Dear all, In a PMF simulation using WHAM, the windows are somehow that the reaction coordinate (RC = COM_group1 ----COM_group2) should have both positive and negative parts along Z direction, e.g COM_group1 locates in the middle of the reaction coordinate more or less. However, what the WHAM gives out is only the positive part of the RC, while all the .tpr and pullf.xvg files for the whole RC are available.
I wonder how I can have PMF along the whole reaction coordinate in this case? Of course, one possible solution might be to run WHAM separately on windows of positive and negative parts of reaction coordinate and then merge the two profiles in a single profile later. But what I found out unexpectedly is that presence of each part (e.g negative part) in gmx WHAM, would affect on the PMF of the another part so that the PMF of the only positive part varies when the windows of the negative part are and are not considered. The -sym yes flag doesn't help as the two end points of the RC don't overlap each other. Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.