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       g_msd - calculates mean square displacements

       VERSION 4.0.1


       g_msd   -f   traj.xtc   -s  topol.tpr  -n  index.ndx  -o  msd.xvg  -mol
       diff_mol.xvg -pdb diff_mol.pdb -[no]h -nice int -b  time  -e  time  -dt
       time  -tu  enum  -[no]w  -[no]xvgr  -type  enum  -lateral enum -[no]ten
       -ngroup int -[no]mw -[no]rmcomm -tpdb  time  -trestart  time  -beginfit
       time -endfit time


       g_msd  computes  the mean square displacement (MSD) of atoms from their
       initial positions. This provides an easy way to compute  the  diffusion
       constant  using  the  Einstein  relation.   The time between additional
       starting points for the MSD calculation is set  with   -trestart.   The
       diffusion  constant  is  calculated by least squares fitting a straight
       line through the MSD from  -beginfit to   -endfit.  An  error  estimate
       given,  which  is the difference of the diffusion coefficients obtained
       from fits over the two halfs of the fit interval.

       There are three, mutually exclusive,  options  to  determine  different
       types  of mean square displacement:  -type,  -lateral and  -ten. Option
       -ten writes the full MSD tensor for each group, the order in the output
       is: trace xx yy zz yx zx zy.

       Option   -mol  plots  the  MSD  for molecules, this implies With option
       -rmcomm center  of  mass  motion  can  be  removed.   For  trajectories
       produced  with  GROMACS  this is usually not necessary as mdrun usually
       already removes the center of mass motion.  When you use this option be
       sure that the whole system is stored in the trajectory file.

         -mw,  i.e.  for  each  inidividual  molecule an diffusion constant is
       computed for its center of mass. The chosen index group will  be  split
       into  molecules.   The  diffusion  coefficient  is determined by linear
       regression of the MSD, where, unlike for the normal output  of  D,  the
       times are weighted according to the number of restart point, i.e. short
       times have a higher weight. Also when  -beginfit=-1,fitting starts at 0
       and  when   -endfit=-1, fitting goes to the end.  Using this option one
       also gets an accurate error estimate based on  the  statistics  between
       individual  molecules.   Note that this diffusion coefficient and error
       estimate are only accurate when the MSD is completely linear  between
       -beginfit and  -endfit.

       Option   -pdb  writes  a  pdb file with the coordinates of the frame at
       time  -tpdb with in the B-factor field the square root of the diffusion
       coefficient of the molecule.  This option implies option  -mol.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -o msd.xvg Output
        xvgr/xmgr file

       -mol diff_mol.xvg Output, Opt.
        xvgr/xmgr file

       -pdb diff_mol.pdb Output, Opt.
        Protein data bank 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)

       -tu enum ps
        Time unit:  ps,  fs,  ns,  us,  ms or  s

        View output xvg, xpm, eps and pdb files

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

       -type enum no
        Compute diffusion coefficient in one direction:  no,  x,  y or  z

       -lateral enum no
        Calculate the lateral diffusion in a plane perpendicular to:  no,   x,
       y or  z

        Calculate the full tensor

       -ngroup int 1
        Number of groups to calculate MSD for

        Mass weighted MSD

        Remove center of mass motion

       -tpdb time 0
        The frame to use for option -pdb (ps)

       -trestart time 10
        Time between restarting points in trajectory (ps)

       -beginfit time -1
        Start time for fitting the MSD (ps), -1 is 10%

       -endfit time -1
        End time for fitting the MSD (ps), -1 is 90%



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                                Thu 16 Oct 2008                       g_msd(1)