Hi, I am trying to use the pull code to keep two peptide monomers near each other during a replica exchange simulation of (homo)dimerization. I do not want any bias if the COM distance between the two is less than some value r_max, as in umbrella sampling, i.e.
E = 0 for r_ij <= r_max; E = k*(r_ij - r_max) for r_ij > r_max Can this be done with the pull code or some other function? Pull=constraint appears to essentially fix the COM distance, which I do not want to do either. Thanks! -- ==================================== Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 -- 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.
