[gmx-users] what factors effetc the simulation during energy minimization

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 25 14:28:50 CET 2009

bhargavi ch wrote:
> hi..
> the sudden shoot up was observed in the RMS because of molecule breakage 
> into monomer and dimer.we  have also mutated some surface hydrophobic 
> aminoacid  and dint observe shoot up in any of the mutation. We have 
> also observed the same shoot in the case of X ray crystallographic 
> structure of template protein, when we did 10 ps simulation. what are 
> the parameters which we need to take to avoid such shoot up??

As Mark pointed out, based on your original description, you are probably seeing 
PBC effects.  Use trjconv to remove periodicity, and analyze the RMSD again.


> thanx
> Bhargavi
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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