[gmx-users] g_hydorder.

dipak sanap dipak94sanap at gmail.com
Mon Aug 31 09:13:23 CEST 2015

Hi all,
I want to calculate tetrahedral order parameter of water (Chau,
P.-L.Hardwick, a. J.) for my simulations.
I made an index file for oxygen atom in water. (oxy.ndx)
For tetrahedral parameter calculation, I issued following command.

g_hydorder -f confout.gro -n oxy.ndx -s md_25ns.tpr -o 1.xpm 2.xpm

Select the group that contains the atoms you want to use for the
tetrahedrality order parameter calculation:
Group     0 (            SOL) has 28521 elements
Group     1 (             OW) has  9507 elements

I selected Group 1
I got an error as follows,

Fatal error:
Internal error in pbc_dx, set_pbc has not been called
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

In my input mdp file, I have set pbc = xyz
My simulation box is dodecahedron.

I would really appreciate, if someone can help me out, thank you very much.

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