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

Justin Lemkul jalemkul at vt.edu
Thu Aug 23 14:02:33 CEST 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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