Re: [gmx-users] About frozen groups

2009-01-20 Thread Justin A. Lemkul
Mohammed Kamal wrote: Many thanks for Justin for your helpful comments, I think I still need your help for the first question... I have included more details about my system below > Mohammed Kamal wrote: > > > Tcoupl = berendsen > > > > tau_t = 0.1 0.1 0.1 0.1 > > > > tc_grps =

RE: [gmx-users] About frozen groups

2009-01-20 Thread Mohammed Kamal
Many thanks for Justin for your helpful comments, I think I still need your help for the first question... I have included more details about my system below > Mohammed Kamal wrote:> > > Tcoupl = berendsen> > > > tau_t = 0.1 0.1 0.1 0.1> > > > > tc_grps = protein T27 SOL Cl ; T27 is the

Re: [gmx-users] About frozen groups

2009-01-20 Thread Justin A. Lemkul
Mohammed Kamal wrote: Tcoupl = berendsen tau_t= 0.1 0.1 0.1 0.1 tc_grps = protein T27 SOL Cl ; T27 is the ligand General advice: do not couple solvent and ions separately. I believe there is a newer version of the tutorial that fixes

[gmx-users] About frozen groups

2009-01-19 Thread Mohammed Kamal
Sorry if this mail was duplicated... I think I have sent it by error to gmx-usres-requ...@gromacs.org Dear Gromacs community, I’m running MD simulation for ligand-enzyme complex with the help of the great tutorial set by Kerrigan using version 3.3.1. In certain stage of my simulation I ne