AMBER Archive (2007)

Subject: Re: AMBER: reporting EPtot and EKtot separately for two molecules

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 12 2007 - 10:25:55 CST

On Mon, Feb 12, 2007, Gabbar S. Daaku wrote:

> While running MD on a complex consisting of t1 protein and 1
> carbohydrate molecule (which I believe would be same as 2 protein
> chains), I was wondering if it possible to print out the potential and
> kinetic energy separately for each molecule (chain)?
>

There is no standard option to do this. The kinetic energy can be split
into "pieces", but generally, the potential energy is not a sum of a
protein part and a carbohydrate part. There is some approximate energy
decomposition analysis in mm-pbsa that might be of use to you.

...good luck...dac

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