From: Rajan Vatassery (r-vatassery_at_northwestern.edu)
Date: Tue Oct 24 2006 - 14:26:47 CDT
Dear NAMD users,
I'm having a bit of trouble understanding the online manual posted
here:
http://www.ks.uiuc.edu/Research/namd/1.5/ug/node64.html
Specifically, I'm interested in deciphering the paragraph included at
the bottom of the page.
The sentence that says "After applying the normal integration
procedure, the atom positions are adjusted to bring the bond lengths
back to their neutral length (ie. the length such that the bond exerts
no force on either atom)" implies to me that there is a straightforward
readjustment of the hydrogen atom position. However, "These adjustments
are applied in such a way that the center of mass of the bonded atoms
does not move" implies that there is a movement of both the hydrogen and
the heavy atom, which wouldn't be as straightforward. The question I
have is, does the heavy atom move during the readjustment of the H-X
bond? If so, it doesn't seem to me that there would be much savings in
computational time. Is this true? Thanks for your time,
Rajan
The rigid bonds module sorts the atoms of interest into one of four data
structures, according to how many hydrogen atoms are bonded to the
parent atom. After applying the normal integration procedure, the atom
positions are adjusted to bring the bond lengths back to their neutral
length (ie. the length such that the bond exerts no force on either
atom). These adjustments are applied in such a way that the center of
mass of the bonded atoms does not move. For the one-hydrogen case, this
is a straightforward calculation, but for the two- or three-hydrogen
cases, an iterative procedure is followed, where each hydrogen-parent
atom pair is adjusted until all the hydrogen bonds are within a certain
tolerance of the desired length, or a maximum number of iterations is
exceeded. These values are set by the rigidTolerance and rigidIterations
parameters. A modified algorithm is applied to waters. Although waters
have only two hydrogens, a constraint is also applied to the distance
between the two hydrogens and the three-bond procedure followed, so that
the angle between the hydrogens is also constrained.
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