[gmx-users] help with g_hydorder and g_polystat

Emmanuel, Alaina A.E.Emmanuel at warwick.ac.uk
Tue Apr 30 12:24:28 CEST 2013

Dear All,

I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time.

For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
Internal error in pbc_dx, set pbc has nor been called
For more information..

I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas?

For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show "nan" values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for "Not a Number", but why do these "nan" values appear and how can I prevent it so that I can read in my results?

Again, thank you for your help.

Kind Regards,


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