[gmx-users] proper use of restraints
pbuscemi at q.com
Thu May 30 02:49:51 CEST 2019
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.
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