g_velacc(1) [debian man page]

g_velacc(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_velacc(1)

NAME

       g_velacc - calculates velocity autocorrelation functions

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_velacc  -f  traj.trr  -s topol.tpr -n index.ndx -o vac.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]m
       -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION

	g_velacc computes the velocity autocorrelation function.  When the  -m option is used, the momentum  autocorrelation  function	is  calcu-
       lated.

       With option  -mol the velocity autocorrelation function of molecules is calculated. In this case the index group should consist of molecule
       numbers instead of atom numbers.

FILES

       -f traj.trr Input
	Full precision trajectory: trr trj cpt

       -s topol.tpr Input, Opt.
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -o vac.xvg Output
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version 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)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]mno
	Calculate the momentum autocorrelation function

       -[no]molno
	Calculate the velocity acf of molecules

       -acflen int -1
	Length of the ACF, default is half the number of frames

       -[no]normalizeyes
	Normalize ACF

       -P enum 0
	Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or	3

       -fitfn enum none
	Fit function:  none,  exp,  aexp,  exp_exp,  vac,  exp5,  exp7,  exp9 or  erffit

       -ncskip int 0
	Skip N points in the output file of correlation functions

       -beginfit real 0
	Time where to begin the exponential fit of the correlation function

       -endfit real -1
	Time where to end the exponential fit of the correlation function, -1 is until the end

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_velacc(1)

g_rotacf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_rotacf(1)

NAME

       g_rotacf - calculates the rotational correlation function for molecules

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]d
       -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION

	g_rotacf calculates the rotational correlation function for molecules. Three atoms (i,j,k) must be given in the index file,  defining  two
       vectors	ij  and  jk. The rotational ACF is calculated as the autocorrelation function of the vector n = ij x jk, i.e. the cross product of
       the two vectors.  Since three atoms span a plane, the order of the three atoms does not matter. Optionally, controlled by the   -d  switch,
       you can calculate the rotational correlation function for linear molecules by specifying two atoms (i,j) in the index file.

       EXAMPLES

	g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0

       This  will  calculate  the  rotational correlation function using a first order Legendre polynomial of the angle of a vector defined by the
       index file. The correlation function will be fitted from 2.5 ps until 20.0 ps to a two-parameter exponential.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -n index.ndx Input
	Index file

       -o rotacf.xvg Output
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version 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)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]dno
	Use index doublets (vectors) for correlation function instead of triplets (planes)

       -[no]averyes
	Average over molecules

       -acflen int -1
	Length of the ACF, default is half the number of frames

       -[no]normalizeyes
	Normalize ACF

       -P enum 0
	Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or	3

       -fitfn enum none
	Fit function:  none,  exp,  aexp,  exp_exp,  vac,  exp5,  exp7,  exp9 or  erffit

       -ncskip int 0
	Skip N points in the output file of correlation functions

       -beginfit real 0
	Time where to begin the exponential fit of the correlation function

       -endfit real -1
	Time where to end the exponential fit of the correlation function, -1 is until the end

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_rotacf(1)