Re: one question about gtp flipping in namd simulation

From: Chris Harrison (
Date: Thu Feb 02 2012 - 13:49:56 CST

It's not clear from your message "how" it flipped. We need much more
information. A dihedral rotated? Which dihedral? By how much? The whole
GTP rotated about its center of mass? How far? And...the environment of
the GTP is not described, which likely (assuming correct GTP parameters)
plays a crucial element in the explanation of the "flip."


On Thu, Feb 2, 2012 at 1:42 PM, Liqun Zhang <> wrote:

> 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,

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 773-570-6078                Fax: 217-244-6078

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:37 CST