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

NAME

       g_energy - writes energies to xvg files and displays averages

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_energy  -f  ener.edr  -f2  ener.edr -s topol.tpr -o energy.xvg -viol violaver.xvg -pairs pairs.xvg -ora orienta.xvg -ort orientt.xvg -oda
       orideva.xvg -odr oridevr.xvg -odt oridevt.xvg -oten oriten.xvg -corr enecorr.xvg -vis visco.xvg -ravg  runavgdf.xvg  -odh  dhdl.xvg  -[no]h
       -[no]version  -nice int -b time -e time -[no]w -xvg enum -[no]fee -fetemp real -zero real -[no]sum -[no]dp -nbmin int -nbmax int -[no]mutot
       -skip int -[no]aver -nmol int -[no]fluc -[no]orinst -[no]ovec -acflen int -[no]normalize -P enum -fitfn enum  -ncskip  int  -beginfit  real
       -endfit real

DESCRIPTION

	 g_energy  extracts  energy  components  or  distance restraint data from an energy file. The user is prompted to interactively select the
       desired energy terms.

       Average, RMSD, and drift are calculated with full precision from the simulation (see printed manual). Drift is calculated by  performing  a
       least-squares  fit  of  the data to a straight line. The reported total drift is the difference of the fit at the first and last point.	An
       error estimate of the average is given based on a block averages over 5 blocks using the full-precision averages. The error estimate can be
       performed  over	multiple  block lengths with the options  -nbmin and  -nbmax.	Note that in most cases the energy files contains averages
       over all MD steps, or over many more points than the number of frames in energy file. This makes the  g_energy statistics output more accu-
       rate than the  .xvg output. When exact averages are not present in the energy file, the statistics mentioned above are simply over the sin-
       gle, per-frame energy values.

       The term fluctuation gives the RMSD around the least-squares fit.

       When the  -viol option is set, the time averaged violations are plotted and the running time-averaged and instantaneous sum  of	violations
       are  recalculated.  Additionally  running  time-averaged and instantaneous distances between selected pairs can be plotted with the  -pairs
       option.

       Options	-ora,  -ort,  -oda,  -odr and  -odt are used for analyzing orientation restraint data.	The first two options  plot  the  orienta-
       tion, the last three the deviations of the orientations from the experimental values.  The options that end on an 'a' plot the average over
       time as a function of restraint. The options that end on a 't' prompt the user for restraint label numbers and plot the data as a  function
       of  time.  Option   -odr  plots	the  RMS  deviation  as  a function of restraint.  When the run used time or ensemble averaged orientation
       restraints, option  -orinst can be used to analyse the instantaneous, not ensemble-averaged orientations and deviations instead of the time
       and ensemble averages.

       Option	-oten  plots  the eigenvalues of the molecular order tensor for each orientation restraint experiment. With option  -ovec also the
       eigenvectors are plotted.

       Option  -odh extracts and plots the free energy data (Hamiltoian differences and/or the Hamiltonian derivative  dhdl)  from  the   ener.edr
       file.

       With  -fee an estimate is calculated for the free-energy difference with an ideal gas state:

	 Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln  e(Upot/kT)

	 Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln  e(Upot/kT)

       where k is Boltzmann's constant, T is set by  -fetemp and the average is over the ensemble (or time in a trajectory).  Note that this is in
       principle only correct when averaging over the whole (Boltzmann) ensemble and using the potential energy. This also allows for  an  entropy
       estimate using:

	 Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (Upot - Delta A)/T

	 Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (Upot + pV - Delta G)/T

       When  a	second energy file is specified ( -f2), a free energy difference is calculated dF = -kT ln  e  -(EB-EA)/kT A , where EA and EB are
       the energies from the first and second energy files, and the average is over the ensemble A. The running average of the free energy differ-
       ence is printed to a file specified by  -ravg.	Note that the energies must both be calculated from the same trajectory.

FILES

       -f ener.edr Input
	Energy file

       -f2 ener.edr Input, Opt.
	Energy file

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

       -o energy.xvg Output
	xvgr/xmgr file

       -viol violaver.xvg Output, Opt.
	xvgr/xmgr file

       -pairs pairs.xvg Output, Opt.
	xvgr/xmgr file

       -ora orienta.xvg Output, Opt.
	xvgr/xmgr file

       -ort orientt.xvg Output, Opt.
	xvgr/xmgr file

       -oda orideva.xvg Output, Opt.
	xvgr/xmgr file

       -odr oridevr.xvg Output, Opt.
	xvgr/xmgr file

       -odt oridevt.xvg Output, Opt.
	xvgr/xmgr file

       -oten oriten.xvg Output, Opt.
	xvgr/xmgr file

       -corr enecorr.xvg Output, Opt.
	xvgr/xmgr file

       -vis visco.xvg Output, Opt.
	xvgr/xmgr file

       -ravg runavgdf.xvg Output, Opt.
	xvgr/xmgr file

       -odh dhdl.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

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

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

       -[no]feeno
	Do a free energy estimate

       -fetemp real 300
	Reference temperature for free energy calculation

       -zero real 0
	Subtract a zero-point energy

       -[no]sumno
	Sum the energy terms selected rather than display them all

       -[no]dpno
	Print energies in high precision

       -nbmin int 5
	Minimum number of blocks for error estimate

       -nbmax int 5
	Maximum number of blocks for error estimate

       -[no]mutotno
	Compute the total dipole moment from the components

       -skip int 0
	Skip number of frames between data points

       -[no]averno
	Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested)

       -nmol int 1
	Number of molecules in your sample: the energies are divided by this number

       -[no]flucno
	Calculate autocorrelation of energy fluctuations rather than energy itself

       -[no]orinstno
	Analyse instantaneous orientation data

       -[no]ovecno
	Also plot the eigenvectors with  -oten

       -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_energy(1)