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g_rmsdist(1) [debian man page]

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

NAME

       g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3
       nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -[no]version -nice int -b time -e time -dt  time  -[no]w  -xvg  enum  -nlevels  int	-max  real
       -[no]sumh -[no]pbc

DESCRIPTION

	 g_rmsdist  computes  the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS
       deviation as computed by  g_rms.  The reference structure is taken from the structure file.  The RMSD at time t is calculated as the RMS of
       the differences in distance between atom-pairs in the reference structure and the structure at time t.

	 g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices
       with NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists of atom pairs with 1/r3 and 1/r6 averaged distance below the  maximum
       distance  ( -max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of
       hydrogens named *[123]). Additionally a list of equivalent atoms can be supplied ( -equiv), each line containing a set of equivalent  atoms
       specified as residue number and name and atom name; e.g.:

	3 SER  HB1 3 SER  HB2

       Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.

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

       -equiv equiv.dat Input, Opt.
	Generic data file

       -o distrmsd.xvg Output
	xvgr/xmgr file

       -rms rmsdist.xpm Output, Opt.
	X PixMap compatible matrix file

       -scl rmsscale.xpm Output, Opt.
	X PixMap compatible matrix file

       -mean rmsmean.xpm Output, Opt.
	X PixMap compatible matrix file

       -nmr3 nmr3.xpm Output, Opt.
	X PixMap compatible matrix file

       -nmr6 nmr6.xpm Output, Opt.
	X PixMap compatible matrix file

       -noe noe.dat Output, Opt.
	Generic data 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

       -nlevels int 40
	Discretize rms in  levels

       -max real -1
	Maximum level in matrices

       -[no]sumhyes
	average distance over equivalent hydrogens

       -[no]pbcyes
	Use periodic boundary conditions when computing distances

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_rmsdist(1)

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

NAME

       g_sgangle - computes the angle and distance between two groups

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_sgangle  -f  traj.xtc	-n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -[no]version
       -nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z

DESCRIPTION

       Compute the angle and distance between two groups.  The groups are defined by a number of atoms given in an index file and may  be  two	or
       three  atoms in size.  If  -one is set, only one group should be specified in the index file and the angle between this group at time 0 and
       t will be computed.  The angles calculated depend on the order in which the atoms are given. Giving, for instance, 5 6 will rotate the vec-
       tor 5-6 with 180 degrees compared to giving 6 5.

       If three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using the formula  P1P2 x P1P3.  The cos
       of the angle is calculated, using the inproduct of the two normalized vectors.

       Here is what some of the file options do:

	-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane	defined  by  those
       three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.

	-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.

	-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.

	-od2: For two planes this option has no meaning.

FILES

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

       -n index.ndx Input
	Index file

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

       -oa sg_angle.xvg Output
	xvgr/xmgr file

       -od sg_dist.xvg Output, Opt.
	xvgr/xmgr file

       -od1 sg_dist1.xvg Output, Opt.
	xvgr/xmgr file

       -od2 sg_dist2.xvg Output, Opt.
	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]oneno
	Only one group compute angle between vector at time zero and time t

       -[no]zno
	Use the  z-axis as reference

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_sgangle(1)
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