g_msd(1) - f14

1g_msd(1)                  GROMACS suite, VERSION 4.5                  g_msd(1)
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NAME

6       g_msd - calculates mean square displacements
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8       VERSION 4.5
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SYNOPSIS

11       g_msd   -f   traj.xtc   -s  topol.tpr  -n  index.ndx  -o  msd.xvg  -mol
12       diff_mol.xvg -pdb diff_mol.pdb -[no]h -[no]version -nice int -b time -e
13       time  -tu  enum  -[no]w  -xvg  enum  -type  enum -lateral enum -[no]ten
14       -ngroup int -[no]mw -[no]rmcomm -tpdb  time  -trestart  time  -beginfit
15       time -endfit time
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DESCRIPTION

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

67       -f traj.xtc Input
68        Trajectory: xtc trr trj gro g96 pdb cpt
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70       -s topol.tpr Input
71        Structure+mass(db): tpr tpb tpa gro g96 pdb
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73       -n index.ndx Input, Opt.
74        Index file
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76       -o msd.xvg Output
77        xvgr/xmgr file
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79       -mol diff_mol.xvg Output, Opt.
80        xvgr/xmgr file
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82       -pdb diff_mol.pdb Output, Opt.
83        Protein data bank file
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OTHER OPTIONS

87       -[no]hno
88        Print help info and quit
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90       -[no]versionno
91        Print version info and quit
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93       -nice int 19
94        Set the nicelevel
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96       -b time 0
97        First frame (ps) to read from trajectory
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99       -e time 0
100        Last frame (ps) to read from trajectory
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102       -tu enum ps
103        Time unit:  fs,  ps,  ns,  us,  ms or  s
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105       -[no]wno
106        View output xvg, xpm, eps and pdb files
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108       -xvg enum xmgrace
109        xvg plot formatting:  xmgrace,  xmgr or  none
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111       -type enum no
112        Compute diffusion coefficient in one direction:  no,  x,  y or  z
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114       -lateral enum no
115        Calculate  the lateral diffusion in a plane perpendicular to:  no,  x,
116       y or  z
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118       -[no]tenno
119        Calculate the full tensor
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121       -ngroup int 1
122        Number of groups to calculate MSD for
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124       -[no]mwyes
125        Mass weighted MSD
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127       -[no]rmcommno
128        Remove center of mass motion
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130       -tpdb time 0
131        The frame to use for option -pdb (ps)
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133       -trestart time 10
134        Time between restarting points in trajectory (ps)
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136       -beginfit time -1
137        Start time for fitting the MSD (ps), -1 is 10%
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139       -endfit time -1
140        End time for fitting the MSD (ps), -1 is 90%
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO