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g_enemat(1) [debian man page]

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

NAME

       g_enemat - extracts an energy matrix from an energy file

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_enemat  -f  ener.edr  -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -[no]version -nice int -b time -e time -dt
       time -[no]w -xvg enum -[no]sum -skip int -[no]mean -nlevels int -max real  -min	real  -[no]coul  -[no]coulr  -[no]coul14  -[no]lj  -[no]lj
       -[no]lj14 -[no]bhamsr -[no]bhamlr -[no]free -temp real

DESCRIPTION

	 g_enemat  extracts an energy matrix from the energy file ( -f).  With	-groups a file must be supplied with on each line a group of atoms
       to be used. For these groups matrix of interaction energies will be extracted from the energy file by looking for energy groups with  names
       corresponding to pairs of groups of atoms, e.g. if your	-groups file contains:

	2

	Protein

	SOL

       then  energy  groups with names like 'Coul-SR:Protein-SOL' and 'LJ:Protein-SOL' are expected in the energy file (although  g_enemat is most
       useful if many groups are analyzed simultaneously). Matrices for different energy types are written out separately, as controlled by  the
       -[no]coul,   -[no]coulr,   -[no]coul14,	  -[no]lj,   -[no]lj14,   -[no]bham and  -[no]free options.  Finally, the total interaction energy
       energy per group can be calculated ( -etot).

       An approximation of the free energy can be calculated using: E(free) = E0 + kT log( exp((E-E0)/kT) ), where '' stands for  time-average.  A
       file  with  reference  free  energies  can be supplied to calculate the free energy difference with some reference state. Group names (e.g.
       residue names) in the reference file should correspond to the group names as used in the  -groups file, but a appended number (e.g. residue
       number) in the  -groups will be ignored in the comparison.

FILES

       -f ener.edr Input, Opt.
	Energy file

       -groups groups.dat Input
	Generic data file

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

       -emat emat.xpm Output
	X PixMap compatible matrix file

       -etot energy.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]sumno
	Sum the energy terms selected rather than display them all

       -skip int 0
	Skip number of frames between data points

       -[no]meanyes
	with  -groups extracts matrix of mean energies instead of matrix for each timestep

       -nlevels int 20
	number of levels for matrix colors

       -max real 1e+20
	max value for energies

       -min real -1e+20
	min value for energies

       -[no]coulyes
	extract Coulomb SR energies

       -[no]coulrno
	extract Coulomb LR energies

       -[no]coul14no
	extract Coulomb 1-4 energies

       -[no]ljyes
	extract Lennard-Jones SR energies

       -[no]ljno
	extract Lennard-Jones LR energies

       -[no]lj14no
	extract Lennard-Jones 1-4 energies

       -[no]bhamsrno
	extract Buckingham SR energies

       -[no]bhamlrno
	extract Buckingham LR energies

       -[no]freeyes
	calculate free energy

       -temp real 300
	reference temperature for free energy calculation

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						       g_enemat(1)

Check Out this Related Man Page

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

NAME

       g_mindist - calculates the minimum distance between two groups

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_mindist  -f  traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h
       -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]matrix -[no]max -d real -[no]group  -[no]pi  -[no]split  -ng
       int -[no]pbc -[no]respertime -[no]printresname

DESCRIPTION

	 g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from
       the respective groups) and the number of contacts within a given distance are written to two  separate  output  files.	With  the   -group
       option  a  contact  of  an atom in other group with multiple atoms in the first group is counted as one contact instead of as multiple con-
       tacts.  With  -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number.

       With option  -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein  has  seen  its
       periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts.  It also plots the maximum
       distance within the group and the lengths of the three box vectors.

       Other programs that calculate distances are  g_dist and	g_bond.

FILES

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

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

       -n index.ndx Input, Opt.
	Index file

       -od mindist.xvg Output
	xvgr/xmgr file

       -on numcont.xvg Output, Opt.
	xvgr/xmgr file

       -o atm-pair.out Output, Opt.
	Generic output file

       -ox mindist.xtc Output, Opt.
	Trajectory: xtc trr trj gro g96 pdb

       -or mindistres.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)

       -tu enum ps
	Time unit:  fs,  ps,  ns,  us,	ms or  s

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

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

       -[no]matrixno
	Calculate half a matrix of group-group distances

       -[no]maxno
	Calculate *maximum* distance instead of minimum

       -d real 0.6
	Distance for contacts

       -[no]groupno
	Count contacts with multiple atoms in the first group as one

       -[no]pino
	Calculate minimum distance with periodic images

       -[no]splitno
	Split graph where time is zero

       -ng int 1
	Number of secondary groups to compute distance to a central group

       -[no]pbcyes
	Take periodic boundary conditions into account

       -[no]respertimeno
	When writing per-residue distances, write distance for each time point

       -[no]printresnameno
	Write residue names

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_mindist(1)
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