[gmx-users] the energy of the individual molecule

[Justin Lemkul]

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

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