Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12

From: Jason Swails <>
Date: Mon, 16 Mar 2015 21:44:53 -0400

On Mon, Mar 16, 2015 at 9:06 PM, Wang Moye <>

> Thank you Jason!
> I do the Temperature-REMD. Set 26 temperatures for the protein. Yes, as
> you said, the WHAM I mentioned is from Grossfield's lab. I don't use biased
> sampling. I saw the section 3 of the toturial. In that toturial the
> metafile contains the dihedral angle information through the script. I am
> confused with that I want to get wham-2D data and how to put the Rg and
> RMSD information into a metafile. After all, in the AMBER output files,
> there is no Rg and RMSD information clearly.

​Ah, so you're trying to reweight the high-temperature replica information
to the low-temperature histograms, yes?

In that case, I don't think Alan Grossfield's code will work for this
particular application (someone can correct me if I'm wrong, but I think it
assumes an umbrella sampling simulation). Alternatives are to use Dan
Sindhikara's modular reweighting code (another, more general WHAM
implementation), here:

Another option is to use MBAR (multi-state Bennett acceptance ratio), with
a python implementation of MBAR available from John Chodera and Michael
Shirts, available here:

You should then be able to take the computed weights for each of the
higher-temperature points and apply those weights to the time series of
whatever property you compute (be it a radius of gyration, a specific
distance, etc.) for each of the temperature.

The *easiest* thing to do is to just take your low-temperature data and use
that directly. What WHAM and MBAR allow you to do is derive *some*
information from the high-temperature replicas that you would otherwise
simply discard. Note, however, that this becomes increasingly inefficient
as the temperature increases (such that *very* high-temperature replicas
will contribute *very* little information to the low-temperature


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 16 2015 - 19:00:02 PDT
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