Gromacs order command not outputting

User discussions
1

Hi all,

I am trying to calculate the tetrahedral order parameter of each water molecule in an ice slab. I used the following command to make an index for the oxygens

gmx_mpi select -f confout.gro -s topol.tpr -select “name OW” -on index-all.ndx

and then I used the following command to calculate the order parameter:

gmx_mpi order -f traj_comp.xtc -s topol.tpr -n index-all.ndx -d z -o order.xvg

however after it runs through the trajectory and says it will print parameters to file, I check the order.xvg and the file is empty, and no matter what I try and change the output file keeps coming up empty as such:

This file was created Mon Oct 5 18:25:50 2020

Created by:

:-) GROMACS - gmx order, 2020.3 (-:

Executable: /home/donadio/Programs/gromacs/bin/gmx_mpi

Data prefix: /home/donadio/Programs/gromacs

Working dir: /home/mberrens/water_run/248_100ns/with_ions

Command line:

gmx_mpi order -f traj_comp.xtc -s topol.tpr -dt 1000 -n index-all.ndx -d z -o order.xvg

gmx order is part of G R O M A C S:

Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm

@ title “Order tensor diagonal elements”
@ xaxis label “Atom”
@ yaxis label “S”
@TYPE xy
~ ~ ~ ~

has anyone else had this issue or may know what is going wrong? and if so could you give some insight on how to fix it? Thanks

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

2

Hi,
The problem can be in the definition of the index.ndx file. You can check the reference given in gmx order -h
Best regards
Alessandra

3

The problem is that you’re using the wrong tool. gmx order is for acyl chain order parameters. What you want is gmx hydorder.

4

Thank you so much!