[gmx-users] Some confusion about calculation of RMSDs

Marc Baaden 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

More information about the gromacs.org_gmx-users mailing list