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)

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COPYRIGHT

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