g_msd_d (1) - Linux Manuals

g_msd_d: calculates mean square displacements

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%