[gmx-users] TOP file question

[Justin Lemkul]

On Fri, Mar 29, 2013 at 1:16 PM, Peter Eastman <peastman at stanford.edu>wrote:

> > Which version of the manual are you using?  I recall the discussion on
> [pairs_nb] being absent in an older version, but manual section 5.3.4 in
> version 4.6.1 has lots of discussion on [pairs_nb].
>
> I was looking at the 4.5.3 manual.  I just downloaded the 4.6.1 manual,
> and I see it now discusses that option.  But here's what it says: "The
> normal pair interactions, intended for 1-4 interactions, have function type
> 1. Function type 2 and the [ pairs_nb ] are intended for free-energy
> simulations."  So that still leaves my question about Coulomb parameters,
> since function type 1 doesn't specify them.
>
>
Coulombic interactions are always scaled by the value of fudgeQQ (see
discussion on [defaults] directive in manual section 5.7.1).

-Justin

-- 

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

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