RE: AMBER: SANDER BOMB: volume of ucell too big

From: Stern, Julie <>
Date: Thu, 12 May 2005 15:34:55 -0400

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: ''
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
there is anything wrong, but there is probably a problem with your

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?


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:
Telephone: 858/784-9290
Fax: 858/784-8688

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Received on Thu May 12 2005 - 20:53:01 PDT
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