Sarah Witzke wrote:
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 :-(
The third mode of tpbconv (make a non-functional .tpr with a subset of
the atoms) might be useful here.
Mark
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