Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions

From: Brian Radak <>
Date: Tue, 24 Dec 2013 17:34:12 -0500

On Sat, Dec 21, 2013 at 8:48 AM, zhongqiao hu <>wrote:

> >Unlike entropy and enthalpy, there is no unique decomposition of PMF's
> into
> >"parts", and this has nothing do with whether or not the potential is
> pairwise
> >additive or not.
> >You could compute a PMF with all charges set to zero, and call that the
> "vdW
> >contribution". Then the difference between that and the full PMF could be
> >called the "electrostatic contribution". But these defintions are
> >arbitrary; whether they offer much insight must depend on the detailed
> >situation.
> >Note that decomposing a PMF is rather different than trying to decompose
> >an alchemical or binding free energy change. For the latter, there are
> >arbitrary but often rather reasonable and helpful ways to decompose the
> >contributions into parts.
> Thanks a lot, dac.
> What I calculated is PMF of protein conformational change. If atomic
> charges are set to zero, protein conformation will be obviously different.
> So I think it is not feasible to get vdw contribuiton simply using neutral
> atoms.
> You could try re-weighting a trajectory with charges to a distribution
with no charges using WHAM or MBAR. This is probably a bit advanced, so if
you don't immediately know what I'm talking about, I wouldn't recommend it.

> One way I am thinking is we need to write out force from electrostatic and
> vdw contributions respectively during umbrella sampling run at each writing
> frame for each window. We can do it in principle, but in reality MD
> software packages (e.g., both amber and gromacs I am using) do not have
> such function to the best of my knowledge. Please correct me if I am wrong.
> AMBER does print these contributions (every ntpr steps); they are
EELEC/1-4 EEL and VDWAALS/1-4 NB, respectively. Note that, depending on how
you do this, you need to watch out for how coordinate and energy
information sync up during printing (due to leapfrog Verlet). Alternatively
you can re-evaluate those components from the mdcrd file using sander with
imin=5 and cpptraj.


> Thanks again,
> Best regards,
> Zhongqiao
> _______________________________________________
> AMBER mailing list

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 Brian Radak                                             :     BioMaPS
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Received on Tue Dec 24 2013 - 15:00:02 PST
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