[gmx-users] about salt bridge (documentation suggestion)

[Justin A. Lemkul]

Justin A. Lemkul wrote:
>  From g_saltbr -h:
> 
> "A minimum distance can be given, (eg. the cut-off), then groups that 
> are never closer than that distance will not be plotted."
> 
> Basically, if a salt bridge occurs within the truncation distance 
> specified by -t, it will be plotted.  Using the default (1000 nm!) will 
> capture all possible salt bridges in the system.

As an aside to the developers, maybe the language of g_saltbr -h can be 
clarified.  The use of the double-negative there can be confusing, especially to 
someone who may not be proficient in the quirks of the English language.

Perhaps something like "A truncation/cut-off distance can be supplied with -t, 
such that only groups interacting within this distance will be plotted in the 
output" would be more clear?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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