[gmx-users] TOP file question

[Justin Lemkul]

On 3/28/13 8:25 PM, Peter Eastman wrote:
> After further study of the documentation, I find myself getting more confused rather than less.  I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not Coulomb parameters.  (There's a function type 2 for [pairs] that does include charges, but the manual says that function type is only used for free energy calculations.)  How do I select the latter when gen-pairs is off?  Is it simply assumed that 1-4 Coulomb interactions are never reduced for force fields that don't use gen-pairs?  Table 5.5 lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as LJ.  But no other mention of this directive appears anywhere else in the manual, there doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that "pairs_nb" never occurs in any file in the entire top directory.
>
> What am I misunderstanding?
>

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].

-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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