one question about gtp flipping in namd simulation

From: Liqun Zhang (lxz79_at_case.edu)
Date: Thu Feb 02 2012 - 13:42:27 CST

Dear namd users:

I ran a namd simulation on rnd1+gtp system, with gtp forcefield parameters
from Mackerell in University of Maryland. After 20 ns, i saw the gtp
flipped. Did anyone of you see such kind of phenomena? Is there any way to
solve the flipping problem by adding constrains in namd simulations, for
example on dihedral angle? Thank you very much.

Kindly regards,

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:42 CST