Hi,
On Thu, Aug 23, 2012 at 8:41 AM, Bala subramanian
<bala.biophysics.gmail.com> wrote:
> If I understand well, col 2 is the average msd of the two atoms, col 3
More specifically, in the "<file>_a.xmgr" file the second column is
the average distance travelled by all the atoms, i.e. sqrt(
SUM[dist^2]/N ), where N is the number of atoms. Columns 3 and 4 in
this case are the distance travelled by each individual atom, i.e.
sqrt( dist^2 ), so col2 should not be equal to the straight average of
cols 3 and 4, but rather col2 = sqrt( (col3^2 + col4^2) / 2), which
you can verify it is.
Hope this helped.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 23 2012 - 12:30:03 PDT
