[gmx-users] Re: hpo4

Justin Lemkul jalemkul at vt.edu
Wed Nov 21 15:53:15 CET 2012

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private Gromacs tutor.

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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