size of water box

From: Mehmet Sen (
Date: Fri Aug 24 2007 - 23:47:41 CDT

Hello Users
I am trying to unfold a protein about 230 residues by SMD. When I start
pulling the C-terminal, I am getting out of the box really easily. How
should I decide the size of the SMD simulation? If I just think of
polypeptide chain size, this corresponds to very huge water box, which takes
ages to calculate?

Additionally, my protein adopts a Rossman fold, where 6 beta sheets are
sandwiched by 7 helices. While pulling, direction of pull is significantly
important where incorrect pull will result in instable condition, and I got
{"ERROR: Constraint failure in RATTLE algorithm for atom 2861"} kind of
error, and just changing the direction get rid of this problem, but I got
same issue in the later stage of SMD. When I looked the dcd file, it seems
like protein start tangling and getting a knot, where rattling atoms are in
close proximity, and cause constraint failure, and concomitant stop of run.
If this is really the case, how can I avoid getting these tangling issue?


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