[gmx-users] umbrella sampling

[Qian Wang]

thanks very much. I will test it. 
 
Sincerely,
Qian

----- Original Message -----
From: chris.neale at utoronto.ca
Date: Sunday, July 31, 2011 8:58 am
Subject: [gmx-users] umbrella sampling
To: gmx-users at gromacs.org

> I've never actually reweighted with F-values. These are the 
> values by which the component PMFs are shifted during WHAM after 
> debiasing the umbrella potentials.
> 
> Look at equations 6 and 7 in "The multicanonical weighted 
> histogram analysis method for the free-energy landscape along 
> structural transition paths" Satoshi Ono, Nobuyuki Nakajima, 
> Junichi Higo and Haruki Nakamura
> 
> My best guess is that you do it like this:
> 
> 1. Run 1-D wham and obtain the F-values.
> 
> 2. create an empty 3D histogram structure for z, rgyrA, and rgyrB.
> 
> 3. Go through the data from each window and add a value to the 
> appropriate location for [z,rgyrA,rgyrB]. This value is not the 
> integer count 1. This value that you add to each histogram bin 
> is a real number:
> 
>   1 * exp(-(1/RT)*-F) * exp(-(1/RT)*0.5K*(z-z0)^2
> 
> 4. Now convert your histogram of probabilities to free energies 
> dG=-RTln(P)
> 
> ** To test this, project your 3-D free energy profile onto each 
> dimension successively and compare it to (z) the profile from 1-
> D wham, and (rgyrA or rgyrB) the profile from 2-D wham with zero 
> force constants as I outlined in my previous post.
> 
> PLEASE NOTE: this email outlines an *idea* of how to accomplish 
> what you want. You must check the match for yourself.
> 
> Chris.
> 
> Qian Wang qwang at mail.uh.edu
> Sat Jul 30 18:05:33 CEST 2011
> 
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> 
> 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.
> 
> Sincerely,
> Qian
> 
> ----- 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.
> >
> >Chris.
> >
> >-- original message --
> >
> >Qian Wang wrote:
> 
> 
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