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

From: Jason Swails <>
Date: Mon, 16 Mar 2015 08:19:18 -0400

On Mon, 2015-03-16 at 15:30 +0800, Wang Moye wrote:
> Hello everyone!
> I am a new user.There is a question in my objection and I need your
> help. I run a REMD process in AMBER12.Now I obtain some output
> files.Like this:
> remd.mdcrd.001
> remd.mdcrd.002
> ...remd.mdcrd.026
> and remd.mdinfo.001.. remd.mdinfo.026
> and remd.rst.001.. remd.rst.002
> and remd.mdout.001.. remd.mdout.026
> Total 26 replicas. I want to get the 3D free energy surface picture
> about my protein. Two coordinates are respectively Rg and RMSD.
> Someone told me the WHAM code can do this. I have the WHAM code now,
> but I don't know how to use the WHAM to deal with my AMBER's output
> files to obtain the metafile. Should I write the Rg and RMSD
> information into a single metafile? How to achieve this using the
> outputfile above? Need I write some scripts to get the value of Rg
> and RMSD?
> If you know how to deal with it, please help me. Thank you very much!

What kind of REMD did you do? Umbrella-REMD? Temperature-REMD?

Also, WHAM is a method, not a program. There are programs that
implement WHAM, like the one from Grossfield's lab (I think that's the
one you're talking about?)

If you did not use biased sampling (like umbrella sampling), then you
don't need a weighted histogram method -- just do unbiased histogramming
and calculate your free energy from that.

If you *did* do biased sampling, then there is an example constructing
the WHAM metafile for Grossfield's program here: (specifically section


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 16 2015 - 05:30:03 PDT
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