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
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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