Actually, I think that if you know and understand what you want, then it is
possible to use that energy in a sensible way. I do this kind of
calculations myself and find them really useful. What you can do is to
extract several frames (50, 100, several hundreds, experiment a little to
find the optimum number) from your trajectory using ptraj, and then, in a
script, do the following:
1) use ambpdb to create a pdb for each frame
2) use leap to load the pdb, use the "remove" command to remove the solvent
in that frame, and then save the parameter and coordinate files.
3) Do a 1 step minimization of each frame in sander, to get the energy of
that frame, i.e., of the solvent.
4) Take an average of all the frames.
Maybe there are more efficient ways to do this, but you can get the idea
from here. And note that in this way, you could also get the other energy
components as well, water-water (by removing the solvent) and solvent-water
(by solving a system of 3 equations, knowing total energy, solvent-solvent
energy and water-water energy).
Ignacio
On Fri, Sep 2, 2011 at 1:40 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 05 2011 - 15:00:03 PDT
