On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <[email protected]> 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 > > >> The deltaG value of my PMF with all the same windows (springs) is the >> exact experimental value but has worse overlap. >> >> Can you advise? >> >> 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
