AMBER Archive (2005)

Subject: RE: AMBER: Leap handling crystallographic waters

From: Ross Walker (
Date: Tue Nov 22 2005 - 14:09:27 CST

Dear Kristina,

> I guess I was thinking of the "fast water routines"--is that no longer
> operational in amber8?

The fast water routine is designed to work with triangulated 'shaken' water.
It works by knowing that the waters are all in a line in memory, essentially
they all come last in the coordinates. In this way the code can do the water
calculations in a way that maximises cache hits.

If your crystallographic waters were defined as having the residue name WAT
and have a TER card between them all and were last in the pdb file then I
believe that they will end up immediately before the solvent waters. They
would then be identified by the fast water routine. If, however, they were
not last in the pdb file then the fast water routine would only work with
the waters that were added by the solvation command. The result of the
simulation would be identical, just a potentially slower algorithm may be
used for the crystallographic waters. Amber 7 used to have a ROWAT flag that
if compiled in would ensure any waters (residues called WAT) were moved to
the end of the array in memory and so could be traversed in a linear
fashion. This disappeared in Amber 8 so I am not sure if such adjustment is
done or not.

In reality, however, the fast water routine really makes only minimal
difference. The effect of having a small percentage of the waters treated
via the regular routine is likely to just get lost in the noise such that
any slowdown would essentially be unnoticeable.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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