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