Please keep all Gromacs-related correspondence on the gmx-users list. I am not
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On 11/21/12 9:50 AM, Kdead wrote:
Hello,
I have another problem after change the parameters.In the 43a1 force
field ga_13 is 109.6 °，but my
ga_13 <90 ° after mdrun by Pymol software。 why？ thank you very much！！
I don't know, aside from suspecting something else is wrong with the topology.
The equilibrium value of the angle should be pretty well maintained during the
simulation, with only slight deviations. If you have some larger collapse of
the structure, something else about the topology is unstable. Again, mapping
everything back to a known entity like ATP is an appropriate course of action.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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