Re: [AMBER] sander bomb: volume of ucell too big

From: case <>
Date: Sat, 6 Mar 2010 09:50:56 -0500

On Sat, Mar 06, 2010, Nancy wrote:

> I tried constant pressure for the first time after a successful
> constant volume equilibration. I received the following error preceded
> by the last time step that ran,What does this mean and What should I do?
> The error is:
> SANDER BOMB in subroutine nonbond_list
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart sander .
> My system is some carbon nanotubes which are packed together as a film,
> and the solvent is water. NPT ensemble is used. Some C atoms are put in
> aperture of carbon nanotubes to stop water flowing through the aperture
> , so water can flow only through carbon nanotubes .

This usually arises because the volume of the system has changed a lot from
its initial value; look at your densities vs. time to see what is happening.

As the message suggests, a restart usually will solve the problem.
Alternatively, consider using pmemd, which handles things in a different way,
and shold be faster as well.


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Received on Sat Mar 06 2010 - 07:00:03 PST
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