Provided by: gromacs-data_4.6.5-1build1_all bug


       g_energy - writes energies to xvg files and displays averages

       VERSION 4.6.5


       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


         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

       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

         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.


       -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


        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

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

        Compute properties based on energy fluctuations, like heat capacity

        Useful only for calculations of fluctuation properties. The drift in the observables will
       be subtracted before computing the fluctuation properties.

        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

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                              g_energy(1)