AMBER Archive (2007)

Subject: Re: AMBER: How to extract energy of molecule from the system with explicit water molecules

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 05 2007 - 09:36:05 CDT

do you mean just the internal energy, or also the interaction with
water? the latter is difficult in a periodic system. if you want just
the peptide energy, you can use ptraj to strip the water and then
make a prmtop of just the peptide without water. then you can
evaluate the energy of the peptide. if you want more specific suggestions
you'll need to make clear what you want- energy for a restart
file, or for all frames in the trajectory, energy with or without
peptide:water
interaction, and so on.

On 7/5/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
>
> Dear All
>
> I am interested in extracting the energy of the molecule i.e peptide only
> from the output file that i obtained from running MD of that peptode in
> explicit solvent (water).
>
> Please suggest me something!
> Regards

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