Re: constraints

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Dec 03 2009 - 16:02:52 CST

have a look at shape-based coarse-graining (SBCG) tutorial. this kind
of constraints are implemented there.

http://www.ks.uiuc.edu/Training/Tutorials/science/coarse-graining/sbcg-tutorial.pdf

On Thu, Dec 3, 2009 at 4:06 PM, doty alexiou <doty_alexiou_at_hotmail.com> wrote:
>
> Hello. I want to ask what kind of constraints should i use in order to keep
> the tertiary structure of a protein in a cg simulation. I guess i should not
> restain atoms  on certain coordinates or on a certain direction, but i
> should constrain the distance between pairs of atoms. So, harmonic bonds
> through steered molecular dynamics would be the right feature of NAMD?Thank
> you.
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-- 
Roman Petrenko
Physics Department
University of Cincinnati

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