On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/12/13 9:57 AM, Steven Neumann wrote: >> >> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 2/12/13 9:40 AM, Steven Neumann wrote: >>>> >>>> >>>> Dear Gmx Users, >>>> >>>> I know it is possible to combine windows with different spring >>>> constants into the one PMF curve using g_wham. >>>> >>>> Do I have to somehow tell g_wham that one or two windows have >>>> different spring constants? >>>> >>> >>> No, they are read from the .tpr files. >>> >>> >>>> For instance - I got the better histogram overlap with lower force >>>> constant in one window. When I replace this window into the window >>>> with the sring constant like all windwos (worse overlap) both PMF >>>> curves differ app. 2kcal/mol which is around 30% of the overall >>>> deltaG. >>>> >>>> Is there any error I should inroduce when one window differ in terms of >>>> k1? >>>> >>> >>> What does g_wham's error analysis suggest? >>> >>> -Justin >> >> >> In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol >> > > Seems like a good result, so what's the problem? > > -Justin
That the better overlap of histograms produce worse deltaG comparing to experiment. With all the same spring constants I get the experimental value of deltaG but there is a poor overlap. There must be (somehow) a correction added to deltaG when introdcuing windows with different spring constants. Steven > > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
