1GMX-MSD(1) GROMACS GMX-MSD(1)
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6 gmx-msd - Compute mean squared displacements
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9 gmx msd [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10 [-o [<.xvg>]] [-mol [<.xvg>]] [-b <time>] [-e <time>]
11 [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
12 [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
13 [-seltype <enum>] [-sel <selection>] [-type <enum>]
14 [-lateral <enum>] [-trestart <real>] [-maxtau <real>]
15 [-beginfit <real>] [-endfit <real>]
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18 gmx 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 is
24 time from the reference positions, not simulation time). An error esti‐
25 mate given, which is the difference of the diffusion coefficients ob‐
26 tained from fits over the two halves of the fit interval.
27 There are three, mutually exclusive, options to determine different
29 types of mean square displacement: -type, -lateral and -ten. Option
30 -ten writes the full MSD tensor for each group, the order in the output
31 is: trace xx yy zz yx zx zy.
32 If -mol is set, gmx msd plots the MSD for individual molecules (includ‐
34 ing making molecules whole across periodic boundaries): for each indi‐
35 vidual molecule a diffusion constant is computed for its center of
36 mass. The chosen index group will be split into molecules. With -mol,
37 only one index group can be selected.
38 The diffusion coefficient is determined by linear regression of the
40 MSD. When -beginfit is -1, fitting starts at 10% and when -endfit is
41 -1, fitting goes to 90%. Using this option one also gets an accurate
42 error estimate based on the statistics between individual molecules.
43 Note that this diffusion coefficient and error estimate are only accu‐
44 rate when the MSD is completely linear between -beginfit and -endfit.
45 By default, gmx msd compares all trajectory frames against every frame
47 stored at -trestart intervals, so the number of frames stored scales
48 linearly with the number of frames processed. This can lead to long
49 analysis times and out-of-memory errors for long/large trajectories,
50 and often the data at higher time deltas lacks sufficient sampling, of‐
51 ten manifesting as a wobbly line on the MSD plot after a straighter re‐
52 gion at lower time deltas. The -maxtau option can be used to cap the
53 maximum time delta for frame comparison, which may improve performance
54 and can be used to avoid out-of-memory issues.
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57 Options to specify input files:
58 -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
60 Input trajectory or single configuration: xtc trr cpt gro g96
61 pdb tng
62 -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
64 Input structure: tpr gro g96 pdb brk ent
65 -n [<.ndx>] (index.ndx) (Optional)
67 Extra index groups
68 Options to specify output files:
70 -o [<.xvg>] (msdout.xvg) (Optional)
72 MSD output
73 -mol [<.xvg>] (diff_mol.xvg) (Optional)
75 Report diffusion coefficients for each molecule in selection
76 Other options:
78 -b <time> (0)
80 First frame (ps) to read from trajectory
81 -e <time> (0)
83 Last frame (ps) to read from trajectory
84 -dt <time> (0)
86 Only use frame if t MOD dt == first time (ps)
87 -tu <enum> (ps)
89 Unit for time values: fs, ps, ns, us, ms, s
90 -fgroup <selection>
92 Atoms stored in the trajectory file (if not set, assume first N
93 atoms)
94 -xvg <enum> (xmgrace)
96 Plot formatting: xmgrace, xmgr, none
97 -[no]rmpbc (yes)
99 Make molecules whole for each frame
100 -[no]pbc (yes)
102 Use periodic boundary conditions for distance calculation
103 -sf <file>
105 Provide selections from files
106 -selrpos <enum> (atom)
108 Selection reference positions: atom, res_com, res_cog, mol_com,
109 mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
110 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
111 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
112 -seltype <enum> (atom)
114 Default selection output positions: atom, res_com, res_cog,
115 mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
116 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
117 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
118 -sel <selection>
120 Selections to compute MSDs for from the reference
121 -type <enum> (unused)
123 : x, y, z, unused
124 -lateral <enum> (unused)
126 : x, y, z, unused
127 -trestart <real> (10)
129 Time between restarting points in trajectory (ps)
130 -maxtau <real> (1.79769e+308)
132 Maximum time delta between frames to calculate MSDs for (ps)
133 -beginfit <real> (-1)
135 Time point at which to start fitting.
136 -endfit <real> (-1)
138 End time for fitting.
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141 gmx(1)
142 More information about GROMACS is available at <‐
144 http://www.gromacs.org/>.
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147 2022, GROMACS development team
1482022.2 Jun 16, 2022 GMX-MSD(1)