1 .TH g_msd 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_msd - calculates mean square displacements
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
12 .BI "\-mol" " diff_mol.xvg "
13 .BI "\-pdb" " diff_mol.pdb "
15 .BI "\-[no]version" ""
23 .BI "\-lateral" " enum "
25 .BI "\-ngroup" " int "
29 .BI "\-trestart" " time "
30 .BI "\-beginfit" " time "
31 .BI "\-endfit" " time "
33 \&g_msd computes the mean square displacement (MSD) of atoms from
34 \&a set of initial positions. This provides an easy way to compute
35 \&the diffusion constant using the Einstein relation.
36 \&The time between the reference points for the MSD calculation
37 \&is set with \fB \-trestart\fR.
38 \&The diffusion constant is calculated by least squares fitting a
39 \&straight line (D*t + c) through the MSD(t) from \fB \-beginfit\fR to
40 \&\fB \-endfit\fR (note that t is time from the reference positions,
41 \¬ simulation time). An error estimate given, which is the difference
42 \&of the diffusion coefficients obtained from fits over the two halves
43 \&of the fit interval.
46 \&There are three, mutually exclusive, options to determine different
47 \&types of mean square displacement: \fB \-type\fR, \fB \-lateral\fR
48 \&and \fB \-ten\fR. Option \fB \-ten\fR writes the full MSD tensor for
49 \&each group, the order in the output is: trace xx yy zz yx zx zy.
52 \&If \fB \-mol\fR is set, g_msd plots the MSD for individual molecules:
53 \&for each individual molecule a diffusion constant is computed for
54 \&its center of mass. The chosen index group will be split into
58 \&The default way to calculate a MSD is by using mass\-weighted averages.
59 \&This can be turned off with \fB \-nomw\fR.
62 \&With the option \fB \-rmcomm\fR, the center of mass motion of a
63 \&specific group can be removed. For trajectories produced with
64 \&GROMACS this is usually not necessary,
65 \&as mdrun usually already removes the center of mass motion.
66 \&When you use this option be sure that the whole system is stored
67 \&in the trajectory file.
70 \&The diffusion coefficient is determined by linear regression of the MSD,
71 \&where, unlike for the normal output of D, the times are weighted
72 \&according to the number of reference points, i.e. short times have
73 \&a higher weight. Also when \fB \-beginfit\fR=\-1,fitting starts at 10%
74 \&and when \fB \-endfit\fR=\-1, fitting goes to 90%.
75 \&Using this option one also gets an accurate error estimate
76 \&based on the statistics between individual molecules.
77 \&Note that this diffusion coefficient and error estimate are only
78 \&accurate when the MSD is completely linear between
79 \&\fB \-beginfit\fR and \fB \-endfit\fR.
82 \&Option \fB \-pdb\fR writes a pdb file with the coordinates of the frame
83 \&at time \fB \-tpdb\fR with in the B\-factor field the square root of
84 \&the diffusion coefficient of the molecule.
85 \&This option implies option \fB \-mol\fR.
89 Trajectory: xtc trr trj gro g96 pdb cpt
91 .BI "\-s" " topol.tpr"
93 Structure+mass(db): tpr tpb tpa gro g96 pdb
95 .BI "\-n" " index.ndx"
103 .BI "\-mol" " diff_mol.xvg"
107 .BI "\-pdb" " diff_mol.pdb"
109 Protein data bank file
113 Print help info and quit
115 .BI "\-[no]version" "no "
116 Print version info and quit
118 .BI "\-nice" " int" " 19"
121 .BI "\-b" " time" " 0 "
122 First frame (ps) to read from trajectory
124 .BI "\-e" " time" " 0 "
125 Last frame (ps) to read from trajectory
127 .BI "\-tu" " enum" " ps"
128 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
131 View output xvg, xpm, eps and pdb files
133 .BI "\-xvg" " enum" " xmgrace"
134 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
136 .BI "\-type" " enum" " no"
137 Compute diffusion coefficient in one direction: \fB no\fR, \fB x\fR, \fB y\fR or \fB z\fR
139 .BI "\-lateral" " enum" " no"
140 Calculate the lateral diffusion in a plane perpendicular to: \fB no\fR, \fB x\fR, \fB y\fR or \fB z\fR
142 .BI "\-[no]ten" "no "
143 Calculate the full tensor
145 .BI "\-ngroup" " int" " 1"
146 Number of groups to calculate MSD for
148 .BI "\-[no]mw" "yes "
151 .BI "\-[no]rmcomm" "no "
152 Remove center of mass motion
154 .BI "\-tpdb" " time" " 0 "
155 The frame to use for option \-pdb (ps)
157 .BI "\-trestart" " time" " 10 "
158 Time between restarting points in trajectory (ps)
160 .BI "\-beginfit" " time" " \-1 "
161 Start time for fitting the MSD (ps), \-1 is 10%
163 .BI "\-endfit" " time" " \-1 "
164 End time for fitting the MSD (ps), \-1 is 90%
169 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.