# Gromacs order command not outputting

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-order-command-not-outputting/912>\
**Category:** User discussions\
**Created:** [October 6, 2020, 1:35am UTC](https://gromacs.bioexcel.eu/t/gromacs-order-command-not-outputting/912 "2020-10-06T01:35:04Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mberrens](https://avatars.discourse-cdn.com/v4/letter/m/d9b06d/32.png) [@mberrens](https://gromacs.bioexcel.eu/u/mberrens)\
**Post date:** [October 6, 2020, 1:35am UTC](https://gromacs.bioexcel.eu/t/gromacs-order-command-not-outputting/912/1 "2020-10-06T01:35:05Z")

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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

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [October 6, 2020, 6:56am UTC](https://gromacs.bioexcel.eu/t/gromacs-order-command-not-outputting/912/2 "2020-10-06T06:56:27Z")

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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

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 6, 2020, 12:30pm UTC](https://gromacs.bioexcel.eu/t/gromacs-order-command-not-outputting/912/3 "2020-10-06T12:30:57Z")

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

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**Author:** ![mberrens](https://avatars.discourse-cdn.com/v4/letter/m/d9b06d/32.png) [@mberrens](https://gromacs.bioexcel.eu/u/mberrens)\
**Post date:** [October 6, 2020, 5:45pm UTC](https://gromacs.bioexcel.eu/t/gromacs-order-command-not-outputting/912/4 "2020-10-06T17:45:19Z")

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Thank you so much!