[gmx-users] question about xaver.pdb from g_rmsf

David spoel at xray.bmc.uu.se
Sat Oct 11 17:44:00 CEST 2003

On Sat, 2003-10-11 at 16:37, Marc Baaden wrote:
> Hi,
> could somebody give some details on how the average coordinates
> in xaver.pdb (generated via g_rmsf -ox) are calculated ? I have
> compared with a homewritten perl script that calculates the average
> by equally averaging all frames.
> If I only analyze the coordinates of a single frame, the result is
> identical.
> For any bigger number of frames there is a deviation.
> I have verified my perl script (by re-calculating the averages by
> hand), and it is correct, eg does the simple average weighting
> every frame the same (ignoring time information).
> What does g_rmsf do differently ?

it also does a LSQ fit by default.

> Thanks in advance,
> Marc
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list