On 2/13/18 11:48 AM, dgfd dgdfg wrote:
Suppose the trajectory of molecular system with interactions between all 
molecules. How is to obtain the time dependence of intramolecular energy of the 
given molecule with unique resname and the total energy of this molecule in the 
system including intermolecular interactions?

Save the subset of coordinates that you care about from the trajectory with trjconv, make a matching subset .tpr with convert-tpr, and use mdrun-rerun.

The values you get may not have any physical meaning, depending on how the force field was parametrized.

-Justin

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

303 Engel Hall
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jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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