[gmx-users] Many energygrps to output

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 20:17:15 CET 2013

On 2/7/13 2:13 PM, Yun Shi wrote:
> Hi all,
> I want to rerun a trajectory to calculate interaction energies between
> each residue of protein A and protein B. In other words, I want to
> calculate interaction energies for pairs A1 - B, A2-B, A3-B, A4-B...,
> A399-B.
> So instead of making an index file with 399 groups of each residue in
> A and typing in rerun.mdp file 400 group names as
> "energygrps = A1 A2 A3 A4 ... A399 B", and issuing g_energy command 399 times,

Writing such lines could probably be scripted in a loop of your favorite 
programming language, but be aware that your .edr file is going to become 
enormous, probably several GB, depending on the length of the trajectory.  You 
won't have 400 energy terms, you will have 400*400 energy terms.

> is there an easier way to do this in Gromacs?

Not in Gromacs, but using scripts to call Gromacs functions and/or write lines 
to files, yes.



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


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