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

[bhargavi ch]

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??

thanx
Bhargavi
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