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       g_energy - writes energies to xvg files and displays averages

       VERSION 4.0.1


       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 -[no]h -nice int -b  time
       -e  time  -[no]w  -[no]xvgr  -[no]fee  -fetemp real -zero real -[no]sum
       -[no]dp -[no]mutot -[no]uni -skip int  -[no]aver  -nmol  int  -ndf  int
       -[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 energy
       terms she wants.

       Average and RMSD are calculated with full precision from the simulation
       (see  printed  manual).  Drift is calculated by performing a LSQ fit of
       the data to a straight line. Total drift is drift multiplied  by  total
       time. The term fluctuation gives the RMSD around the LSQ 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

       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.

       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 andthe 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.  NOTE that the energies must  both  be  calculated
       from the same trajectory.


       -f ener.edr Input
        Energy file: edr ene

       -f2 ener.edr Input, Opt.
        Energy file: edr ene

       -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


        Print help 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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

        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

        Compute the total dipole moment from the components

        Skip non-uniformly spaced frames

       -skip int 0
        Skip number of frames between data points

        Print also the X1,t and sigma1,t, only if only 1 energy is requested

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

       -ndf int 3
        Number  of  degrees of freedom per molecule. Necessary for calculating
       the heat capacity

        Calculate autocorrelation of energy fluctuations  rather  than  energy

        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

       -fitfn enum none
        Fit function:  none,  exp,  aexp,   exp_exp,   vac,   exp5,   exp7  or

       -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 till the end



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                    g_energy(1)