NAME

       g_msd - calculates mean square displacements

       VERSION 4.6.5

SYNOPSIS

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

DESCRIPTION

        g_msd computes the mean square  displacement  (MSD)  of  atoms  from  a  set  of  initial
       positions.  This provides an easy way to compute the diffusion constant using the Einstein
       relation.  The time between the reference points for  the  MSD  calculation  is  set  with
       -trestart.   The diffusion constant is calculated by least squares fitting a straight line
       (D*t + c) through the MSD(t) from  -beginfit to  -endfit (note that t  is  time  from  the
       reference  positions,  not  simulation  time).  An  error  estimate  given,  which  is the
       difference of the diffusion coefficients obtained from fits over the two halves 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.

       If  -mol is set,  g_msd plots the MSD for individual molecules (including making molecules
       whole across periodic boundaries): for each individual molecule a  diffusion  constant  is
       computed for its center of mass. The chosen index group will be split into molecules.

       The default way to calculate a MSD is by using mass-weighted averages.  This can be turned
       off with  -nomw.

       With the option  -rmcomm, the center of mass motion of a specific group  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.

       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  reference
       points,  i.e.  short times have a higher weight. Also when  -beginfit=-1,fitting starts at
       10% and when  -endfit=-1, fitting goes to  90%.   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.

FILES

       -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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        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

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

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -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

       -[no]tenno
        Calculate the full tensor

       -ngroup int 1
        Number of groups to calculate MSD for

       -[no]mwyes
        Mass weighted MSD

       -[no]rmcommno
        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%

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                          Mon 2 Dec 2013                                 g_msd(1)