Hi Gleb,
g_rmsdist calculates a matrix of interatomic distances, averages these
and calculates the average deviation from the average. g_rms
superimposes two structures (superimposes the averages) and calculates
the average deviation over the pairs of equal atoms in the structures.
Hope I am clear enough...
Best,
Tsjerk
On 3/15/07, Gleb Solomentsev <[EMAIL PROTECTED]> wrote:
Hello,
I am trying to figure out what the difference between these two
applications is. The calculation is of the RMSD for a protein unfolding
trajectory and I get different results with g_rms and g_rmsdist. I have
looked at the manual and all I can find is that:
"g_rmsdist computes the root mean square deviation of atom distances, which
has the advantage that no fit is needed like in standard RMS deviation as
computed by g_rms."
What fit is this referring to and would this be the source of my
differences?
I am getting larger RMSD values using g_rms.
Thanks,
Gleb
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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