[gmx-users] Some confusion about calculation of RMSDs

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 9 10:32:00 CEST 2003

On Wed, 2003-04-09 at 09:32, Marc Baaden wrote:
> Hi,
> I just checked the RMSD definitions given in the Gromacs manual
> and was a bit surprised to find that the mass-weighted RMSD is
> the value calculated by default. I thought that by default RMSD
> meant equal contribution of each atom you include in the calculation
> *unless* you state/define otherwise. Is there any "standard" ?
> Also I am a bit unsure about the fitting part. My guess would be
> that fitting is equally weighted ? Or is it also mass-weighted ?
I think it is mass weighted too. It doesn't make a big difference though
(especially when you only use C-alpha).

If in doubt, use the source... It can be changed quite simple too.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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://xray.bmc.uu.se/~spoel

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