[gmx-users] Bug in g_rms -> calculate RhoSc ??

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 17 11:37:22 CET 2002

On Tue, 2002-12-17 at 08:07, K.A. Feenstra wrote:
> Marc Baaden wrote:
> > Hi,
> > 
> > I was trying to use the alternative similarity measures Rho
> > and Rho Scaled from the Crippen and Maiorov paper. Rho looks
> > fine, but Rho scaled doesn't make sense, in the way that it
> > even looks like a bug to me ..
> I haven't yet looked at your examples, but I was the one that implemented
> the rho/rho_sc measures in g_rms. I've definitely fixed some bugs before
> I was satisfied, and have checked several peptide conformations visually
> to see whether the calculated figures made any sense in comparison with
> the 'visual overlap' of the structures. Also, the behavior corresponds
> qualitatively to the description in the Crippen & Maiorov paper.
> Other than that, there is no straightforward way of rigorously testing
> it, since I don't have reference structures to test against. Perhaps
> I (we?) could contact (one of) the authors to ask for a few structures
> with known rho/rho_sc differences. Do feel free, in the meantime, to
> check my implementation against the formulae in the paper. I did do
> some re-writing to get a more straightforward implementation.
Did you look at MArc's figures? It seemed like PBC errors to me... Or
maybe lsq fitting errors.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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