xiongxuqiong wrote:
To whom it may concern，
when I used g_saltbr to compute some salt bridges in my system, I
couldn't understand the option "-t". The tutorial tell me that it's
trunc distance and the default is 1000. Then I want to find the
definition of the salt bridge in Gromacs. However, I couldn't find it.
Could you like to tell me the relative definition in Gromacs? And what
is a proper value for the option t?
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.
-Justin
Look forward to your early reply,
Regards,
mary
2009-04-23
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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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