Dear users and experts I'm doing an umbrella-samplig calculation to obtain the PMF when two structure (A and B) are at various X distances. I setted my md-umbrella.mdp file as in follows:
; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella pull_geometry = distance pull_dim = Y N N pull_start = yes pull_nstxout = 1000 pull_nstfout = 1000 ; Number of pull groups pull_ngroups = 1 pull_group0 = A pull_group1 = B pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_kB1 = 1000 but when I run the program g_wham: g_wham -it tpr-files.dat -if pullf-files.dat -o profile.xvg -hist histo.xvg the profile I obtain is respect to the z coordinate (PMF as a function of z). My question is: is this only a problem of xvg text, or the PMF is effectively calculated with respect to the z variable, although I selected pull_dim = Y N N? Thank you very much Anna -- 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
