<DIV>thanks very much. I will test it. </DIV>
<DIV> </DIV>
<DIV>Sincerely,</DIV>
<DIV>Qian<BR><BR>----- Original Message -----<BR>From: chris.neale@utoronto.ca<BR>Date: Sunday, July 31, 2011 8:58 am<BR>Subject: [gmx-users] umbrella sampling<BR>To: gmx-users@gromacs.org<BR><BR>> I've never actually reweighted with F-values. These are the <BR>> values by which the component PMFs are shifted during WHAM after <BR>> debiasing the umbrella potentials.<BR>> <BR>> Look at equations 6 and 7 in "The multicanonical weighted <BR>> histogram analysis method for the free-energy landscape along <BR>> structural transition paths" Satoshi Ono, Nobuyuki Nakajima, <BR>> Junichi Higo and Haruki Nakamura<BR>> <BR>> My best guess is that you do it like this:<BR>> <BR>> 1. Run 1-D wham and obtain the F-values.<BR>> <BR>> 2. create an empty 3D histogram structure for z, rgyrA, and rgyrB.<BR>> <BR>> 3. Go through the data from each window and add a value to the <BR>> appropriate location for [z,rgyrA,rgyrB]. This value is not the <BR>> integer count 1. This value that you add to each histogram bin <BR>> is a real number:<BR>> <BR>> 1 * exp(-(1/RT)*-F) * exp(-(1/RT)*0.5K*(z-z0)^2<BR>> <BR>> 4. Now convert your histogram of probabilities to free energies <BR>> dG=-RTln(P)<BR>> <BR>> ** To test this, project your 3-D free energy profile onto each <BR>> dimension successively and compare it to (z) the profile from 1-<BR>> D wham, and (rgyrA or rgyrB) the profile from 2-D wham with zero <BR>> force constants as I outlined in my previous post.<BR>> <BR>> PLEASE NOTE: this email outlines an *idea* of how to accomplish <BR>> what you want. You must check the match for yourself.<BR>> <BR>> Chris.<BR>> <BR>> Qian Wang qwang at mail.uh.edu<BR>> Sat Jul 30 18:05:33 CEST 2011<BR>> <BR>> * Previous message: [gmx-users] umbrella sampling<BR>> * Next message: [gmx-users] OPLSAA parameters<BR>> * Messages sorted by: [ date ] [ thread ] [ <BR>> subject ] [ author ]<BR>> <BR>> Thanks very much.<BR>> I am sorry I did not describe my question very clear. In my <BR>> system, I am going to obtain three things. (1) the free energy <BR>> versus distance, which I can obtain from g_wham. (2) the free <BR>> energy versus, eg, the radius of gyration of the object A. (3) <BR>> the 2-D free energy as a function of the radius of gyration of A <BR>> and the radius of gyration of B. I do not know how to get (2) <BR>> and (3).<BR>> Your first method can help me obtain (2), but I can not obtain <BR>> (3) because then it needs a 3-D WHAM code, am I correct? For <BR>> your second method, I do not quite understand how to re-<BR>> weighting using the F-values from 1D-WHAM. Could you please <BR>> explain it? Thanks.<BR>> <BR>> Sincerely,<BR>> Qian<BR>> <BR>> ----- Original Message -----<BR>> From: chris.neale at utoronto.ca<BR>> Date: Friday, July 29, 2011 11:00 pm<BR>> Subject: [gmx-users] umbrella sampling<BR>> To: gmx-users at 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>> <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>