Hydorder output

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hi,

I want to use the hydorder tool to compute the tetrahedral order parameter of water molecules. When using:

gmx hydorder -s box.tpr -f traj.xtc -b 5000 -n index_oxygens.ndx -o file1.xpm -or file1.out

it gives…

Taking z axis as normal to the membrane

-------------------------------------------------------
Program:     gmx hydorder, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxana/gmx_hydorder.cpp (line 695)

Fatal error:
No or not correct number (2) of output-files: 1

But, If I use (according to How to use gmx hydorder to calculate tetrahedral order parameter of water):

gmx hydorder -s ../box.tpr -f ../traj.xtc -b 5000 -n index_oxygens.ndx -o file1.xpm file2.xpm -or file1.out file2.out

… it starts reading the frames (very slowly though).

Why do I need more than 2 output files with options -o and -or? Also, my systems is just a simple water box, not a membrane system.

Thanks in advance.

Best,
-Yasser

2

I think I am a bit late with a reply, but also came across this error. Basically, as you say, you need to put 2 file names after the -o or -or option

gmx hydorder -n orderICE.ndx -b 4500 -o test_1 test_2 -or test_4 test_5
Hope this helps someone also searching