[gmx-users] PMF decompostion
salman.zarrini at gmail.com
Sat Dec 3 16:29:50 CET 2016
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.
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
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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