[gmx-users] radius of gyration taking bound water into account

[David van der Spoel]

Fabrizio Mancinelli wrote:
> Dear users,
> in computing radius of gyration of a protein in water (g_gyrate), I have 
> found values that are rather smaller than what found experimentally, 
> maybe because bound water isn't taken into account within g_gyrate 
> routine. Is there any way to overcome this limitation?
yes and no.

you can reorder your waters using trjorder and then redo the 
calculation. the problem ofcourse is where to stop. AFAIK these 
experiments are not very accurate, as the e.g. assume spherical proteins.

> Thanks in advance,
> Giovanni
> 
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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://folding.bmc.uu.se
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