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

[Anton Feenstra]

mario wrote:

> 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?

It depends on the timescales you want to study the viscoelastic response
of your protein. Typically, for a large protein like a-lactin (mus be
about 900 residues, right?) you won't get more than 10-100 ns in any
reasonable simulation time (depending on your hardware). So, relaxation
on the timescales of microseconds or larger, cannot be studied.

There have been studies of 'AFM' pulling on some proteins, actin comes
to mind. Don't have references handy now...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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