[gmx-users] rigid body

[David]

On Thu, 2003-05-08 at 18:31, Ram'on Garc'ia Fern'andez wrote:
> I don't think Gromacs supports rigid bodies. However, you can achieve a similar
> result using enough constrains between the atoms involved; and removing forces
> between them. That will not be as efficient as a program that supports rigid bodies;
> but it might be enough.
Since this is meant to be a simulation under physiological conditions,
the computer time lost in computing protein internal degrees of freedom
is negligeable. This will be a salt and water plus impurity simulation
(doing one myself too...). 

The only thing that could be worthwhile is too limit the flexibility of
the protein somewhat, for instance by adding some long range distance
restraints within the molecule (like the spokes in a wheel). In
particular when you want to study relaxation, you need the
intramolecular flexibility I would think...


> 
> Supporting rigid bodies would make the code more complex, because the
> physics of a rigid body are more complex than the physics of
> atoms. Compared to atoms, rigid bodies do have orientation in addition
> to position, torques in addition to forces and rotation in addition to
> traslation.
> 
> In addition, there might be subtle problems related to the metric tensor
> so that even using constrains in a molecule that has a flexible part
> might be incorrect. You should check this.
You are probably right here, and as I see it the benefits are not that
large...


> Ramon
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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