thanks very much. I will test it. Sincerely, Qian ----- Original Message ----- From: chris.ne...@utoronto.ca Date: Sunday, July 31, 2011 8:58 am Subject: [gmx-users] umbrella sampling To: gmx-users@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 > > * 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 thewww > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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