It is a periodic simulation of alkylthiol chains. The sulfurs
are restrained, but apparently did not stay in place. There is
no solvent at all. I did look at the simulation (22 frames at
..1 ps/frame was all I got). The volume expanded roughly 6 angstroms
in both the x and y directions but hardly anything in the z-direction.
I had run a successful constant volume simulation before, so all I
really did was to change to constant pressure:
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0
Any more suggestions of what to try?
-----Original Message-----
From: Michael Crowley
To: Stern, Julie
Cc: 'amber.scripps.edu'
Sent: 5/12/2005 1:10 PM
Subject: Re: AMBER: SANDER BOMB: volume of ucell too big
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
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Received on Thu May 12 2005 - 20:53:01 PDT
