Re: [AMBER] cutoff

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 4 Jun 2010 10:12:50 -0700

> When we do MD simulations using amber, does cutoff = 10 angstrom will
> make much difference from 8 angstrom?

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.

> When choosing 8 angstrom, the calculation will be much faster than
> 10 angstrom?

Yes, you can try it and see what the difference is for your system.

> How should we choose?

I would read the literature for experiments similar to yours.
Without knowing what you are studying, there is no way to know.


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Received on Fri Jun 04 2010 - 10:30:05 PDT
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