Johnny Lam wrote:
Hi again,
I am trying to pull apart a CG protein (to verify CG results with those of
already published works using atomistic MD). Using the previous
suggestions, my new pull code is the following:
By "pull apart," do you mean to unwind the secondary structure of the protein?
If so, I don't think it will work. Doesn't MARTINI fix certain backbone
parameters such that secondary structure remains very rigid over time?
If that's the case, then the vibrations you're seeing are just the structure
trying to resist being pulled apart.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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