[gmx-developers] Restraining the radius of gyration
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
>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)
(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.
More information about the gromacs.org_gmx-developers