AMBER Archive (2004)

Subject: AMBER: extra points

From: richard dimelow (r.dimelow_at_stud.man.ac.uk)
Date: Thu Sep 16 2004 - 11:21:05 CDT

I have a question about the source code and how it deals with these extra
points (like the fourth massless point in the tip4p molecule).

I am assuming that the arrays X and V in runmd.f contain the coordinates and
velocities of all atoms plus these extra points. Also, is it correct that
the force.f routine calculates the forces on these extra points but
transforms them into equivalent forces acting on the real atoms? If this is
the case then during the leap frog algorithm the time evolution of the
coordinates and velocities will be correct. But what part of the source code
then recalculates the new positions of these extra points.

Many thanks

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