Help automating gmx pairwise on a bash script using ctrl + D

User discussions
1

GROMACS version: 2020.3
GROMACS modification: Yes/No No
Here post your question:

I am trying to use a bash script to automate gmx pairdist. My input goes like:

gmx pairdist -f RaLPS_DPPC_6us_GIIKS_noPBC.xtc -n RaLPS_DPPC_6us_GIIKS.ndx -o pep1.xvg -sel -ref << EOF

17

18

19

etc. (there are 24 index groups and 1 reference)

For the next part I need to input control + D followed by my reference index and then all the pairwise distances will be completed, I have currently

# ctrl + d

17 (my reference)

EOF

But it’s not working at all and I’m super stuck on how to automate this!

Thanks!

2

Hi!

I think you can use -ref 17 instead of supplying it via input redirection. That way, you only need to provide “selection” via the standard input.

3

Thank you so much this worked! So much time has been saved thank you!