Re:Re: [AMBER] cutoff

From: fancy2012 <>
Date: Sat, 5 Jun 2010 21:20:38 +0800 (CST)

Dear Bill,
Thanks very much for your explanation! what I study is doing MD simulation of EGFR in complex with an inhibitor, so is cutoff of 8 angstrom enough? Or 10 is better? Thanks!
All the best,

2010-06-05"Bill Ross" <ross.cgl.ucsf.EDU> д
>> 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 Sat Jun 05 2010 - 06:30:03 PDT
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