[gmx-users] Protein potential energy

Justin Lemkul jalemkul at vt.edu
Mon Jun 18 20:59:48 CEST 2018

On 6/18/18 4:15 AM, Ming Tang wrote:
> Dear list,
> I pulled a protein in water. In order to get the trend of the potential energy terms of the protein, I defined energygrps and reran the system. May I ask can I get the right trend of the protein potential energy terms using this approach?

No. You'd have to strip away all non-protein components from the 
trajectory, make a matching .tpr file, and use mdrun -rerun. Then you'll 
get the protein's potential energy, which also happens to be a 
meaningless quantity.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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