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
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
