NAME

       gmx-msd - Calculates mean square displacements

SYNOPSIS

          gmx msd [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                  [-o [<.xvg>]] [-mol [<.xvg>]] [-pdb [<.pdb>]] [-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

       gmx  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, gmx 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 gmx 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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xvg>] (msd.xvg)
              xvgr/xmgr file

       -mol [<.xvg>] (diff_mol.xvg) (Optional)
              xvgr/xmgr file

       -pdb [<.pdb>] (diff_mol.pdb) (Optional)
              Protein data bank file

       Other options:

       -b <time> (0)
              First frame (ps) to read from trajectory

       -e <time> (0)
              Last frame (ps) to read from trajectory

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum>
              xvg plot formatting: xmgrace, xmgr, none

       -type <enum> (no)
              Compute diffusion coefficient in one direction: no, x, y, z

       -lateral <enum> (no)
              Calculate the lateral diffusion in a plane perpendicular to: no, x, y, z

       -[no]ten (no)
              Calculate the full tensor

       -ngroup <int> (1)
              Number of groups to calculate MSD for

       -[no]mw (yes)
              Mass weighted MSD

       -[no]rmcomm (no)
              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

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team

5.1.2                                           February 03, 2016                                     GMX-MSD(1)