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 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.
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_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 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]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/>.