[gmx-users] PMF decompostion
David van der Spoel
spoel at xray.bmc.uu.se
Sat Dec 3 07:19:42 CET 2016
On 02/12/16 23:40, Christopher Neale wrote:
> PMF gives free energy, which can not be decomposed into VDW and Q without leaving a remainder, though I guess that doesn't affect your question. Enthalpy is simply the average potential energy plus the pressure volume component. So you can compute average potential energy VDW and Q components at each umbrella if you want (from the .edr files with gmx energy). Be aware that the statistical uncertainty on the enthalpy tends to be greater than the relevant differences on achievable simulation timescales (i.e., convergence is hard), so you'll want to evaluate error explicitly.
Agree with Chris here, that enthalpy and entropy are the
thermodynamically meaningful components here. VDW and Q does not mean
anything outside the force field definition since they can not be
measured in any way. For more info on decomposing into enthalpy and
entropy, see this paper: http://pubs.acs.org/doi/abs/10.1021/ct400404q
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Salman Zarrini <salman.zarrini at gmail.com>
> Sent: 02 December 2016 17:16:15
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PMF decompostion
> Dear gromacs user,
> I was wondering if something has been already implemented in gromacs to
> make possible the potential of mean force (PMF) decomposition into the van
> der waals and electrostatic energies?
> Would you please also let me know if the desolvation energy originated from
> protein-water or in my case solid surface-water interaction, will be taken
> into account automatically when one calculates the PMF in aqueous solution
> in gromacs?
> Salman Zarrini
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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