[gmx-users] Residue interaction energy

Justin A. Lemkul jalemkul at vt.edu
Sat Dec 19 17:07:47 CET 2009

abelius wrote:
> Dear Justin,
> Thank you for your reply... Just to check if I made any mistakes is the 
> following procedure acceptable?
> 1) make NDX file with extra groups RES and Protein_Without_RES
> 2) add options to the MDP file:
>    energygrps = RES Protein_Without_RES  non-Protein
>    unconstrained_start = yes     ;For mdrun -rerun
> 3) mdrun -rerun <TRR file> -s <new TPR>

Seems fine to me.  Rather than waiting for confirmation, you could always go 
ahead and try it :)  Gromacs will give an error if there are any problems.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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