Gmx dipoles doesnt work

[jshinsato1]

when using gromacs.dipoles it produces an error, I assume that this is because when run normally through the terminal gmx dipoles prompts the user to select a group to analyze, similar to how gmx energy or gmx pdb2gmx would do. Is there a workaround for this or will commands like that simply not work.

[orbeckst]

If a command requires input then in gromacswrapper use the input=[...] kwarg as described under Simple Usage:

gromacs.dipoles(corr="mol", P=1, temp=298, 
                f="md0.trr", s="md0.tpr", 
                o="Mtot0.xvg", d="dipdist0.xvg", c="dipcorr0.xvg",
                input=["Water"])

I didn't try it but something like the above should work. It's the equivalent of piping into the command from the command line

printf "Water\n" | gmx dipoles -corr mol -P 1 -s md0.tpr ...

[orbeckst]

To see the equivalent shell command to a GromacsWrapper command, start logging with

gromacs.start_logging()