[gmx-users] gmx hydorder

Jessica Leuchter jessica.leuchter at gmail.com
Thu Jul 16 14:34:57 CEST 2015

Hi gromacs users,
I want to use gmx hydorder to get the local tetrahedral arrangement of
water surrounding protein within .1 nm . If I understand correctly from
this paper in the gromacs manual (P.-L. Chau and A.J. Hardwick, Mol. Phys.,
93, (1998)) I think I should get tetrahedrality for each frame as a
function of time. I am having difficulty understanding the output in this
case .xpm and file1 and file 2 (see my input below).

gmx hydorder -s md_0_1.tpr -f npt.gro -o hydorder_test.xpm
hydorder_test2.xpm -n index_water_prot.ndx -or file1 file2

Thank you for the help!


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