[gmx-users] Re: What is the purpose of the [ pairs ] section?

[Justin Lemkul]

On 12/10/12 3:27 PM, Andrew DeYoung wrote:
> Hi again,
>
> I forgot to mention that in my system I always set nrexcl = 3 (while
> explicitly specifying 1-4 interactions in [ pairs ], as I mentioned in my
> last message).  Does this mean that if gen-pairs = yes, then 1-5, 1-6, 1-7,
> ..., 1-Infinity nonbonded interactions will automatically be taken into
> account?
>

They are calculated like any other nonbonded interaction in the system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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