SYNOPSISg_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
DESCRIPTIONg_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
Run input file: tpr tpb tpa
Print help info and quit
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
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
Do a free energy estimate
-fetemp real 300
Reference temperature for free energy calculation
-zero real 0
Subtract a zero-point energy
Sum the energy terms selected rather than display them all
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
Compute the total dipole moment from the components
-skip int 0
Skip number of frames between data points
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
Calculate autocorrelation of energy fluctuations rather than energy itself
Analyse instantaneous orientation data
Also plot the eigenvectors with -oten
-acflen int -1
Length of the ACF, default is half the number of frames
-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