[gmx-users] Pulling in GROMACS 4.0.3

Johnny Lam johntus at berkeley.edu
Tue Aug 4 21:13:34 CEST 2009

Hi Justin,

Thx for the reply. By pull apart, I just wanted to expose an 'activation
site' by using a force. It is somewhat similar to pulling two domains of a
protein away from each other. I'm not aiming to undo any secondary
structure. I hope this is clearer. Thanks again!


> 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
> ========================================

Johnny Lam
ISPE Berkeley Chapter External Vice President
Department of Bioengineering
College of Engineering
University of California, Berkeley
Tel: (408) 655- 6829
Email: johntus at berkeley.edu

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