Provided by: gromacs-data_2018.1-1_all bug


       gmx-energy - Writes energies to xvg files and display averages


          gmx energy [-f [<.edr>]] [-f2 [<.edr>]] [-s [<.tpr>]] [-o [<.xvg>]]
                     [-viol [<.xvg>]] [-pairs [<.xvg>]] [-corr [<.xvg>]]
                     [-vis [<.xvg>]] [-evisco [<.xvg>]] [-eviscoi [<.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>]


       gmx  energy  extracts  energy  components  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).

       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


       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

       -corr [<.xvg>] (enecorr.xvg) (Optional)
              xvgr/xmgr file

       -vis [<.xvg>] (visco.xvg) (Optional)
              xvgr/xmgr file

       -evisco [<.xvg>] (evisco.xvg) (Optional)
              xvgr/xmgr file

       -eviscoi [<.xvg>] (eviscoi.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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              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



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