g_msd(1)

NAME
g_msd VERSION 3.2.0

SYNOPSIS
g_msd -f traj.xtc -s topol.tpr -n index.ndx -o msd.xvg -mol diff_mol.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -type enum -lateral enum -ngroup int -[no]mw -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 diffusion constant is calculated by least squares fitting a straight line through the MSD from -beginfit to -endfit of the diffusion coefficients obtained from fits over the two halfs of the fit interval. Option -mol plots the MSD for molecules, this implies -mw , i.e. for each inidividual molecule an diffusion constant is computed. When using an index file, it should contain molecule numbers instead of atom numbers. Using this option one also gets an accurate error estimate based on the statistics between individual molecules. Since one usually is interested in self-diffusion at infinite dilution this is probably the most useful number.

FILES
-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt.
 Index file -o msd.xvg Output
 xvgr/xmgr file -mol diff_mol.xvg Output, Opt.
 xvgr/xmgr file

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -tu enum ps
 Time unit: ps , fs , ns , us , ms , s , m or h -[no]w no
 View output xvg, xpm, eps and pdb files -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 -ngroup int 1
 Number of groups to calculate MSD for -[no]mw yes
 Mass weighted MSD -trestart time 0
 Time between restarting points in trajectory (ps) -beginfit time 0
 Start time for fitting the MSD (ps) -endfit time -1
 End time for fitting the MSD (ps), -1 is till end