[gmx-users] Pulling in GROMACS 4.0.3

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 4 21:06:37 CEST 2009

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


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