David A. Case writes:
> On Mon, Jun 13, 2005, Li Su wrote:
>
>> I'm simulating alanine dipeptide in vaccum using sander, but everytime
>> after around 350 ps, it stops and tells me the "The system has extended
>> beyond the extent of the virtual box. Restarting sander will recalculat a
>> new virtual box with 30 Angstroms extra on each side, if there is a restart
>> file for this configuration." The I use the rst file to restart , but after
>> about the same period the same problem happens.
>
> I suspect that you are seeing translational diffusion, that moves you out of
> the virtual box. You should visualize your trajectory to see if this is the
> case. You should be able to fix this up by setting your cutoff to 999. (which
> is probably not much different from 12 for such a small molecule), and also
> to set ntnb to some value bigger than the total number of steps you are
> requesting. That way, the code will never try to update the list.
>
> Basically, the current Amber code is not well designed for long time-scale
> vacuum simulations. These problems do not exist for gb or periodic
> simulations, which is what most people use. But I hope that the workaround
> listed above will fix your problem.
>
> ...dac
>
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Thank you for your suggestion,but what is ntnb, I could not find this flag
anywhere in the mannual.
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Received on Tue Jun 14 2005 - 22:53:02 PDT
