[gmx-users] rigid body

[Anton Feenstra]

Tatiana Hushcha wrote:
> Dear GROMACS developers,
> 
> We would like to simulate realistic behavior of the whole human serum
> albumin (HSA) molecule at the physiological conditions. We plan to use the
> modeled time characteristics of conformational transitions to interpret our
> experimental relaxation data, so the simulated times should be correct.
> 
> It is our belief that the only way to solve our problem by computational
> resources available, is to treat several fragments of HSA molecule as rigid
> bodies. We studied Molecular Modeling software available, and GROMACS in
> general seems extremely attractive in view of our purposes. But we had no
> success in finding in the GROMACS User Manual the feature of treatment the
> HSA molecule as a number of rigid bodies. GROMACS Freeze Group concept would
> be of use in the case of a single rigid fragment, but employing of several
> rigid body fragments is absolutely necessary for us.
> So, we would be grateful if you give us explicit confirmation that GROMACS
> can't be used to treat a large biomolecule as a system of several rigid
> bodies. Or maybe this feature is still available? It may be not documented
> yet, for example.

No, it is not possible in the current implementation.

It is also questionable whether such a treatment would in fact
lead to an increased performance with respect to a fully flexible
treatment. The time consuming part is calculating all (atom) pair
interactions, and that does not change if you make several
rigid fragments, unless your fragments are so large that a
considerable fraction of the atoms is inside the fragments, far
enough from the surface of the fragment to be excluded from the
calculations. That does not seem realistic, for example, a 500
residue protein would be about 3-4 nm diameter. A 0.5 nm surface
layer would still be more than half of the system!

(We've thought about this type of simplifications a lot in the
MD group in Groningen, in the context of doing ab-inito protein
folding simulations.)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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