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

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 24 05:14:22 CEST 2009

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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