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.
-Justin
Thanking you
Shahid Nayeem
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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