Hi Wang,
Are you running this simulation in explicit solvent? If so then the PME
routines etc are not strictly pairwise decomposable so you can't actually
evaluate the energy of a single molecule. You can, however, obtain the
internal energy for a molecule (bonds, angles, dihedrals etc). If you are
running implicit solvent GB then you can do a pairwise decomposition to find
an individual molecules contribution to the total energy.
See idecomp on page 26 of the AMBER 10 manual.
Good luck,
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of WANG,YING
> Sent: Friday, May 23, 2008 6:08 PM
> To: amber.scripps.edu
> Subject: AMBER: how to extract energy
>
> Hi, Dear ambers,
>
> My system contain some molecules. The mdout give me the total
> energy of the whole system. if I want to know the energy of one of
> the molecules but not the total energy of the whole system, how
> can I do?
>
> If you know how to do could you tell me? Thanks a lot!!
>
>
> Ying
>
>
>
>
>
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Received on Sun May 25 2008 - 06:08:03 PDT
