From: Chris Harrison (charris5_at_gmail.com)
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."
Best,
Chris
On Thu, Feb 2, 2012 at 1:42 PM, Liqun Zhang <lxz79_at_case.edu> 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 char_at_ks.uiuc.edu Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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