SV: [gmx-users] g_saltbr

[Justin A. Lemkul]

Sarah Witzke wrote:
> Dear gmx users,
> 
> 
> 
> I'm sorry to continue an old thread - here's a summary:
> 
> I have a DMPC bilayer surrounded by water and a small organic molecule with a
> deprotonated carboxylic acid. The small molecule diffuses near the membrane
> interface/into the membrane. I would like to calculate any formed salt bridge
> between the negative carboxylic acid of the small molecule and the positive
> charge of the DMPC choline nitrogen. To do this I use these two commands:
> 
> g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 100000
> 
> g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 100000 -sep
> 
> The first command I use to get the files min-min.xvg, plus-plus.xvg and
> plus-min.xvg. Here I am interested in plus-min.xvg to tell me which of the
> salt bridges between the small molecule and DMPC is between the negative acid
> and the positive choline (as opposed to between the negative acid and the
> negative phosphate of DMPC).
> 
> Then I run the command again with -sep to get the individual graphs of each
> interaction. This is unfortunately a rather tedious exercise since very many
> files are generated for all sort of charged interactions (DMPC-DMPC,
> smallmolecule-smallmolecule, counterion-counterion, and pairs thereof), and
> then I have to select the wanted ones by looking through plus-min.xvg. I
> guess I could make some sort of script to make it easier, but I just want to
> check if there is absolutely no way to include an .ndx file or only choose
> plus-min interactions?
> 

Per the documentation, the only options that can be passed to g_saltbr are -s 
and -f, so no, you cannot use any index groups.

> 
> 
> Another thing, when running the second command several of each files are
> generated, for instance:
> 
> sb-DMPC144:DMPC154.xvg
> 
> #sb-DMPC144:DMPC154.xvg.3#
> 
> Etc
> 
> The files are not identical when checked with "diff" or looked at in xmgrace.
> 
> 
> I suppose the last generated files are the "correct" one, but what are all
> the other files?
> 

Previous attempts at running the command generate backups.  These sb-*.xvg files 
only come from using the -sep option, so issuing only the two commands above 
would not generate any backups (the ones that are flanked by #).  Have you run 
different g_saltbr commands in the same directory?  Perhaps using different 
values of -b and/or -t?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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