NAME

       gmx-msd - Compute mean squared displacements

SYNOPSIS

          gmx msd [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                  [-o [<.xvg>]] [-mol [<.xvg>]] [-b <time>] [-e <time>]
                  [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
                  [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
                  [-seltype <enum>] [-sel <selection>] [-type <enum>]
                  [-lateral <enum>] [-trestart <real>] [-maxtau <real>]
                  [-beginfit <real>] [-endfit <real>]

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.  With  -mol,  only  one  index  group  can  be
       selected.

       The  diffusion  coefficient is determined by linear regression of the MSD.  When -beginfit is -1, fitting
       starts at 10% and when -endfit is -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.

       By  default, gmx msd compares all trajectory frames against every frame stored at -trestart intervals, so
       the number of frames stored scales linearly with the number of frames processed. This can  lead  to  long
       analysis  times  and  out-of-memory errors for long/large trajectories, and often the data at higher time
       deltas lacks sufficient sampling, often manifesting as a wobbly line on the MSD plot after  a  straighter
       region  at  lower  time  deltas.  The  -maxtau option can be used to cap the maximum time delta for frame
       comparison, which may improve performance and can be used to avoid out-of-memory issues.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
              Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Input structure: tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Extra index groups

       Options to specify output files:

       -o [<.xvg>] (msdout.xvg) (Optional)
              MSD output

       -mol [<.xvg>] (diff_mol.xvg) (Optional)
              Report diffusion coefficients for each molecule in selection

       Other options:

       -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 if t MOD dt == first time (ps)

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

       -fgroup <selection>
              Atoms stored in the trajectory file (if not set, assume first N atoms)

       -xvg <enum> (xmgrace)
              Plot formatting: xmgrace, xmgr, none

       -[no]rmpbc (yes)
              Make molecules whole for each frame

       -[no]pbc (yes)
              Use periodic boundary conditions for distance calculation

       -sf <file>
              Provide selections from files

       -selrpos <enum> (atom)
              Selection  reference  positions:  atom,  res_com,  res_cog,   mol_com,   mol_cog,   whole_res_com,
              whole_res_cog,    whole_mol_com,    whole_mol_cog,   part_res_com,   part_res_cog,   part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -seltype <enum> (atom)
              Default selection output positions:  atom,  res_com,  res_cog,  mol_com,  mol_cog,  whole_res_com,
              whole_res_cog,    whole_mol_com,    whole_mol_cog,   part_res_com,   part_res_cog,   part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -sel <selection>
              Selections to compute MSDs for from the reference

       -type <enum> (unused)
              : x, y, z, unused

       -lateral <enum> (unused)
              : x, y, z, unused

       -trestart <real> (10)
              Time between restarting points in trajectory (ps)

       -maxtau <real> (1.79769e+308)
              Maximum time delta between frames to calculate MSDs for (ps)

       -beginfit <real> (-1)
              Time point at which to start fitting.

       -endfit <real> (-1)
              End time for fitting.

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                        GMX-MSD(1)