[gmx-users] umbrella sampling
qwang at mail.uh.edu
Sat Jul 30 18:05:33 CEST 2011
Thanks very much.
I am sorry I did not describe my question very clear. In my system, I am going to obtain three things. (1) the free energy versus distance, which I can obtain from g_wham. (2) the free energy versus, eg, the radius of gyration of the object A. (3) the 2-D free energy as a function of the radius of gyration of A and the radius of gyration of B. I do not know how to get (2) and (3).
Your first method can help me obtain (2), but I can not obtain (3) because then it needs a 3-D WHAM code, am I correct? For your second method, I do not quite understand how to re-weighting using the F-values from 1D-WHAM. Could you please explain it? Thanks.
----- Original Message -----
From: chris.neale at utoronto.ca
Date: Friday, July 29, 2011 11:00 pm
Subject: [gmx-users] umbrella sampling
To: gmx-users at gromacs.org
> format your data for 2D-WHAM with 1D being the distance and the
> 2nd-D being your other coordinate of interest. Specify a value
> of zero for the force constants for your 2nd-D. Run 2D-WHAM.
> Boltzmann project the 2D PMF onto your 2nd-D.
> I think you can also do essentially the same thing by re-
> weighting using the F-values from 1D-WHAM, but I find the above
> method to be the simplest. It also provides you with a 2D free
> energy profile, which can be informative both biologically and
> to indicate on sampling problems.
> Note that you're very likely going to run into convergence
> problems since your 2nd-D will rely on brute-force to converge,
> and worse: the umbrellas in 1D can force the sampling in the 2nd-
> D to surmount energy barriers that might be circumvented in
> unrestrained sampling.
> -- original message --
> Qian Wang wrote:
> I used umbrella sampling method to restrain the distance of two
> molecules at several distances. Then I can use g_wham to get the free
> energy as a function of the distance. Is there any way that I
> can get
> the free energy as a function of another parameter? Thanks a lot.
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