[gmx-users] energy of each residue??
kotanmd at gmail.com
Tue May 1 22:49:01 CEST 2007
Thanks a lot Tsjerk !
I joined SOL and Cl into one index group and removed Protein and SOLCL (the
new one with SOL and CL) from energy monitoring list. It works now. i got
the energy of a particular residue.
thanks for the help.
On 5/1/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Kota,
> So in your case, the solution is to make an index group
> Protein_not_met1 or something like that. Note that you can always get
> information about energies and energy contributions by using mdrun
> -rerun and feeding a trajectory.
> Now there's one other thing:
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = berendsen
> > tc-grps = Protein SOL Cl
> > tau_t = 0.1 0.1 0.1
> > ref_t = 300 300 300
> This is bad! Check the archives on temperature coupling groups (hint:
> check last weeks archive), and think a bit about heat-baths.
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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