[gmx-users] Residue interaction energy

[abelius]

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
>>
>