Hi all, Using umbrella sampling and WHAM I am calculating the PMF of a single molecule (A) diffusion from water into a thin film made out of another molecule. The thin film is supposed to be an infinite film along X-Y (or have periodicity laterally), also the pbc for the whole system is ON for all three directions pbc = xyz. The reaction coordinate is the film_com to A_com along Z axis.
By default the "comm-mode = Linear" for the whole system, however the thin film translate during the PMF simulation in each window causing some artifact in the resulted PMF. Now, for such system my question is that if I am allowed to use: "comm-grps = thin film" and also "comm-mode = Linear-acceleration-correction" ? 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.
