Provided by: gromacs-data_5.1.2-1ubuntu1_all 
NAME
gmx-energy - Writes energies to xvg files and display averages
SYNOPSIS
gmx energy [-f [<.edr>]] [-f2 [<.edr>]] [-s [<.tpr>]] [-o [<.xvg>]]
[-viol [<.xvg>]] [-pairs [<.xvg>]] [-ora [<.xvg>]]
[-ort [<.xvg>]] [-oda [<.xvg>]] [-odr [<.xvg>]]
[-odt [<.xvg>]] [-oten [<.xvg>]] [-corr [<.xvg>]]
[-vis [<.xvg>]] [-ravg [<.xvg>]] [-odh [<.xvg>]]
[-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>] [-beginfit <real>] [-endfit <real>]
DESCRIPTION
gmx 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 gmx 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 gmx 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.
OPTIONS
Options to specify input files:
-f [<.edr>] (ener.edr)
Energy file
-f2 [<.edr>] (ener.edr) (Optional)
Energy file
-s [<.tpr>] (topol.tpr) (Optional)
Portable xdr run input file
Options to specify output files:
-o [<.xvg>] (energy.xvg)
xvgr/xmgr file
-viol [<.xvg>] (violaver.xvg) (Optional)
xvgr/xmgr file
-pairs [<.xvg>] (pairs.xvg) (Optional)
xvgr/xmgr file
-ora [<.xvg>] (orienta.xvg) (Optional)
xvgr/xmgr file
-ort [<.xvg>] (orientt.xvg) (Optional)
xvgr/xmgr file
-oda [<.xvg>] (orideva.xvg) (Optional)
xvgr/xmgr file
-odr [<.xvg>] (oridevr.xvg) (Optional)
xvgr/xmgr file
-odt [<.xvg>] (oridevt.xvg) (Optional)
xvgr/xmgr file
-oten [<.xvg>] (oriten.xvg) (Optional)
xvgr/xmgr file
-corr [<.xvg>] (enecorr.xvg) (Optional)
xvgr/xmgr file
-vis [<.xvg>] (visco.xvg) (Optional)
xvgr/xmgr file
-ravg [<.xvg>] (runavgdf.xvg) (Optional)
xvgr/xmgr file
-odh [<.xvg>] (dhdl.xvg) (Optional)
xvgr/xmgr file
Other options:
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
-[no]fee (no)
Do a free energy estimate
-fetemp <real> (300)
Reference temperature for free energy calculation
-zero <real> (0)
Subtract a zero-point energy
-[no]sum (no)
Sum the energy terms selected rather than display them all
-[no]dp (no)
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]mutot (no)
Compute the total dipole moment from the components
-skip <int> (0)
Skip number of frames between data points
-[no]aver (no)
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_props (no)
Compute properties based on energy fluctuations, like heat capacity
-[no]driftcorr (no)
Useful only for calculations of fluctuation properties. The drift in the
observables will be subtracted before computing the fluctuation properties.
-[no]fluc (no)
Calculate autocorrelation of energy fluctuations rather than energy itself
-[no]orinst (no)
Analyse instantaneous orientation data
-[no]ovec (no)
Also plot the eigenvectors with -oten
-acflen <int> (-1)
Length of the ACF, default is half the number of frames
-[no]normalize (yes)
Normalize ACF
-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-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
gmx(1)
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