[gmx-users] TOP file question

[Peter Eastman]

Ok, thanks.

Peter


On Mar 29, 2013, at 10:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> 
> -- 
> 
> ========================================
> 
> 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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