1GMX-MSD(1)                          GROMACS                         GMX-MSD(1)
2
3
4

NAME

6       gmx-msd - Compute mean squared displacements
7

SYNOPSIS

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>]
16

DESCRIPTION

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
28       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
33       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
39       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
46       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.
55

OPTIONS

57       Options to specify input files:
58
59       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
60              Input  trajectory  or  single configuration: xtc trr cpt gro g96
61              pdb tng
62
63       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
64              Input structure: tpr gro g96 pdb brk ent
65
66       -n [<.ndx>] (index.ndx) (Optional)
67              Extra index groups
68
69       Options to specify output files:
70
71       -o [<.xvg>] (msdout.xvg) (Optional)
72              MSD output
73
74       -mol [<.xvg>] (diff_mol.xvg) (Optional)
75              Report diffusion coefficients for each molecule in selection
76
77       Other options:
78
79       -b <time> (0)
80              First frame (ps) to read from trajectory
81
82       -e <time> (0)
83              Last frame (ps) to read from trajectory
84
85       -dt <time> (0)
86              Only use frame if t MOD dt == first time (ps)
87
88       -tu <enum> (ps)
89              Unit for time values: fs, ps, ns, us, ms, s
90
91       -fgroup <selection>
92              Atoms stored in the trajectory file (if not set, assume first  N
93              atoms)
94
95       -xvg <enum> (xmgrace)
96              Plot formatting: xmgrace, xmgr, none
97
98       -[no]rmpbc (yes)
99              Make molecules whole for each frame
100
101       -[no]pbc (yes)
102              Use periodic boundary conditions for distance calculation
103
104       -sf <file>
105              Provide selections from files
106
107       -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
113       -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
119       -sel <selection>
120              Selections to compute MSDs for from the reference
121
122       -type <enum> (unused)
123              : x, y, z, unused
124
125       -lateral <enum> (unused)
126              : x, y, z, unused
127
128       -trestart <real> (10)
129              Time between restarting points in trajectory (ps)
130
131       -maxtau <real> (1.79769e+308)
132              Maximum time delta between frames to calculate MSDs for (ps)
133
134       -beginfit <real> (-1)
135              Time point at which to start fitting.
136
137       -endfit <real> (-1)
138              End time for fitting.
139

SEE ALSO

141       gmx(1)
142
143       More     information    about    GROMACS    is    available    at    <‐
144       http://www.gromacs.org/>.
145
147       2022, GROMACS development team
148
149
150
151
1522022.2                           Jun 16, 2022                       GMX-MSD(1)
Impressum