Dear Justin My system contains lipid + drug + water molecules.
At first, I put drug molecule in middle of bilayer. Based on your tutorial, after minimization and equilibration, I generated configurations. After using distance.pl script, summary_distances.dat file is irregular such that no increasing trend is not seen in the distances. Some times distance increased and some time decreased. Is there problem in generating configuration step? pull code part of mdp file is as follows: pull = constraint pull_geometry = distance pull_constr_tol = 1e-6 pull_dim = N N Y pull_ngroups = 1 pull_group0 = CHOL_DOPC pull_group1 = drug pull_vec1 = 0 0 1 pull_rate1= 0 pull-start = yes How to resolve this issue? Best wishes -- 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.
