[gmx-users] PMF decompostion
jalemkul at vt.edu
Mon Dec 5 00:08:02 CET 2016
On 12/3/16 10:29 AM, Salman Zarrini wrote:
> Thanks David and Christopher for your responses.
> I do not understand why vdW and Q are not meaningful contributors of PMF as
> a biasing method, as I think one can loop over the trajectory of all the
> biasing method either from US or Metadynamics and recompute the force
> separating vdW and electrostatic and then project them on to the reaction
> coordinate ... , after doing a little math, averaging, integration and
> scripting you have the portion of each energy.
These are force field quantities, not real physical quantities. Depending on
how the force field was parametrized, decomposing the total energy may be
completely unphysical and therefore useless. Sometimes inclusion of a term in
vdW is a compensation for inadequate electrostatic representations and/or
deficiencies in LJ combination rules. Take, for a simple example, NBFIX in
CHARMM between ions. There is no way to change the ion parameters in the
additive force field (they have to be, e.g. +1 or -1 charge), and their LJ
reproduce individual ion hydration free energies, so we mitigate overly
attractive cation-anion interactions in some cases by modifying LJ specifically
for their interaction while leaving ion-water interactions (default combination
So, sure, you can recompute and/or decompose these energies, but they don't
necessarily mean anything.
> Concerning to the entropy and enthalpy portions, I am using covar and
> anaeig to calculate eigenvectors over "non-water" ingredients for both
> analyzing and fitting, and then quasihamonic approximation and Schlitter's
> formula for the entropy, but the problem is that, already the difference
> between the entropy out of these two methods is something around "43 kcal/
> mol" in each windows, if this is normal?
> Both analyzing and fitting are "non-mass wighted" in my calculations.
> Do you think I should get something close to the entropy of the
> quasihamonic approximation Schlitter's formula if I use the method proposed
> by you?
> Salman Zarrini
> On Sat, Dec 3, 2016 at 7:19 AM, David van der Spoel <spoel at xray.bmc.uu.se>
>> 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
>>> 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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Justin A. Lemkul, Ph.D.
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