man g_msd (Commandes) - g_msd VERSION 3.3_beta_20050823
NAME
g_msd VERSION 3.3_beta_20050823
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 -[no]xvgr -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 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 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 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 , s , m or h
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes 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
-ngroup int 1 Number of groups to calculate MSD for
-[no]mw yes Mass weighted MSD
-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%