On Fri, Sep 2, 2011 at 1:31 PM, Mattei, Alessandra <ale.mattei.uky.edu>wrote:
> 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.
>
As long as your solvent is in your system, that's impossible (and arbitrary,
as well). Do you want solvation effects included in your calculation, or
just in the gas phase? I would suggest using MMPBSA.py if you want
solvation effects included (either via GB, PB, or RISM solvation models).
However you plan on doing this, though, you'll need to create a topology
file *without* the solvent and a corresponding trajectory file (which
MMPBSA.py does for you).
HTH,
Jason
> Regards,
> Alessandra
>
> ---
> Alessandra Mattei
> Graduate Student
> University of Kentucky
> Department of Pharmaceutical Sciences
> 787 S. Limestone St. Rm 356
> Lexington, KY 40536
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 02 2011 - 11:00:03 PDT
