gmx-msd(1) GROMACS Manual gmx-msd(1)NAMEgmx-msd - Calculates mean square displacements
SYNOPSIS
gmx msd [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-o [<.xvg>]] [-mol [<.xvg>]] [-pdb [<.pdb>]] [-nice <int>]
[-b <time>] [-e <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
[-type <enum>] [-lateral <enum>] [-[no]ten] [-ngroup <int>]
[-[no]mw] [-[no]rmcomm] [-tpdb <time>] [-trestart <time>]
[-beginfit <time>] [-endfit <time>]
DESCRIPTION
gmx msd computes the mean square displacement (MSD) of atoms from a set
of initial positions. This provides an easy way to compute the diffu‐
sion constant using the Einstein relation. The time between the refer‐
ence points for the MSD calculation is set with -trestart. The diffu‐
sion constant is calculated by least squares fitting a straight line
(D*t + c) through the MSD(t) from -beginfit to -endfit (note that t is
time from the reference positions, not simulation time). An error esti‐
mate given, which is the difference of the diffusion coefficients
obtained from fits over the two halves of the fit interval.
There are three, mutually exclusive, options to determine different
types of mean square displacement: -type, -lateral and -ten. Option
-ten writes the full MSD tensor for each group, the order in the output
is: trace xx yy zz yx zx zy.
If -mol is set, gmx msd plots the MSD for individual molecules (includ‐
ing making molecules whole across periodic boundaries): for each indi‐
vidual molecule a diffusion constant is computed for its center of
mass. The chosen index group will be split into molecules.
The default way to calculate a MSD is by using mass-weighted averages.
This can be turned off with -nomw.
With the option -rmcomm, the center of mass motion of a specific group
can be removed. For trajectories produced with GROMACS this is usually
not necessary, as gmx mdrun usually already removes the center of mass
motion. When you use this option be sure that the whole system is
stored in the trajectory file.
The diffusion coefficient is determined by linear regression of the
MSD, where, unlike for the normal output of D, the times are weighted
according to the number of reference points, i.e. short times have a
higher weight. Also when -beginfit=-1,fitting starts at 10% and when
-endfit=-1, fitting goes to 90%. Using this option one also gets an
accurate error estimate based on the statistics between individual mol‐
ecules. Note that this diffusion coefficient and error estimate are
only accurate when the MSD is completely linear between -beginfit and
-endfit.
Option -pdb writes a .pdb file with the coordinates of the frame at
time -tpdb with in the B-factor field the square root of the diffusion
coefficient of the molecule. This option implies option -mol.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (msd.xvg) (Output)
xvgr/xmgr file
-mol [<.xvg>] (diff_mol.xvg) (Output, Optional)
xvgr/xmgr file
-pdb [<.pdb>] (diff_mol.pdb) (Output, Optional)
Protein data bank file
Other options:
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-tu <enum> (ps)
Time unit: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-type <enum> (no)
Compute diffusion coefficient in one direction: no, x, y, z
-lateral <enum> (no)
Calculate the lateral diffusion in a plane perpendicular to: no, x,
y, z
-[no]ten (no)
Calculate the full tensor
-ngroup <int> (1)
Number of groups to calculate MSD for
-[no]mw (yes)
Mass weighted MSD
-[no]rmcomm (no)
Remove center of mass motion
-tpdb <time> (0)
The frame to use for option -pdb (ps)
-trestart <time> (10)
Time between restarting points in trajectory (ps)
-beginfit <time> (-1)
Start time for fitting the MSD (ps), -1 is 10%
-endfit <time> (-1)
End time for fitting the MSD (ps), -1 is 90%
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-msd(1)
