SV: SV: [gmx-users] g_saltbr

Sarah Witzke sawit02 at
Wed Dec 2 00:58:28 CET 2009

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.

I thought so :-(

> 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?

There are no old xvg files in the directory. I have used "rm -rf *xvg*" to clean up and checked with "ls -alt". Just now I also ran the command in a folder that I have not analyzed before - with the same huge amount og #-files. Also note the dates of the files are within minutes, eg.:
-rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 sb-DMPC191:DMPC192.xvg
-rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.1#
-rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.2#
-rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.3#



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

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