Subject: Re: CCL:CHARMm disappearing waters?

From: [email-masked] (Ryszard Czerminski X 217)
Date: Wed, 11 Oct 1995 15:04:41 -0400

Please note that charmm is using logical function INITIA
to determine if coordinates for an atom are defined or not.
For this purpose it is comparing X,Y and Z coordinates with
a parameter (which is set to 9999.). For this function to return
TRUE all three coordinates have to be smaller then 9999.
Therefore it is possible to get "undefined" coordinates if
some atoms fly far away ( with X > 9999 or Y > 9999 or Z > 9999 ).
Note also that "undefined" coordinates will not happen for 
atoms which fly away in opposite direction i.e. if
X < -9999 or Y < -9999 or Z < -9999.

I am not quite sure if this is what happens in troubled run,
but it is definitely a possibility.

Ryszard