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

From: zhongqiao hu <>
Date: Sat, 21 Dec 2013 21:48:42 +0800

>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
>additive or not.

>You could compute a PMF with all charges set to zero, and call that the
>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

>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

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.

Thanks again,
Best regards,
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Received on Sat Dec 21 2013 - 06:00:02 PST
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