Re: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Apr 03 2019 - 14:52:38 CDT

You can kind of do it using NAMD and the pairInteraction command. For US simulations, you just loop over all DCDs, re-bin the data according to the value of your reaction coordinate in each frame, and then average. It’s not precisely the decomposition of the free energy but it works reasonably well.

We did it in this paper: https://www.ncbi.nlm.nih.gov/pubmed/24179453

Best,
JC

On Apr 3, 2019, at 12:24 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:

Not without running more simulations. I could imagine approximating a "vdW" contribution from a REUS calculation where the psf has been altered to have zero charge everywhere. Then, assuming the bonded contributions are identical, you could say that the difference between the two free energies is the electrostatic component. But by default, WHAM only cares about population statistics, not the underlying forces that drive the population statistics, so I've never seen this done before.

-Josh



On 2019-04-02 18:31:19-06:00 owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> wrote:

Hello,
I'm post-processing some long REUS simulations and would like to decompose
the free energy I obtain from WHAM into its vdW and electrostatic components. Is there any way to do this?
Thanks a lot,
Sebastian

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