Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_energy - writes energies to xvg files and displays averages
VERSION 4.6.5
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]fluct_props -[no]driftcorr -[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 accurate than the .xvg output. When
exact averages are not present in the energy file, the statistics mentioned above are simply over the
single, per-frame energy values.
The term fluctuation gives the RMSD around the least-squares fit.
Some fluctuation-dependent properties can be calculated provided the correct energy terms are selected,
and that the command line option -fluct_props is given. The following properties will be computed:
Property Energy terms needed
---------------------------------------------------
Heat capacity C_p (NPT sims): Enthalpy, Temp
Heat capacity C_v (NVT sims): Etot, Temp
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility: Vol, Temp
Adiabatic bulk modulus: Vol, Temp
---------------------------------------------------
You always need to set the number of molecules -nmol. The C_p/C_v computations do not include any
corrections for quantum effects. Use the g_dos program if you need that (and you do).
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 orientation, 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_idealgas(N,V,T) = kT ln(exp(U_pot/kT))
Delta G = G(N,p,T) - G_idealgas(N,p,T) = kT ln(exp(U_pot/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_idealgas(N,V,T) = (U_pot - Delta A)/T
Delta S(N,p,T) = S(N,p,T) - S_idealgas(N,p,T) = (U_pot + pV - Delta G)/T
When a second energy file is specified ( -f2), a free energy difference is calculated
dF = -kT ln(exp(-(E_B-E_A)/kT)_A) , where E_A and E_B 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 difference 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]fluct_propsno
Compute properties based on energy fluctuations, like heat capacity
-[no]driftcorrno
Useful only for calculations of fluctuation properties. The drift in the observables will be subtracted
before computing the fluctuation properties.
-[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 this many 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 2 Dec 2013 g_energy(1)