[gmx-users] interface_enrgy

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 7 14:20:37 CET 2011

shahid nayeem wrote:
> Dear User
> I am doing MD on protein complex keeping backbone as well as side
> chain of all residues which is not on th interface fixed. For this I
> prepared posre_backbone_sidechain.itp and defined this in .top file
> for full MD. Now I want to know from the trajectory the best side
> chain conformation of the interface residues for which I want to see
> the change in total energy of the interface residues throught the
> trajectory. I prepared index file for interface residues. But g_energy
> command does not takes -n index.ndx to calculate energy of these
> groups. How can I do that. Please suggest.

You can set energygrps in the .mdp file and use mdrun -rerun to re-calculate the 
components of the nonbonded interaction energy between different groups.  You 
cannot decompose the total energy or bonded terms.  If you've used PME, the 
long-range term cannot be decomposed, either.


> Thanking you
> Shahid Nayeem


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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