<DIV>Thanks very much. </DIV>
<DIV>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).</DIV>
<DIV>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.</DIV>
<DIV> </DIV>
<DIV>Sincerely,</DIV>
<DIV>Qian<BR><BR>----- Original Message -----<BR>From: chris.neale@utoronto.ca<BR>Date: Friday, July 29, 2011 11:00 pm<BR>Subject: [gmx-users] umbrella sampling<BR>To: gmx-users@gromacs.org<BR><BR>> format your data for 2D-WHAM with 1D being the distance and the <BR>> 2nd-D being your other coordinate of interest. Specify a value <BR>> of zero for the force constants for your 2nd-D. Run 2D-WHAM. <BR>> Boltzmann project the 2D PMF onto your 2nd-D.<BR>> <BR>> I think you can also do essentially the same thing by re-<BR>> weighting using the F-values from 1D-WHAM, but I find the above <BR>> method to be the simplest. It also provides you with a 2D free <BR>> energy profile, which can be informative both biologically and <BR>> to indicate on sampling problems.<BR>> <BR>> Note that you're very likely going to run into convergence <BR>> problems since your 2nd-D will rely on brute-force to converge, <BR>> and worse: the umbrellas in 1D can force the sampling in the 2nd-<BR>> D to surmount energy barriers that might be circumvented in <BR>> unrestrained sampling.<BR>> <BR>> Chris.<BR>> <BR>> -- original message --<BR>> <BR>> Qian Wang wrote:<BR>> Hi,<BR>> <BR>> I used umbrella sampling method to restrain the distance of two<BR>> molecules at several distances. Then I can use g_wham to get the free<BR>> energy as a function of the distance. Is there any way that I <BR>> can get<BR>> the free energy as a function of another parameter? Thanks a lot.<BR>> <BR>> <BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at <BR>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use thewww <BR>> interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</DIV>