[gmx-users] Residue interaction energy

abelius abelius at gmail.com
Sat Dec 19 16:14:49 CET 2009

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>


Justin A. Lemkul wrote:
> abelius wrote:
>> Dear All,
>> Is there a way to calculated the interaction energy of a single 
>> residue with its environment?
>> I would like to compare two simulations with a W residue in an 
>> alternative rotameric position.
> Read in the manual about the energygrps .mdp keyword.
> -Justin
>> Thank you in advance,
>> Abel

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