[gmx-users] umbrella sampling
qwang at mail.uh.edu
Sun Jul 31 18:12:44 CEST 2011
thanks very much. I will test it.
----- 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
> ** 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.
> 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.
> ----- 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:
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