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

From: Wang Moye <>
Date: Thu, 19 Mar 2015 09:21:21 +0800 (GMT+08:00)

Hi Jason!

Thank you for reply! It is very helpful for me. Thank you very much.
> -----原始邮件-----
> 发件人: "Jason Swails" <>
> 发送时间: 2015年3月17日 星期二
> 收件人: "AMBER Mailing List" <>
> 抄送:
> 主题: Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
> On Mon, Mar 16, 2015 at 9:06 PM, Wang Moye <>
> wrote:
> >
> > 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
> statistics).
> HTH,
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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Received on Wed Mar 18 2015 - 18:30:02 PDT
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