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>
Cheers,
Abel
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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