1GMX-MSD(1)                          GROMACS                         GMX-MSD(1)
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NAME

6       gmx-msd - Calculates mean square displacements
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SYNOPSIS

9          gmx msd [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                  [-o [<.xvg>]] [-mol [<.xvg>]] [-pdb [<.pdb>]] [-b <time>]
11                  [-e <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
12                  [-type <enum>] [-lateral <enum>] [-[no]ten] [-ngroup <int>]
13                  [-[no]mw] [-[no]rmcomm] [-tpdb <time>] [-trestart <time>]
14                  [-beginfit <time>] [-endfit <time>]
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DESCRIPTION

17       gmx msd computes the mean square displacement (MSD) of atoms from a set
18       of initial positions. This provides an easy way to compute  the  diffu‐
19       sion constant using the Einstein relation.  The time between the refer‐
20       ence points for the MSD calculation is set with -trestart.  The  diffu‐
21       sion  constant  is  calculated by least squares fitting a straight line
22       (D*t + c) through the MSD(t) from -beginfit to -endfit (note that t  is
23       time from the reference positions, not simulation time). An error esti‐
24       mate given, which is  the  difference  of  the  diffusion  coefficients
25       obtained from fits over the two halves of the fit interval.
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27       There  are  three,  mutually  exclusive, options to determine different
28       types of mean square displacement: -type,  -lateral  and  -ten.  Option
29       -ten writes the full MSD tensor for each group, the order in the output
30       is: trace xx yy zz yx zx zy.
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32       If -mol is set, gmx msd plots the MSD for individual molecules (includ‐
33       ing  making molecules whole across periodic boundaries): for each indi‐
34       vidual molecule a diffusion constant is  computed  for  its  center  of
35       mass. The chosen index group will be split into molecules.
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37       The  default way to calculate a MSD is by using mass-weighted averages.
38       This can be turned off with -nomw.
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40       With the option -rmcomm, the center of mass motion of a specific  group
41       can  be removed. For trajectories produced with GROMACS this is usually
42       not necessary, as gmx mdrun usually already removes the center of  mass
43       motion.   When  you  use  this  option be sure that the whole system is
44       stored in the trajectory file.
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46       The diffusion coefficient is determined by  linear  regression  of  the
47       MSD,  where,  unlike for the normal output of D, the times are weighted
48       according to the number of reference points, i.e. short  times  have  a
49       higher  weight.  Also  when  -beginfit is -1, fitting starts at 10% and
50       when -endfit is -1, fitting goes to 90%.  Using this  option  one  also
51       gets  an  accurate error estimate based on the statistics between indi‐
52       vidual molecules.  Note that this diffusion coefficient and error esti‐
53       mate  are  only  accurate  when  the  MSD  is completely linear between
54       -beginfit and -endfit.
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56       Option -pdb writes a .pdb file with the coordinates  of  the  frame  at
57       time  -tpdb with in the B-factor field the square root of the diffusion
58       coefficient of the molecule.  This option implies option -mol.
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OPTIONS

61       Options to specify input files:
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63       -f [<.xtc/.trr/…>] (traj.xtc)
64              Trajectory: xtc trr cpt gro g96 pdb tng
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66       -s [<.tpr/.gro/…>] (topol.tpr)
67              Structure+mass(db): tpr gro g96 pdb brk ent
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69       -n [<.ndx>] (index.ndx) (Optional)
70              Index file
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72       Options to specify output files:
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74       -o [<.xvg>] (msd.xvg)
75              xvgr/xmgr file
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77       -mol [<.xvg>] (diff_mol.xvg) (Optional)
78              xvgr/xmgr file
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80       -pdb [<.pdb>] (diff_mol.pdb) (Optional)
81              Protein data bank file
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83       Other options:
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85       -b <time> (0)
86              Time of first frame to read from trajectory (default unit ps)
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88       -e <time> (0)
89              Time of last frame to read from trajectory (default unit ps)
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91       -tu <enum> (ps)
92              Unit for time values: fs, ps, ns, us, ms, s
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94       -[no]w (no)
95              View output .xvg, .xpm, .eps and .pdb files
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97       -xvg <enum> (xmgrace)
98              xvg plot formatting: xmgrace, xmgr, none
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100       -type <enum> (no)
101              Compute diffusion coefficient in one direction: no, x, y, z
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103       -lateral <enum> (no)
104              Calculate the lateral diffusion in a plane perpendicular to: no,
105              x, y, z
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107       -[no]ten (no)
108              Calculate the full tensor
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110       -ngroup <int> (1)
111              Number of groups to calculate MSD for
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113       -[no]mw (yes)
114              Mass weighted MSD
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116       -[no]rmcomm (no)
117              Remove center of mass motion
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119       -tpdb <time> (0)
120              The frame to use for option -pdb (ps)
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122       -trestart <time> (10)
123              Time between restarting points in trajectory (ps)
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125       -beginfit <time> (-1)
126              Start time for fitting the MSD (ps), -1 is 10%
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128       -endfit <time> (-1)
129              End time for fitting the MSD (ps), -1 is 90%
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SEE ALSO

132       gmx(1)
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134       More     information    about    GROMACS    is    available    at    <‐
135       http://www.gromacs.org/>.
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138       2019, GROMACS development team
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1432018.7                           May 29, 2019                       GMX-MSD(1)
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