.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_msd - calculates mean square displacements

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_msd\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " msd.xvg "
.BI "\-mol" " diff_mol.xvg "
.BI "\-pdb" " diff_mol.pdb "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-type" " enum "
.BI "\-lateral" " enum "
.BI "\-[no]ten" ""
.BI "\-ngroup" " int "
.BI "\-[no]mw" ""
.BI "\-[no]rmcomm" ""
.BI "\-tpdb" " time "
.BI "\-trestart" " time "
.BI "\-beginfit" " time "
.BI "\-endfit" " time "
.SH DESCRIPTION
\&\fB g_msd\fR 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 \fB \-trestart\fR.
\&The diffusion constant is calculated by least squares fitting a
\&straight line (D*t + c) through the MSD(t) from \fB \-beginfit\fR to
\&\fB \-endfit\fR (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: \fB \-type\fR, \fB \-lateral\fR
\&and \fB \-ten\fR. Option \fB \-ten\fR writes the full MSD tensor for
\&each group, the order in the output is: trace xx yy zz yx zx zy.


\&If \fB \-mol\fR is set, \fB g_msd\fR 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 \fB \-nomw\fR.


\&With the option \fB \-rmcomm\fR, the center of mass motion of a 
\&specific group can be removed. For trajectories produced with 
\&GROMACS this is usually not necessary, 
\&as \fB mdrun\fR 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 \fB \-beginfit\fR=\-1,fitting starts at 10%
\&and when \fB \-endfit\fR=\-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
\&\fB \-beginfit\fR and \fB \-endfit\fR.


\&Option \fB \-pdb\fR writes a \fB .pdb\fR file with the coordinates of the frame
\&at time \fB \-tpdb\fR with in the B\-factor field the square root of
\&the diffusion coefficient of the molecule.
\&This option implies option \fB \-mol\fR.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " msd.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-mol" " diff_mol.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-pdb" " diff_mol.pdb" 
.B Output, Opt.
 Protein data bank file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-type"  " enum" " no" 
 Compute diffusion coefficient in one direction: \fB no\fR, \fB x\fR, \fB y\fR or \fB z\fR

.BI "\-lateral"  " enum" " no" 
 Calculate the lateral diffusion in a plane perpendicular to: \fB no\fR, \fB x\fR, \fB y\fR or \fB z\fR

.BI "\-[no]ten"  "no    "
 Calculate the full tensor

.BI "\-ngroup"  " int" " 1" 
 Number of groups to calculate MSD for

.BI "\-[no]mw"  "yes   "
 Mass weighted MSD

.BI "\-[no]rmcomm"  "no    "
 Remove center of mass motion

.BI "\-tpdb"  " time" " 0     " 
 The frame to use for option \fB \-pdb\fR (ps)

.BI "\-trestart"  " time" " 10    " 
 Time between restarting points in trajectory (ps)

.BI "\-beginfit"  " time" " \-1    " 
 Start time for fitting the MSD (ps), \-1 is 10%

.BI "\-endfit"  " time" " \-1    " 
 End time for fitting the MSD (ps), \-1 is 90%

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.