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

From: zhongqiao hu <>
Date: Thu, 26 Dec 2013 22:10:34 +0800

Hi Brian,

Thank you for your kind reply. I am not not sure what you are talking is
what I need. Simply speaking, for umbrella sampling, amber writes out
instantaneous value of reaction coordinate, which is equivalent with force
on reaction coordinate. If I can get decomposed components of this force
from electrostatic and vdw contributions for each writing frame, then I can
evaluate electrostatic and vdw parts. What I need is not electrostatic and
vdw energies of the whole system. If you think cpptraj (or any others like
MBAR) can postprocess trajectory to give electrostatic and vdw terms
specifically for reaction coordinate, then please tell me some details so
that I can follow.

Thanks a lot,

Zhongqiao Hu

> >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
> >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
> 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
> 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.

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Received on Thu Dec 26 2013 - 06:30:03 PST
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