Re: [AMBER] free energy profile

From: <>
Date: Thu, 10 Jun 2010 03:23:29 -0400 (EDT)


> Great. Thanks for response. I made myself a simple reaction coordinate
> to start with: the angle between three domains. Calculated that with
> ptraj, and measured min and max values of this.

Especially important would be the overlap of both. Plot your histograms
and see if they sufficiently overlap, you need lots of data at every point
along the coordinate.

> As input to WHAM, I used the measured angles, and 0 as spring constant
> for the biasing potential:
> "wham Pval 74.1 131.5 200 0.0001 300.0 0 angle_metadatafile angle.pmf"
> where 74 and 131 are min and max angles, 200 is the number of bins,
> 0.0001 is the wham convergence tolerance, and 300 is the temperature.

Each of your bins will only be .3 degree wide. Look at the point where
both histograms are most sparsely populated. How many data point per bin
would you have? If too few, reduce the number of bins accordingly, or do
you really need such a finely resolved reaction coordinate?

> Does this sound reasonable in order to get some sort of free energy
> profile as a function of the domain angles?

Im no WHAM expert, but that sounds ok to me. You are one stroke of the
'Enter' key away from finding out :-D

> I guessing I'm a bit off here since you say "by hand", and two-window..?

You have two-windows because you have two (endpoint) simulations that
provide you with histograms. I said by hand because Im not sure if WHAM
will accept a zero force constant. All the better if it does.

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Jun 10 2010 - 00:30:03 PDT
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