Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions

From: zhongqiao hu <>
Date: Fri, 20 Dec 2013 10:35:41 +0800

Dear Brian,

Thank you very much for your reply. I used Amber12 to do umbrella sampling
to get PMF. I want to decompose it into electrostatic and van der Waals
contributions. it is something like decomposition into enthalpic and
entropic contributions.

I agree this decomposition needs pairwise potential that maybe beyond the
PME. I can not find any clue in amber manual to use MM/GBSA or MM/PBSA to
do it. Do you suggest it in detail if you know it.

Thank again,

Best regards,
Zhongqiao Hu
Bioinformatics Institute, A*STAR, Singapore

Message: 5
Date: Thu, 19 Dec 2013 09:39:58 -0500
From: Brian Radak <>
Subject: Re: [AMBER] How to decompose PMF into electrostatic and van
        der Waals contributions.
To: AMBER Mailing List <>
Content-Type: text/plain; charset=ISO-8859-1

I'm not sure this is an AMBER specific question. Do you mean how to write
down such a decomposition with the AMBER force field form?

My understanding of energy decomposition (which is limited) is that it
requires the assumption of a pairwise potential. This is not strictly true
for either PME or GB simulations, but can be done approximately in order to
gain some physical insights. I'm not sure where in the manual to read about
how this is done, but I'd imagine it is in the sections describing MM/GBSA
and MM/PBSA.

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Received on Thu Dec 19 2013 - 19:00:03 PST
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