Provided by: gromacs-data_2019.1-1_all bug


       gmx-msd - Calculates mean square displacements


          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>]


       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

       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 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.

       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 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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -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> (xmgrace)
              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%



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       2019, GROMACS development team