[gmx-developers] Restraining the radius of gyration

David Bostick dbostick at scripps.edu
Fri Aug 11 20:02:40 CEST 2006

I cannot speak for all users of gmx, but I see many others, especially in 
the protein folding field, who make use of Rg restraints. Often Rg is used 
as one of many types of "order parameter" to gauge the progress of protein 
folding. Often umbrella sampling is used in order to calculate the PMF 
along the Rg coordinate, among other coordinates.

Berk is correct that sometimes unrealistic things may occur, but of course 
the usefulness of Rg restraints will be dependent on the model one chooses 
to use and on the context in which it is used. All in all, these 
considerations are true of any kind of restraint.

I suppose I am trying to say that I actually do think that if it were 
implemented properly, it would expand the versatility and usefulness of 
the package. But that's my 2 cents worth.


David Bostick
The Scripps Research Institute
Dept. of Molecular Biology, TPC 6 
10550 N. Torrey Pines Rd.
La Jolla, CA 92037

Phone: 858-784-9614
Fax:   858-784-8688
Email: dbostick at scripps.edu
Web:   http://www.scripps.edu/~dbostick

On Fri, 11 Aug 2006, Berk Hess wrote:

> 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.
> OK.
> 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 
> distance
> and therefore it might be favourable for a molecule to move just a few atoms
> far outward instead of the whole molecule expanding slightly.
> Berk.
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