NAME¶
g_msd - calculates mean square displacements
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS¶
g_msd -f traj.xtc -s topol.tpr -n
index.ndx -o msd.xvg -mol diff_mol.xvg
-pdb diff_mol.pdb -[no]h
-[no]version -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¶
g_msd computes the mean square displacement (MSD) of atoms from a set of
initial positions. This provides an easy way to compute the diffusion constant
using the Einstein relation. The time between the reference points for the MSD
calculation is set with
-trestart. The diffusion 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 estimate 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,
g_msd plots the MSD for individual molecules
(including making molecules whole across periodic boundaries): for each
individual 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
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 molecules. 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.
FILES¶
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-o msd.xvg Output
xvgr/xmgr file
-mol diff_mol.xvg Output, Opt.
xvgr/xmgr file
-pdb diff_mol.pdb Output, Opt.
Protein data bank file
OTHER OPTIONS¶
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-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 or
s
-[no]wno
View output
.xvg,
.xpm,
.eps and
.pdb files
-xvg enum xmgrace
xvg plot formatting:
xmgrace,
xmgr or
none
-type enum no
Compute diffusion coefficient in one direction:
no,
x,
y or
z
-lateral enum no
Calculate the lateral diffusion in a plane perpendicular to:
no,
x,
y or
z
-[no]tenno
Calculate the full tensor
-ngroup int 1
Number of groups to calculate MSD for
-[no]mwyes
Mass weighted MSD
-[no]rmcommno
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 ALSO¶
gromacs(7)
More information about
GROMACS is available at
<
http://www.gromacs.org/>.