Hi Gleb,
Apparently I wasn't clear enough. g_rmsdist calculates the average
distance for each pair of atoms over time and then calculates, for
each frame, the deviations from the average distance for each pair of
atoms. Per frame, these deviations are summed and the square root is
taken.
You're right regarding g_rms.
Best,
Tsjerk
On 4/3/07, Gleb Solomentsev <[EMAIL PROTECTED]> wrote:
Hi Tsjerk,
Thanks very much for the response. Just to make sure I understand correctly,
g_rmsdist calculates an
average interatom distance value for the reference structure. At a time t, a
similar average interatom
distance is calculated and the observed deviation is the difference between
this value and the average
interatom distance for the reference structure.
g_rms, at each time t, superimposes as best it can, the current structure
and the reference structure,
and calculates the distance deviation between equivalent atoms.
Also, if this is not too complicated of a question, which value is more
significant? Or does the
Maiorov & Crippen, PROTEINS 22, 273 (1995)
reference go into this.
Thanks again,
Gleb
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
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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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