[gmx-users] ASP-LIG Interaction Energy : MDRUN

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 12 15:20:50 CEST 2008

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.


> Kindly advice.
> regards,
> nahren
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list