1GMX-MSD(1) GROMACS GMX-MSD(1)
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6 gmx-msd - Calculates mean square displacements
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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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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.
26 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.
31 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.
36 The default way to calculate a MSD is by using mass-weighted averages.
38 This can be turned off with -nomw.
39 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.
45 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.
55 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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61 Options to specify input files:
62 -f [<.xtc/.trr/…>] (traj.xtc)
64 Trajectory: xtc trr cpt gro g96 pdb tng
65 -s [<.tpr/.gro/…>] (topol.tpr)
67 Structure+mass(db): tpr gro g96 pdb brk ent
68 -n [<.ndx>] (index.ndx) (Optional)
70 Index file
71 Options to specify output files:
73 -o [<.xvg>] (msd.xvg)
75 xvgr/xmgr file
76 -mol [<.xvg>] (diff_mol.xvg) (Optional)
78 xvgr/xmgr file
79 -pdb [<.pdb>] (diff_mol.pdb) (Optional)
81 Protein data bank file
82 Other options:
84 -b <time> (0)
86 Time of first frame to read from trajectory (default unit ps)
87 -e <time> (0)
89 Time of last frame to read from trajectory (default unit ps)
90 -tu <enum> (ps)
92 Unit for time values: fs, ps, ns, us, ms, s
93 -[no]w (no)
95 View output .xvg, .xpm, .eps and .pdb files
96 -xvg <enum> (xmgrace)
98 xvg plot formatting: xmgrace, xmgr, none
99 -type <enum> (no)
101 Compute diffusion coefficient in one direction: no, x, y, z
102 -lateral <enum> (no)
104 Calculate the lateral diffusion in a plane perpendicular to: no,
105 x, y, z
106 -[no]ten (no)
108 Calculate the full tensor
109 -ngroup <int> (1)
111 Number of groups to calculate MSD for
112 -[no]mw (yes)
114 Mass weighted MSD
115 -[no]rmcomm (no)
117 Remove center of mass motion
118 -tpdb <time> (0)
120 The frame to use for option -pdb (ps)
121 -trestart <time> (10)
123 Time between restarting points in trajectory (ps)
124 -beginfit <time> (-1)
126 Start time for fitting the MSD (ps), -1 is 10%
127 -endfit <time> (-1)
129 End time for fitting the MSD (ps), -1 is 90%
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132 gmx(1)
133 More information about GROMACS is available at <‐
135 http://www.gromacs.org/>.
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138 2019, GROMACS development team
1392018.7 May 29, 2019 GMX-MSD(1)