[gmx-users] energy of each residue??

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 1 14:40:02 CEST 2007

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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