[gmx-users] can gromacs investigate mechanical properties of a molecule?

mario kurtz219 at yahoo.it
Wed Feb 11 15:58:01 CET 2004

dear gmx crew,

I'm working on a project which is aimed to study the mechanical features of alpha-actinin, a 100 kDa protein involved in the structure of cell's cytoskeleton.

This is what I'd like to do: after optimization of the .pdb file, perform some elongation simulation, by restraining the distance between the two terminal atoms (I've already done some testing like that with a software called "hyperchem", but every elongation step required almost ten hours...). So, I'll eventually get the relation between Energy and elongation. 

Then it would be nice to reproduce the viscoelastic behaviour of the protein, performing some creep or stress relaxation test.

Do you guys think that gromacs can do that? Has anybody already done something similar?


mario orsi

dipartimento di bioingegneria, politecnico di milano, italy.

" You know Dude, I myself dabbled with pacifism at one point. Not in Nam, of course... " -the big lebowski

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