Main Table of Contents

Fri 5 Jul 2013


Compute 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).

The program 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.


-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input Index file
-nr index.ndx Input Index file
-s topol.tpr Input Run input file: tpr tpb tpa
-o order.xvg Output xvgr/xmgr file
-od deuter.xvg Output xvgr/xmgr file
-ob eiwit.pdb Output Protein data bank file
-os sliced.xvg Output xvgr/xmgr file
-Sg sg-ang.xvg Output, Opt. xvgr/xmgr file
-Sk sk-dist.xvg Output, Opt. xvgr/xmgr file
-Sgsl sg-ang-slice.xvg Output, Opt. xvgr/xmgr file
-Sksl sk-dist-slice.xvg Output, Opt. xvgr/xmgr file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-d enum z Direction of the normal on the membrane: z, x or y
-sl int 1 Calculate order parameter as function of box length, dividing the box into this number of slices.
-[no]szonly bool no Only give Sz element of order tensor. (axis can be specified with -d)
-[no]unsat bool no Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
-[no]permolecule bool no Compute per-molecule Scd order parameters
-[no]radial bool no Compute a radial membrane normal
-[no]calcdist bool no Compute distance from a reference