
[gmx-users] dihedral restraint MD Lin Huang
[gmx-users] rare huge forces in constraint simulation with direction_periodic Jochen Hub
[gmx-users] rare huge forces in constraint simulation with direction_periodic Jochen Hub
[gmx-users] Bootstrapping using g_wham Jochen Hub
[gmx-users] Force constant in g_wham Jochen Hub
[gmx-users] GPU-GROMACS and OPLS-AA Igor1963
[gmx-users] GPU-GROMACS and OPLS-AA Igor1963
[gmx-users] (no subject) Pathumwadee Intharathep
[gmx-users] problem regarding installation of gromacs-4.5.5 Nidhi Jatana
[gmx-users] problem regarding installation of gromacs-4.5.5 Nidhi Jatana
[gmx-users] problem regarding installation of gromacs-4.5.5 Nidhi Jatana
[gmx-users] problem regarding installation of gromacs-4.5.5 Nidhi Jatana
[gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system Sangita Kachhap
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system Sangita Kachhap
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system Sangita Kachhap
[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12? Bao Kai
[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12? Bao Kai
[gmx-users] What does this message mean? Bao Kai
[gmx-users] Re:What does this message mean? Bao Kai
[gmx-users] Cannot get correct pressure value with MTTK pressure coupling Bao Kai
[gmx-users] Can Gromacs functions be called by some other codes? Bao Kai
[gmx-users] Re: Can Gromacs functions be called by some other codes? Bao Kai
[gmx-users] What does --enable-fahcore mean? Bao Kai
[gmx-users] Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Positive Potential Energy after equilibration Satish Kamath
[gmx-users] Re: Fatal error: Atomtype O2 not found Gurunath Katagi
[gmx-users] Total energy of a group of atoms Markus Kaukonen
[gmx-users] Total energy of a group of atoms Markus Kaukonen
[gmx-users] dodssp segmentation fault Denis Kazakiewicz
[gmx-users] dodssp segmentation fault SOLVED for DEBIAN Denis Kazakiewicz
[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface Klniu
[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface Klniu
[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface Klniu
[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type? Klniu
[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type? Klniu
[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type? Klniu
[gmx-users] (no subject) Klniu
[gmx-users] wrong distances with g_dist Dmytro Kovalskyy
[gmx-users] Rhamnose on 53a6 Thales Kronenberger
[gmx-users] energy conservation: shift vs shifted user potential Anja Kuhnhold
[gmx-users] Re: energy conservation: shift vs shifted user potential Anja Kuhnhold
[gmx-users] Re: Re: energy conservation: shift vs shifted user potential Anja Kuhnhold
[gmx-users] Re: energy conservation: shift vs shifted user potential Anja Kuhnhold
[gmx-users] Water molecules cannot be settled, why? John Ladasky
[gmx-users] Berger lipid Peter Lai
[gmx-users] Writing and compiling new analyses for gromacs Peter C. Lai
[gmx-users] Writing and compiling new analyses for gromacs Peter C. Lai
[gmx-users] Trajectories Peter C. Lai
[gmx-users] How to add DMSO as solvent? Peter C. Lai
[gmx-users] mdrun -v output Peter C. Lai
[gmx-users] Insertion protein in the membrane via G_membed Peter C. Lai
[gmx-users] no SOL in topology file after genbox command Peter C. Lai
[gmx-users] Berger lipid Peter C. Lai
[gmx-users] Berger lipid Peter C. Lai
[gmx-users] Electrostatic interactions and atoms with nul charge Laurence Leherte
[gmx-users] Electrostatic interactions and atoms with nul charge Laurence Leherte
[gmx-users] umbrella windows... Justin A. Lemkul
[gmx-users] Incomplete frame Justin A. Lemkul
[gmx-users] Incomplete frame Justin A. Lemkul
[gmx-users] Configurational bias Monte Carlo Justin A. Lemkul
[gmx-users] About extend the run,, Justin A. Lemkul
[gmx-users] About extend the run,, Justin A. Lemkul
[gmx-users] how to run production MD for only a fragment of protein Justin A. Lemkul
[gmx-users] Atomtype 1 Justin A. Lemkul
[gmx-users] Atomtype 1 Justin A. Lemkul
[gmx-users] Atomtype 1 Justin A. Lemkul
[gmx-users] Re: dangling bond at at one of the terminal ends Justin A. Lemkul
[gmx-users] Re: dangling bond at at one of the terminal ends Justin A. Lemkul
[gmx-users] Water molecules cannot be settled, why? Justin A. Lemkul
[gmx-users] Writing and compiling new analyses for gromacs Justin A. Lemkul
[gmx-users] Writing and compiling new analyses for gromacs Justin A. Lemkul
[gmx-users] trajectory analysis Justin A. Lemkul
[gmx-users] Trajectories Justin A. Lemkul
[gmx-users] Selecting atom indices of residues whose centers of mass match a position range Justin A. Lemkul
[gmx-users] How to add DMSO as solvent? Justin A. Lemkul
[gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue Justin A. Lemkul
[gmx-users] Question regarding genion Justin A. Lemkul
[gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system Justin A. Lemkul
[gmx-users] Atomtype OW_tip4p not found Justin A. Lemkul
[gmx-users] Atomtype OW_tip4p not found Justin A. Lemkul
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system Justin A. Lemkul
[gmx-users] Cannot get correct pressure value with MTTK pressure coupling Justin A. Lemkul
[gmx-users] GPU crashes Justin A. Lemkul
[gmx-users] GPU crashes Justin A. Lemkul
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system Justin A. Lemkul
[gmx-users] Regarding g_sham Justin A. Lemkul
[gmx-users] How to set up constraint distcance pulling Justin A. Lemkul
[gmx-users] Regarding Free Energy calculation tutorial Justin A. Lemkul
[gmx-users] How to set up constraint distcance pulling Justin A. Lemkul
[gmx-users] dssp doubt Justin A. Lemkul
[gmx-users] About Umbrella sampling Justin A. Lemkul
[gmx-users] Atomtype OW_tip4p not found Justin A. Lemkul
[gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters Justin A. Lemkul
[gmx-users] Trouble with packing lipids around a protein using InflateGRO Justin A. Lemkul
[gmx-users] Electrostatic interaction energy Justin A. Lemkul
[gmx-users] parameters for bond types for GROMOS force field. Justin A. Lemkul
[gmx-users] parameters for bond types for GROMOS force field. Justin A. Lemkul
[gmx-users] Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] Re: Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] RE: Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] RE: Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] RE: Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] RE: Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] Fatal error: Atomtype O2 not found Justin A. Lemkul
[gmx-users] Re: Fatal error: Atomtype O2 not found Justin A. Lemkul
[gmx-users] Re: Fatal error: Atomtype O2 not found Justin A. Lemkul
[gmx-users] Re: Fatal error: Atomtype O2 not found Justin A. Lemkul
[gmx-users] Re: Automated Topology Builder job partially completed Justin A. Lemkul
[gmx-users] parameters for bond types for GROMOS force field. Justin A. Lemkul
[gmx-users] Temperature in NVT file Justin A. Lemkul
[gmx-users] parameters for bond types for GROMOS force field. Justin A. Lemkul
[gmx-users] Capping error in pdb2gmx Justin A. Lemkul
[gmx-users] Question about documentation of -a switch in g_hbond Justin A. Lemkul
[gmx-users] Re : Capping error in pdb2gmx Justin A. Lemkul
[gmx-users] Regarding error. Justin A. Lemkul
[gmx-users] radius of gyration Justin A. Lemkul
[gmx-users] Coordinate file for lipid bilayer Justin A. Lemkul
[gmx-users] Rhamnose on 53a6 Justin A. Lemkul
[gmx-users] LINCS warnings Justin A. Lemkul
[gmx-users] Positive Potential Energy after equilibration Justin A. Lemkul
[gmx-users] radius of gyration Justin A. Lemkul
[gmx-users] radius of gyration Justin A. Lemkul
[gmx-users] radius of gyration Justin A. Lemkul
[gmx-users] Re: Fatal error: Atomtype O2 not found Justin A. Lemkul
[gmx-users] RE: Bonds and atom-pairs in g_hbond Justin A. Lemkul
[gmx-users] simulated annealing mdp Justin A. Lemkul
[gmx-users] Re: Positive Potential Energy after equilibration Justin A. Lemkul
[gmx-users] mdrun_mpi segmentation fault for run in vacuum Justin A. Lemkul
[gmx-users] mdrun_mpi segmentation fault for run in vacuum Justin A. Lemkul
[gmx-users] Press Equilibration Justin A. Lemkul
[gmx-users] g_rdf (lyzozyme tutorial) Justin A. Lemkul
[gmx-users] g_rdf (lyzozyme tutorial) Justin A. Lemkul
[gmx-users] mdrun_mpi segmentation fault for run in vacuum Justin A. Lemkul
[gmx-users] mdrun_mpi segmentation fault for run in vacuum Justin A. Lemkul
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] simulated annealing mdp Justin A. Lemkul
[gmx-users] Re: Positive Potential Energy after equilibration Justin A. Lemkul
[gmx-users] mdrun_mpi segmentation fault for run in vacuum Justin A. Lemkul
[gmx-users] simulated annealing mdp Justin A. Lemkul
[gmx-users] mdrun_mpi segmentation fault for run in vacuum Justin A. Lemkul
[gmx-users] Hbonds and PBC Justin A. Lemkul
[gmx-users] RE: Energy Minimization - not getting correct lipid area Justin A. Lemkul
[gmx-users] Re: bond autocorrelation function Justin A. Lemkul
[gmx-users] problems occur during simulation Justin A. Lemkul
[gmx-users] Re: Positive Potential Energy after equilibration Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] unknown residue (BGC) Justin A. Lemkul
[gmx-users] input/output error in production grompp Justin A. Lemkul
[gmx-users] unknown residue (BGC) Justin A. Lemkul
[gmx-users] Errors in Minimization using grompp Justin A. Lemkul
[gmx-users] unknown residue (BGC) Justin A. Lemkul
[gmx-users] input/output error in production grompp Justin A. Lemkul
[gmx-users] Errors in Minimization using grompp Justin A. Lemkul
[gmx-users] input/output error in production grompp Justin A. Lemkul
[gmx-users] input/output error in production grompp Justin A. Lemkul
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation Justin A. Lemkul
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation Justin A. Lemkul
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation Justin A. Lemkul
[gmx-users] Error in production run Justin A. Lemkul
[gmx-users] unable to access redmine Justin A. Lemkul
[gmx-users] Re: Dihedral Constraints Justin A. Lemkul
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation Justin A. Lemkul
[gmx-users] Regarding error. Justin A. Lemkul
[gmx-users] help!! Justin A. Lemkul
[gmx-users] Bootstrapping using g_wham Justin A. Lemkul
[gmx-users] Re: Positive Potential Energy after equilibration Justin A. Lemkul
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED] Justin A. Lemkul
[gmx-users] problem regarding installation of gromacs-4.5.5 Justin A. Lemkul
[gmx-users] problem regarding installation of gromacs-4.5.5 Justin A. Lemkul
[gmx-users] simulation box shape and length Justin A. Lemkul
[gmx-users] Tutorial KALP-15 in DPPC Justin A. Lemkul
[gmx-users] Tutorial KALP-15 in DPPC Justin A. Lemkul
[gmx-users] protein near the edges of simulation box Justin A. Lemkul
[gmx-users] protein near the edges of simulation box Justin A. Lemkul
[gmx-users] Simple question (confout) Justin A. Lemkul
[gmx-users] protein near the edges of simulation box Justin A. Lemkul
[gmx-users] simulating dimer proteins Justin A. Lemkul
[gmx-users] problem in making a trajectory Justin A. Lemkul
[gmx-users] simulating dimer proteins Justin A. Lemkul
[gmx-users] problem in making a trajectory Justin A. Lemkul
[gmx-users] problem in making a trajectory Justin A. Lemkul
[gmx-users] How to compare two pdb files Justin A. Lemkul
[gmx-users] How to compare two pdb files Justin A. Lemkul
[gmx-users] How to compare two pdb files Justin A. Lemkul
[gmx-users] How to compare two pdb files Justin A. Lemkul
[gmx-users] pressure-lyzozyme tutorial Justin A. Lemkul
[gmx-users] About Mike Harms python script Justin A. Lemkul
[gmx-users] Distance of pull group is larger than half the box size Justin A. Lemkul
[gmx-users] SDF-error Justin A. Lemkul
[gmx-users] spatial distribution function Justin A. Lemkul
[gmx-users] Strange behaviour of bonds Justin A. Lemkul
[gmx-users] jalemkul at vt.edu Justin A. Lemkul
[gmx-users] Strange behaviour of bonds Justin A. Lemkul
[gmx-users] problem regarding installation of gromacs-4.5.5 Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] hello Justin A. Lemkul
[gmx-users] Solvation Free Energy calculation (g_bar) Justin A. Lemkul
[gmx-users] Re: Solvation Free Energy calculation (g_bar) Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Analysis of the torsion Chi angles dynamics during simulation Justin A. Lemkul
Fw: [gmx-users] segmentation fault-g_spatial Justin A. Lemkul
[gmx-users] to know about constraints Justin A. Lemkul
[gmx-users] pair interaction energy decomposition analysis Justin A. Lemkul
[gmx-users] to know about constraints Justin A. Lemkul
[gmx-users] Regarding pdb file of a polymer Justin A. Lemkul
[gmx-users] Re: Regarding pdb file of a polymer Justin A. Lemkul
[gmx-users] only three options for genrestr Justin A. Lemkul
[gmx-users] plzz help Justin A. Lemkul
[gmx-users] Residue 'DUM' not found in residue topology database Justin A. Lemkul
[gmx-users] Residue 'DUM' not found in residue topology database Justin A. Lemkul
[gmx-users] Residue 'DUM' not found in residue topology database Justin A. Lemkul
[gmx-users] center an atomic group Justin A. Lemkul
[gmx-users] Top file Justin A. Lemkul
[gmx-users] Rotation aroud the z axis Justin A. Lemkul
[gmx-users] H-atoms in .hdb file Justin A. Lemkul
[gmx-users] H-atoms in .hdb file Justin A. Lemkul
[gmx-users] H-atoms in .hdb file Justin A. Lemkul
[gmx-users] H-atoms in .hdb file Justin A. Lemkul
[gmx-users] Lipid-protein simulation.... Justin A. Lemkul
[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial Justin A. Lemkul
[gmx-users] H-atoms in .hdb file Justin A. Lemkul
[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology Justin A. Lemkul
[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial Justin A. Lemkul
[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial Justin A. Lemkul
[gmx-users] H-atoms in .hdb file Justin A. Lemkul
[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp Justin A. Lemkul
[gmx-users] Pulling ligand - Different Profiles (Force vs time) Justin A. Lemkul
[gmx-users] Pulling ligand - Different Profiles (Force vs time) Justin A. Lemkul
[gmx-users] make index Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] Re: pdb2gmx error Justin A. Lemkul
[gmx-users] NVT, NPT and then pulling? Justin A. Lemkul
[gmx-users] Free energy between residues Justin A. Lemkul
[gmx-users] Justin's Paper Justin A. Lemkul
[gmx-users] Free energy between residues Justin A. Lemkul
[gmx-users] editbox removes dummy atoms Justin A. Lemkul
[gmx-users] g_bar ... the right answer for the wrong reason? Justin A. Lemkul
[gmx-users] editbox removes dummy atoms Justin A. Lemkul
[gmx-users] g_bar ... the right answer for the wrong reason? Justin A. Lemkul
[gmx-users] Berger lipid Justin A. Lemkul
[gmx-users] Berger lipid Justin A. Lemkul
[gmx-users] Berger lipid Justin A. Lemkul
[gmx-users] Berger lipid Justin A. Lemkul
[gmx-users] editconf do not center protein Justin A. Lemkul
[gmx-users] Structure optimization failure Justin A. Lemkul
[gmx-users] problem with git/4.6 Justin A. Lemkul
[gmx-users] Structure optimization failure Justin A. Lemkul
[gmx-users] error with grompp Justin A. Lemkul
[gmx-users] COM Pulling Justin A. Lemkul
[gmx-users] error with grompp Justin A. Lemkul
[gmx-users] Structure optimization failure Justin A. Lemkul
[gmx-users] error with grompp Justin A. Lemkul
[gmx-users] error with grompp Justin A. Lemkul
[gmx-users] Re: COM Pulling Justin A. Lemkul
[gmx-users] problem with git/4.6 Justin A. Lemkul
[gmx-users] Structure optimization failure Justin A. Lemkul
[gmx-users] pdb file of polymer Justin A. Lemkul
[gmx-users] .top file incoherent with the values in the ffbonded.itp file Justin A. Lemkul
[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file Justin A. Lemkul
[gmx-users] error with grompp Justin A. Lemkul
[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file Justin A. Lemkul
[gmx-users] Berger lipid Justin A. Lemkul
[gmx-users] Berger lipid Justin A. Lemkul
[gmx-users] Can Gromacs functions be called by some other codes? Da-Wei Li
[gmx-users] Re: Can Gromacs functions be called by some other codes? Da-Wei Li
[gmx-users] the error in "bondfree.c" when installing gromacs 4.5.4 Xingcheng Lin
[gmx-users] the error in "bondfree.c" when installing gromacs 4.5.4 Xingcheng Lin
[gmx-users] Results of the GROMACS user survey & NVIDIA board winners Erik Lindahl
[gmx-users] Diameter of the micelle Angie Paola Macias Lozano
[gmx-users] Steered MD Mike M
[gmx-users] Steered MD Mike M
[gmx-users] question about pdb file Mike M
[gmx-users] query on table potential Sanku M
[gmx-users] tip5p tip, not good, energy can only get -39, not -45 MD
[gmx-users] Error in grompp steps of position restrained Malai
[gmx-users] Error in grompp steps of position restrained Malai
[gmx-users] Error in grompp steps of position restrained Malai
[gmx-users] input/output error in production grompp Malai
[gmx-users] input/output error in production grompp Malai
[gmx-users] input/output error in production grompp Malai
[gmx-users] input/output error in production grompp Malai
[gmx-users] Error in production run Malai
[gmx-users] Error in production run Malai
[gmx-users] Code precision is double message Allen Mao
[gmx-users] Re : How GROMACS calculate the energy of hydrogen bond Erik Marklund
[gmx-users] MD Training Erik Marklund
[gmx-users] Re : How GROMACS calculate the energy of hydrogen bond Erik Marklund
[gmx-users] Writing and compiling new analyses for gromacs Erik Marklund
[gmx-users] Trajectories Erik Marklund
[gmx-users] Trajectories Erik Marklund
[gmx-users] Trajectories Erik Marklund
[gmx-users] Regarding error. Erik Marklund
[gmx-users] Bonds and atom-pairs in g_hbond Erik Marklund
[gmx-users] dodssp segmentation fault SOLVED for DEBIAN Erik Marklund
[gmx-users] multi-chain pdbs with mdrun? Erik Marklund
[gmx-users] protein near the edges of simulation box Erik Marklund
[gmx-users] Numbering for pbc_atom0 Erik Marklund
[gmx-users] Numbering for pbc_atom0 Erik Marklund
[gmx-users] to know about constraints Marzinek, Jan
[gmx-users] to know about constraints Marzinek, Jan
[gmx-users] to know about constraints Marzinek, Jan
[gmx-users] QM/MM Calculation with Orca Minos Matsoukas
[gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas) Minos Matsoukas
[gmx-users] Simple question (confout) Dariush Mohammadyani
[gmx-users] Selecting atom indices of residues whose centers of mass match a position range Teemu Murtola
[gmx-users] (3x3) Hessian matrix without minimization Hyuntae Na
[gmx-users] (3x3) Hessian matrix without minimization Hyuntae Na
[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface Christopher Neale
[gmx-users] unit conversion of a force constant Christopher Neale
[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface Christopher Neale
[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type? Christopher Neale
[gmx-users] floating point exception in .xtc file Christopher Neale
[gmx-users] floating point exception in .xtc file Christopher Neale
[gmx-users] unable to access redmine Christopher Neale
[gmx-users] Diameter of the micelle Christopher Neale
[gmx-users] segmentation fault-g_spatial Christopher Neale
[gmx-users] Regarding umbrella sampling simulations along H-bonds Christopher Neale
[gmx-users] Berger lipid Christopher Neale
[gmx-users] Segmentation fault - pdb2gmx specbond.dat Steven Neumann
[gmx-users] Pulling - ligand outside the box Steven Neumann
[gmx-users] Hbonds and PBC Steven Neumann
[gmx-users] Re: Hbonds and PBC Steven Neumann
[gmx-users] Hbonds and PBC Steven Neumann
[gmx-users] Pulling ligand - Different Profiles (Force vs time) Steven Neumann
[gmx-users] Pulling ligand - Different Profiles (Force vs time) Steven Neumann
[gmx-users] Pulling ligand - Different Profiles (Force vs time) Steven Neumann
[gmx-users] NVT, NPT and then pulling? Steven Neumann
[gmx-users] Free energy between residues Steven Neumann
[gmx-users] NVT, NPT and then pulling? Steven Neumann
[gmx-users] Free energy between residues Steven Neumann
[gmx-users] Free energy between residues Steven Neumann
[gmx-users] Justin's Paper Steven Neumann
[gmx-users] Force constant - units Steven Neumann
[gmx-users] Re: pair interaction energy decomposition analysis Son Tung Ngo
[gmx-users] Re: pair interaction energy decomposition analysis Son Tung Ngo
[gmx-users] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option PAVAN PAYGHAN
[gmx-users] gmx-users Digest, Vol 98, Issue 42 PAVAN PAYGHAN
[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp PAVAN PAYGHAN
[gmx-users] RMS fluctuations and error estimate from block averaging Atila Petrosian
[gmx-users] Re: dangling bond at at one of the terminal ends Thomas Piggot
[gmx-users] Trajectories Thomas Piggot
[gmx-users] Berger lipid Thomas Piggot
[gmx-users] Re: Possible bug: energy changes with the number of nodes for energy minimization Szilárd Páll
[gmx-users] GPU Szilárd Páll
[gmx-users] RIMSP calculation R.S.K.Vijayan
[gmx-users] RIMSP calculation R.S.K.Vijayan
[gmx-users] chi1/chi2 Raj
[gmx-users] COM Pulling Raj
[gmx-users] Re: COM Pulling Raj
[gmx-users] Re: Thermodynamic Integration Glu -> Ala Mutation Sai Kumar Ramadugu
[gmx-users] FEP Sai Kumar Ramadugu
[gmx-users] g_msd and MSD analysis Mr Bernard Ramos
[gmx-users] Trajectories Blake Rankin
AW: [gmx-users] Structure optimization failure Rausch, Felix
[gmx-users] g_sas Meisam Rezaei
[gmx-users] OPLS parameters for amine oxide sulatha M. S
[gmx-users] OPLS parametrs for aminoxide sulatha M. S
[gmx-users] Furthest distance between 2 atoms Catarina Santos
[gmx-users] DNA simulations SatyaK
[gmx-users] Re: boundaries in PMF Thomas Schlesier
[gmx-users] vsite as interaction site for COM of benzene Thomas Schlesier
[gmx-users] vsite as interaction site for COM of benzene Thomas Schlesier
[gmx-users] Residue 'DUM' not found in residue topology database Thomas Schlesier
[gmx-users] Residue 'DUM' not found in residue topology database Thomas Schlesier
[gmx-users] GPU Ehud Schreiber
[gmx-users] Dispersion Corrections Erica Schulz
[gmx-users] Re: [gmx-developers] issue on benchmarking FEP calculations in Gromacs and NAMD Roland Schulz
[gmx-users] hello Anik Sen
[gmx-users] to know about constraints Anik Sen
[gmx-users] to know about constraints Anik Sen
[gmx-users] to know about constraints Anik Sen
[gmx-users] to know about constraints Anik Sen
[gmx-users] to know about constraints Anik Sen
[gmx-users] to know about constraints Anik Sen
[gmx-users] md.log i/o error in futil.c +459 Inon Sharony
[gmx-users] Re: md.log i/o error in futil.c +459 Inon Sharony
[gmx-users] Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain Inon Sharony
[gmx-users] How to add DMSO as solvent? Yun Shi
[gmx-users] Configurational bias Monte Carlo Michael Shirts
[gmx-users] What does --enable-fahcore mean? Michael Shirts
[gmx-users] Unusual g_order with CHARMM36 Ricardo O. S. Soares
[gmx-users] CMAP in Gromacs Vs. CHARMM Andy Somogyi
[gmx-users] BAR gives different result than TI David van der Spoel
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] Re: Automated Topology Builder job partially completed James Starlight
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] parameters for bond types for GROMOS force field. James Starlight
[gmx-users] Coordinate file for lipid bilayer James Starlight
[gmx-users] analysing of the long trajectories James Starlight
[gmx-users] analysing of the long trajectories James Starlight
[gmx-users] Insertion protein in the membrane via G_membed James Starlight
[gmx-users] Insertion protein in the membrane via G_membed James Starlight
[gmx-users] analysing of the long trajectories James Starlight
[gmx-users] analysing of the long trajectories James Starlight
[gmx-users] Insertion protein in the membrane via G_membed James Starlight
[gmx-users] Expanding existing biphastic Box James Starlight
[gmx-users] Analysis of the torsion Chi angles dynamics during simulation James Starlight
[gmx-users] Insertion protein in the membrane via G_membed James Starlight
[gmx-users] Insertion protein in the membrane via G_membed James Starlight
[gmx-users] Insertion protein in the membrane via G_membed James Starlight
[gmx-users] Analysis of buried water dynamics James Starlight
[gmx-users] Force constant - units Oliver Stueker
[gmx-users] Regarding error Seera Suryanarayana
[gmx-users] Regarding error Seera Suryanarayana
[gmx-users] Regarding error Seera Suryanarayana
[gmx-users] Regarding error. Seera Suryanarayana
[gmx-users] Regarding error Seera Suryanarayana
[gmx-users] Regarding error. Seera Suryanarayana
[gmx-users] Regarding error. Seera Suryanarayana
[gmx-users] Regarding error Seera Suryanarayana
[gmx-users] Regarding minim.mdp file. Seera Suryanarayana
[gmx-users] Regarding .mdp files. Seera Suryanarayana
[gmx-users] Regarding error. Seera Suryanarayana
[gmx-users] (no subject) Seera Suryanarayana
[gmx-users] Regarding error. Seera Suryanarayana
[gmx-users] Fwd: Regarding error. Seera Suryanarayana
[gmx-users] Regarding error. Seera Suryanarayana
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] Writing and compiling new analyses for gromacs Shay Teaching
[gmx-users] dssp doubt Emine Deniz Tekin
[gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules Surya Prakash Tiwari
[gmx-users] bond autocorrelation function Tom
[gmx-users] pair interaction energy decomposition analysis Ngo Son Tung
[gmx-users] Scaling/performance on Gromacs 4 Manu Vajpai
[gmx-users] How to calculate chemical shift? Xianwei Wang
[gmx-users] cluster fomation in triolein simulation Dallas Warren
[gmx-users] Regarding error Dallas Warren
[gmx-users] analysing of the long trajectories Tsjerk Wassenaar
[gmx-users] Re: Can Gromacs functions be called by some other codes? Tsjerk Wassenaar
[gmx-users] Protein near the edges of simulation box Tsjerk Wassenaar
[gmx-users] Bootstrapping using g_wham Tsjerk Wassenaar
[gmx-users] protein near the edges of simulation box Tsjerk Wassenaar
[gmx-users] PBC Tsjerk Wassenaar
[gmx-users] RIMSP calculation Tsjerk Wassenaar
[gmx-users] Dielectric Constants Size Zheng
[gmx-users] analysing of the long trajectories a a
[gmx-users] problems occur during simulation abhidon89
[gmx-users] radius of gyration delara aghaie
[gmx-users] MD continuation delara aghaie
[gmx-users] Parallel MD performance delara aghaie
[gmx-users] radius of gyration delara aghaie
[gmx-users] radius of gyration delara aghaie
[gmx-users] radius of gyration delara aghaie
[gmx-users] radius of gyration delara aghaie
[gmx-users] radius of gyration delara aghaie
[gmx-users] g_rdf (lyzozyme tutorial) delara aghaie
[gmx-users] question about pdb file delara aghaie
[gmx-users] g_rdf (lyzozyme tutorial) delara aghaie
[gmx-users] pdb2gmx error delara aghaie
[gmx-users] unknown residue (BGC) delara aghaie
[gmx-users] simulating dimer proteins delara aghaie
[gmx-users] simulating dimer proteins delara aghaie
[gmx-users] simulating dimer proteins delara aghaie
[gmx-users] simulating dimer proteins delara aghaie
[gmx-users] simulating dimer proteins delara aghaie
[gmx-users] simulating dimer proteins delara aghaie
[gmx-users] How to compare two pdb files delara aghaie
[gmx-users] How to compare two pdb files delara aghaie
[gmx-users] How to compare two pdb files delara aghaie
[gmx-users] How to compare two pdb files delara aghaie
[gmx-users] How to compare two pdb files delara aghaie
[gmx-users] pressure-lyzozyme tutorial delara aghaie
[gmx-users] pressure-lyzozyme tutorial delara aghaie
[gmx-users] simulation time delara aghaie
[gmx-users] structural analysis delara aghaie
[gmx-users] spatial distribution function delara aghaie
[gmx-users] SDF-error delara aghaie
[gmx-users] segmentation fault-g_spatial delara aghaie
Fw: [gmx-users] segmentation fault-g_spatial delara aghaie
[gmx-users] Re: umbrella sampling with distances larger than half box size anaome
[gmx-users] Re: Effect of vdwradii.dat anna.duncan
[gmx-users] Tabulated potentials for dihedrals - regd ramesh cheerla
[gmx-users] Tabulated potentials for dihedrals - regd ramesh cheerla
[gmx-users] Tabulated potentials for dihedrals - regd ramesh cheerla
[gmx-users] user specified non bonded potentials - regd ramesh cheerla
[gmx-users] Checking interaction energies - regd ramesh cheerla
[gmx-users] umbrella windows... rama david
[gmx-users] About extend the run,, rama david
[gmx-users] About extend the run,, rama david
[gmx-users] About extend the run,, rama david
[gmx-users] LINCS warnings rama david
[gmx-users] LINCS warnings rama david
[gmx-users] LINCS warnings rama david
[gmx-users] LINCS warnings rama david
[gmx-users] simulated annealing mdp rama david
[gmx-users] Press Equilibration rama david
[gmx-users] simulated annealing mdp rama david
[gmx-users] Re: Press Equilibration rama david
[gmx-users] Press Equilibration rama david
[gmx-users] simulated annealing mdp rama david
[gmx-users] simulated annealing mdp rama david
[gmx-users] Lipid-protein simulation.... rama david
[gmx-users] Re: Lipid-protein simulation.... rama david
[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial rama david
Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial rama david
[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial rama david
[gmx-users] Fwd: Determine sec structure by MD rama david
[gmx-users] umbrella sampling with distances larger than half box size anaome at fundp.ac.be
[gmx-users] email id for posting sreeta gorripaty
[gmx-users] Re: Dihedral Constraints bharat gupta
[gmx-users] Re: Dihedral Constraints bharat gupta
[gmx-users] Re: Dihedral Constraints bharat gupta
[gmx-users] Re: Dihedral Constraints bharat gupta
[gmx-users] Re: Dihedral Constraints bharat gupta
[gmx-users] Re: Dihedral Constraints bharat gupta
[gmx-users] Dihedral restraints bharat gupta
[gmx-users] Dihedral restraints bharat gupta
[gmx-users] Capping error in pdb2gmx siddhant jain
[gmx-users] Re : Capping error in pdb2gmx siddhant jain
[gmx-users] cluster fomation in triolein simulation mahnam karim
[gmx-users] selenomethionine OPLS ff tarak karmakar
[gmx-users] (no subject) tarak karmakar
[gmx-users] pdb2gmx error tarak karmakar
[gmx-users] current directory files tarak karmakar
[gmx-users] current directory files tarak karmakar
[gmx-users] current directory files tarak karmakar
[gmx-users] simulation box shape and length tarak karmakar
[gmx-users] pdb file of polymer Parvez khan
[gmx-users] pdb file of polymer Parvez khan
[gmx-users] ewald_geometry 3dc with wall gives high pressure zifeng li
[gmx-users] What's the effect of non-neotron charge group? zifeng li
[gmx-users] Can I set the dielectric constant for polymer and water separately zifeng li
[gmx-users] How Coulomb energy terms are calculated? vincenzo moreschini
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation ms
[gmx-users] Re: Strong egative energy drift (losing energy) in explicit water AMBER protein simulation ms
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation ms
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation ms
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation ms
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED] ms
[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED] ms
[gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules ms
[gmx-users] Structure optimization failure ms
[gmx-users] Calculate surface tension cuong nguyen
[gmx-users] help!! ankita oindrila
[gmx-users] (no subject) ankita oindrila
[gmx-users] (no subject) ankita oindrila
[gmx-users] plzz help ankita oindrila
[gmx-users] Writing and compiling new analyses for gromacs francesco oteri
[gmx-users] floating point exception in .xtc file francesco oteri
[gmx-users] CMAP and Free Energy francesco oteri
[gmx-users] dodssp segmentation fault SOLVED for DEBIAN raf ponsaerts
[gmx-users] Force constant in g_wham rainy908
[gmx-users] Bootstrapping using g_wham rainy908
[gmx-users] Re: dangling bond at at one of the terminal ends ramaraju801
[gmx-users] Re: dangling bond at at one of the terminal ends ramaraju801
[gmx-users] Re: dangling bond at at one of the terminal ends ramaraju801
[gmx-users] Fatal error: Atomtype O2 not found ramaraju801
[gmx-users] Re: Fatal error: Atomtype O2 not found ramaraju801
[gmx-users] Re: Fatal error: Atomtype O2 not found ramaraju801
[gmx-users] Re: Fatal error: Atomtype O2 not found ramaraju801
[gmx-users] Re: Fatal error: Atomtype O2 not found ramaraju801
[gmx-users] Re: Fatal error: Atomtype O2 not found ramaraju801
[gmx-users] Trajectories rankinb
[gmx-users] Trajectories lloyd riggs
[gmx-users] Trajectories lloyd riggs
[gmx-users] GPU crashes lloyd riggs
[gmx-users] About Mike Harms python script lloyd riggs
[gmx-users] umbrella sampling with distances larger than half box size lloyd riggs
[gmx-users] Re: umbrella sampling with distances larger than half box size lloyd riggs
[gmx-users] wrong distances with g_dist lloyd riggs
[gmx-users] Free energy between residues lloyd riggs
[gmx-users] Free energy between residues lloyd riggs
[gmx-users] Regarding umbrella sampling simulations along H-bonds lloyd riggs
[gmx-users] mdrun_mpi segmentation fault for run in vacuum reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] mdrun_mpi segmentation fault for run in vacuum reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] mdrun_mpi segmentation fault for run in vacuum reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] mdrun_mpi segmentation fault for run in vacuum reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] mdrun_mpi segmentation fault for run in vacuum reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] mdrun_mpi segmentation fault for run in vacuum reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error in grompp run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error in grompp run reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Errors in Minimization using grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Errors in Minimization using grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Errors in Minimization using grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Errors in Minimization using grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] only three options for genrestr reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] only three options for genrestr reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Residue 'DUM' not found in residue topology database reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Residue 'DUM' not found in residue topology database reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Residue 'DUM' not found in residue topology database reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Residue 'DUM' not found in residue topology database reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] Rotation aroud the z axis reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] make index reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] editbox removes dummy atoms reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] editbox removes dummy atoms reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] editconf do not center protein reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] no SOL in topology file after genbox command reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error with grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error with grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error with grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] error with grompp reisingere at rostlab.informatik.tu-muenchen.de
[gmx-users] About Umbrella sampling vidhya sankar
[gmx-users] About Mike Harms python script vidhya sankar
[gmx-users] jalemkul at vt.edu vidhya sankar
[gmx-users] Regarding Free energy (Energy barrier) calculation neeru sharma
[gmx-users] Regarding Free Energy calculation tutorial neeru sharma
[gmx-users] Re: gmx-users Digest, Vol 98, Issue 44 neeru sharma
[gmx-users] Regarding umbrella sampling simulations along H-bonds neeru sharma
[gmx-users] Re: pair interaction energy decomposition analysis shounakb
[gmx-users] Re: pdb2gmx error shounakb
[gmx-users] Re: pdb2gmx error shounakb
[gmx-users] Re: pdb2gmx error shounakb
[gmx-users] Re: pdb2gmx error shounakb
[gmx-users] Re: pdb2gmx error shounakb
[gmx-users] Re: pdb2gmx error shounakb
[gmx-users] GPU ifat shub
[gmx-users] Regarding g_sham bipin singh
[gmx-users] questiones about dihedral restrain mircial at sjtu.edu.cn
[gmx-users] Regarding pdb file of a polymer sreeta.g
[gmx-users] Re: Regarding pdb file of a polymer sreeta.g
[gmx-users] Re: Regarding pdb file of a polymer sreeta.g
[gmx-users] .top file incoherent with the values in the ffbonded.itp file sreeta.g
[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file sreeta.g
[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file sreeta.g
[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file sreeta.g
[gmx-users] problem in making a trajectory francesca vitalini
[gmx-users] problem in making a trajectory francesca vitalini
[gmx-users] problem in making a trajectory francesca vitalini
[gmx-users] problem in making a trajectory francesca vitalini
[gmx-users] chirality changes during the simulation mu xiaojia
[gmx-users] How to set up constraint distcance pulling xiaowu759
[gmx-users] How to set up constraint distcance pulling xiaowu759
[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for xi zhao
[gmx-users] Atomtype 1 xi zhao
[gmx-users] Atomtype 1 xi zhao
[gmx-users] Atomtype 1 xi zhao
[gmx-users] Atomtype 1 xi zhao
[gmx-users] Atomtype 1 xi zhao
[gmx-users] Atomtype 1 xi zhao

Last message date: Sat Jun 30 23:31:13 CEST 2012
Archived on: Thu Nov 14 12:13:02 CET 2013

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