Dear Amber Mailing List,
I am running MD simulation of a solute molecule surrounded by water molecules. I would like to determine the energy of the solute molecule only, without solvent molecules, during the equilibration phase and plot the energy of the molecule versus time. From the output file I can only see the energy of the all system. I would like to know how I can do that.
Any suggestion is really appreciated. Thanks in advance for your help.
Regards,
Alessandra
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Alessandra Mattei
Graduate Student
University of Kentucky
Department of Pharmaceutical Sciences
787 S. Limestone St. Rm 356
Lexington, KY 40536
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Received on Fri Sep 02 2011 - 11:00:02 PDT
