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

    * Previous message: [gmx-users] umbrella sampling
    * Next message: [gmx-users] OPLSAA parameters
    * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

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:


--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to