Re: [AMBER] cutoff

From: Dean Cuebas <>
Date: Sat, 5 Jun 2010 17:39:27 -0500

I have a quick question:

I'm just curious as to the theoretical explanation for why the box clearance
should be greater than your cutoff?

If I did 10A clearance for my protein in a water box, and used 10A for my
cutoff, what would be the deleterious results?

I always thought that the minimum of about 10A box clearance was so that a
protein would never be closer than about 20A to its nearest image, to
minimize image-to-image interactions. In that case, a 10A cutoff would still
be 10A away from its image. Or is that too close to the nearest image so
that artifacts would arise?

Thanks for your your responses in advance!


> In principle over a long simulation it might. Another aspect is that
> box clearance should be > cutoff, so with 10A cut you would need a
> bigger box, so the expense increases due to more water as well as
> more pair evaluations.

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Received on Sat Jun 05 2010 - 16:00:05 PDT
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