Yet, my system is composed of POPC and POPS with oleoyl and palmitoyl tails. I have created an index file for each tail type containing just the carbon atoms for each chain. For instance
gmx make_ndx -f proMD.tpr -o index_ol.ndx
2 & a C12 C13 C14 C15 C16 C17 C18 C19 C110 C111 C112 C113 C114 C115 C116
name 10 ol_tails
del 0-9
And then I use the command order to obtain the order parameters:
gmx order -s proMD.tpr -f proMD.xtc -n index_ol.ndx -d z -od order_ol.xvg
However, the .xvg created is empty. Can anyone help me solve this issue?
Yes, the number 2 should be a group of species inside my simulation box. For the OL tail, it should actually be 4 (I changed the commands to make it easier to understand my question, but I forgot to change the number 2 to number 4 - the number 2 should be for the PA tail). The correct set of commands for the OL tail should be:
gmx make_ndx -f proMD.tpr -o index_ol.ndx
4 & a C12 C13 C14 C15 C16 C17 C18 C19 C110 C111 C112 C113 C114 C115 C116
name 10 ol_tails
del 0-9
The selection seems not to be empty, as the number of atoms is exactly the same as expected (I calculated the number of atoms knowing the number of phospholipids in the box and the number of atoms per tail).
You need each different carbon of the tails in individual groups. Take a closer look at the tutorial you linked to and what it shows.
Worth mentioning is that you should probably use a different tool for this analysis than gmx order as it won’t do the unsaturated carbon atoms correctly and is also designed for united-atom membranes.
