| GMX-ORDER(1) | GROMACS | GMX-ORDER(1) |
gmx-order - Compute the order parameter per atom for carbon tails
gmx order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nr [<.ndx>]]
[-s [<.tpr>]] [-o [<.xvg>]] [-od [<.xvg>]] [-ob [<.pdb>]]
[-os [<.xvg>]] [-Sg [<.xvg>]] [-Sk [<.xvg>]]
[-Sgsl [<.xvg>]] [-Sksl [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-d <enum>] [-sl <int>]
[-[no]szonly] [-[no]unsat] [-[no]permolecule] [-[no]radial]
[-[no]calcdist]
gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. The index file should contain only the groups to be used for calculations, with each group of equivalent carbons along the relevant acyl chain in its own group. There should not be any generic groups (like System, Protein) in the index file to avoid confusing the program (this is not relevant to tetrahedral order parameters however, which only work for water anyway).
gmx order can also give all diagonal elements of the order tensor and even calculate the deuterium order parameter Scd (default). If the option -szonly is given, only one order tensor component (specified by the -d option) is given and the order parameter per slice is calculated as well. If -szonly is not selected, all diagonal elements and the deuterium order parameter is given.
The tetrahedrality order parameters can be determined around an atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details.
Options to specify input files:
Options to specify output files:
Other options:
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2019, GROMACS development team
| February 15, 2019 | 2019.1 |