Dear Users, I’ve modeled a simple polymer ( nylon ), 600 atoms aligned in the x direction . I create a restraint file for one molecule using the top file indices and fx,fy fz = 10000 0 0 then place 10 to 100 copies in a box On equilibration, they exhibit the expected hydrogen bonding using the gromos54a7 ff. Under npt pcouple - surface tension, the molecules remain elongated and some coalesce into groups but do not fully group with ref p = 1 1 and comp = 4e-5 0 . Just why the y direction does not shrink is a puzzle but not the main concern. The x dimension fo the box remains constant too but I assumed that is because the ends of the polymers are fixed, But there is room for packing in the y dimension.
Under p couple = isotropic, the ends re-enter the opoosite (x) sides as the box collapses in x, y x directions ( the original xyz 300 300 40 A. I was under the impression that under relatively strong x restraint, the x direction would not collapse because the x direction is fixed at the ends ??? Or is the way to look at it, the end ARE fixed, but the world around them is shrinking ? Any comments ( well most any good ones ) would be appreciate. Reference is made to the restraint file both in the molecule itp, and the base top file as an include statement - which is probably redundant if not outright wrong. Paul -- 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.
