nahren manuel wrote:
Dear Gromacs Users,
I have just completed one (5ns ) mdrun.
Now If i want to calculate the interaction energy between two residues,
my ligand and ASP104, how should I go about calculating the same.
The one option I know is by creating .ndx . But I did not expect this
residue to play an important role when i started my simulation. So i did
not include this protein residue ASP104 as a seperate group.
What you're looking for is mdrun -rerun. Make the appropriate index groups, and
include them in your .mdp as energy-grps when creating a new .tpr file. I think
you will also need to set nstenergy = 1 in the new .mdp file for the re-run.
-Justin
Kindly advice.
regards,
nahren
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========================================
Justin A. Lemkul
Graduate Research Assistant
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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