Man Linux: Main Page and Category List


       g_order - computes the order parameter per atom for carbon tails

       VERSION 4.0.1


       g_order  -f  traj.xtc  -n  index.ndx  -s  topol.tpr  -o  order.xvg  -od
       deuter.xvg -os sliced.xvg -Sg sg-ang.xvg -Sk sk-dist.xvg  -[no]h  -nice
       int  -b  time  -e  time  -dt  time  -[no]w  -[no]xvgr  -d  enum -sl int
       -[no]szonly -[no]unsat


       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 has to
       contain a group with all equivalent atoms in all tails  for  each  atom
       the order parameter has to be calculated for. 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

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -o order.xvg Output
        xvgr/xmgr file

       -od deuter.xvg Output
        xvgr/xmgr file

       -os sliced.xvg Output
        xvgr/xmgr file

       -Sg sg-ang.xvg Output
        xvgr/xmgr file

       -Sk sk-dist.xvg Output
        xvgr/xmgr file


        Print help 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)

        View output xvg, xpm, eps and pdb files

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -d enum z
        Direction of the normal on the membrane:  z,  x or  y

       -sl int 1
        Calculate  order  parameter as function of boxlength, dividing the box
       in nr slices.

        Only give Sz element of order tensor. (axis can be specified with -d)

        Calculate order parameters for unsaturated  carbons.  Note  that  this
       cannot be mixed with normal order parameters.



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                     g_order(1)