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.ne...@utoronto.ca Date: Friday, July 29, 2011 11:00 pm Subject: [gmx-users] umbrella sampling To: gmx-users@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: > Hi, > > 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. > > > -- > 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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