[gmx-users] residue-ligand interaction energy using rerun option in mdrun

[Justin Lemkul]

On 8/23/18 6:34 AM, vijayakumar gosu wrote:
> Dear gromacs users,
>
> I want to calculate the interaction energies of one particular residue with
> RNA using rerun option. however i indexed the residue with RNA. in my mdp
> file i have given energy groups as a r_100 RNA.
> i ended up with an error Fatal error:
> "21510 atoms are not part of any of the T-Coupling groups". in T-Coupling i
> have provided r_100_RNA. I guess the error is because of T-Coupling
> considers the whole protein rather than one residue, because my protein
> dimer has  21528 atoms. The residue which i am looking has18 atoms. can
> anyone suggest me how can I rectify this....

You don't need to change anything about tc-grps to recompute an 
interaction energy. Just specify the groups you want in energygrps and 
leave everything else alone.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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