[gmx-users] How can I calculate Potential Energy of the segment divided by index file?

Justin Lemkul jalemkul at vt.edu
Fri Jan 6 19:41:04 CET 2017

On 1/5/17 3:58 PM, 大木啓輔 wrote:
> Dear Gromacs users
> I want to calculate Potential Energy of segment of the structure.
> For example, segment that coordinations in z axis are 7.2 Å in the structure.
> I could specify that segment of atom numbers by writing index file.
> But gmx energy has no option of specifying segments by index file.
> Then, how should I get the Potential Energy of segments?
> Could you tell me how to solve this problem, please?

You can create an index file with gmx select, extract those coordinates from the 
trajectory, create a matching .tpr file with convert-tpr, then use mdrun -rerun 
to recalculate the energies.  I'm not sure what use those values will be, but 
that's how you'd compute them.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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