Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

: > > > Joanne Martin wrote: > >> Hi Justin, thanks so much for the swift reply. >> With regards to the mdp setting >> >> >> > The proper setting for the "dihre" keyword is either "yes" or "no." >> >> How to I sp

Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

Joanne On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul wrote: > > > Joanne Martin wrote: > >> Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version >> 4.04. >> I have read through all posts on the mailing list regarding this query, &

[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version 4.04. I have read through all posts on the mailing list regarding this query, and although Chris Neale did explain how to set the restraints for Gromacs 3, these options are now obsolete for 4.04 I get the followi

[gmx-users] 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group

Hi im trying to run an NVT equilibration, and im getting the following errors these are my commands for solvating the box... any suggestions would be greatly appreciated J editconf -f 2VVSET_complex.gro -o 2VVSET_complex_conf.gro -box 12 genbox -cp 2VVSET_complex_conf.gro -cs /programs/gro