NAME
g_msd - calculates mean square displacements
VERSION 4.0.1
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 -nice int -b time -e time -dt
time -tu enum -[no]w -[no]xvgr -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 their
initial positions. This provides an easy way to compute the diffusion
constant using the Einstein relation. The time between additional
starting points for the MSD calculation is set with -trestart. The
diffusion constant is calculated by least squares fitting a straight
line through the MSD from -beginfit to -endfit. An error estimate
given, which is the difference of the diffusion coefficients obtained
from fits over the two halfs 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.
Option -mol plots the MSD for molecules, this implies With option
-rmcomm center of mass motion 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.
-mw, i.e. for each inidividual molecule an diffusion constant is
computed for its center of mass. The chosen index group will be split
into molecules. 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 restart point, i.e. short
times have a higher weight. Also when -beginfit=-1,fitting starts at 0
and when -endfit=-1, fitting goes to the end. 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
-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
-dt time 0
Only use frame when t MOD dt = first time (ps)
-tu enum ps
Time unit: ps, fs, ns, us, ms or s
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-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/>.
Thu 16 Oct 2008 g_msd(1)