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

From: Nancy <>
Date: Sun, 7 Mar 2010 15:13:43 +0800 (CST)

Thank you case. I have looked at the densities vs. time . THe density became smaller and smaller with time ,and volume is bigger and bigger. can you tell me why and what is wrong?

Nancy<br><br>在2010-03-06 22:50:56,case <> 写道:
>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.
>AMBER mailing list

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Received on Sat Mar 06 2010 - 23:30:03 PST
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