Dear All: I encountered a problem when doing umbrella sampling. The distance calculated by grompp and g_dist is different, as shown by the following:
grompp z component of g_dist(since I am constraining the distance between two groups along the z direction, I should calculate the z component of the distance, right?) 2.986 2.96 2.953 2.95 2.931 2.92 2.936 2.9355 2.844 2.83 There is an obvious difference between the distance calculated by the grompp and the g_dist, I also found that some post similar problems in the maillist, but I didn't found answers for the following questions. (1)Why there is a such difference? (2)Also, does anyone know which value is used in the umbrella sampling simulations, the grompp result or the g_dist result? (3)how to choose the right starting conformations since there is such a difference? I also pasted the pull code I used as follows: pull = umbrella pull_geometry = direction pull_dim = N N Y pull_start = yes pull_nstxout = 500 pull_nstfout = 500 pull_ngroups = 1 pull_group0 = Protein pull_group1 = AMA pull_init1 = 0 pull_rate1 = 0.000;nm/ps pull_k1 = 4500 ;kJ/mol/nm^2 Thanks in advance!! Best regards, Ruo-Xu Gu -- 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
