[gmx-users] Some confusion about calculation of RMSDs
baaden at smplinux.de
Wed Apr 9 09:33:01 CEST 2003
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 ?
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baaden at smplinux.de - http://www.marc-baaden.de
FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
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