[gmx-users] Avoiding calculation on some degrees of freedom

[David van der Spoel]

On Tue, 2005-05-17 at 11:56 +0200, gianluca.santarossa wrote:
> >> For example, if atoms A and B are bonded, and some force
> >> acts on A, I want to keep the A-B distance constant, 
> >>moving B
> >> as much as A, and B not affecting force on A.
> > Apart from constraints you mean?
> Well, AFAIK contraints are not applied on angles or 
> dihedrals.
You can constrain angles using a MDP option.

> 
> My idea was to 'simplify' a topology of a non-proteic 
> molecule
> to move it in a subspace of the whole phase space, for 
> example
> allowing only dihedrals to change, and see what happens.
> So, there are some connections I want to take into account 
> without
> calculation of forces from them.
> 
> Thanks
> Gianluca
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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