[gmx-developers] Restraining the radius of gyration

Berk Hess hessb at mpip-mainz.mpg.de
Fri Aug 11 10:31:57 CEST 2006

Albert Mao wrote:

>(Let me know if I should reply to just Dr. Berk Hess instead of the whole
>mailing list)
>Your answer was surprising to me because g_gyrate shows the radius of gyration
>converging towards and oscillating around my desired value, but I can see how
>the code could be incorrect yet still produce this result.
>I thought that I inserted the call to restrain_rg at a point where the
>coordinates x are already shifted to take periodic boundary conditions into
>account.  I admit that I don't have a thorough understanding of how periodic
>boundary conditions work in Gromacs.  Is there a place I can insert my call to
>restrain_rg so that it will handle everything correctly, or should I modify the
>function somehow, or what?
>We want to use the restraint potential for a number of things, but one of them
>is generating a population of starting configurations in order to calculate
>transition probabilities between regions in Rg space.
So that means that the code would work for when applied to (a subset of) 
a molecule
(not a cluster of molecules) with pbc=no or pbc=xyz (not pbc=full)
and when the molecule is not split over mutiple cpu's.
So I guess that for your simulations the code is correct.

One problem that I can forsee is that Rg depends quadratically on the 
and therefore it might be favourable for a molecule to move just a few atoms
far outward instead of the whole molecule expanding slightly.


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