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
--
========================================
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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