Dear Julie,
Please send some more information that will help deciding what to do.
Your system has expanded in at least one direction beyond the limits set
inside sander as worst case expansion. This does not necessarily mean that
there is anything wrong, but there is probably a problem with your system.
The data that would help is:
Is it a non-periodic simulation?
What is the nature of the simulation: Are you trying to unfold a
macromolecule? Is it unfolding?
Is there unrestrained water in a nonperiodic system?
Do you have enough output to show what is happening to the volume of the
simulation if it is periodic?
Sincerely,
Mike
-----------------------------------------------------------------
Physical mail: Dr. Michael F. Crowley
Department of Molecular Biology, TPC6
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, California 92037
Electronic mail: crowley.scripps.edu
Telephone: 858/784-9290
Fax: 858/784-8688
-----------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu May 12 2005 - 18:53:01 PDT
