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.
Regards,
Brian
On Thu, Dec 19, 2013 at 4:44 AM, zhongqiao hu <zhongqiao.hu.gmail.com>wrote:
> Dear all,
>
> I just constructed conformational potential of mean force (PMF) of one
> protein using umbrella sampling. Is it possible to decompose PMF into
> electrostatic and van der Waals contributions? I want to do it because it
> may provide some clues about effect of different forces on conformational
> PMF.
>
> Thanks in advance
>
> Best regards,
> Zhongqiao
> Bioinformatics Institute, A*STAR, Singapore
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Dec 19 2013 - 07:00:03 PST
