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>]] [-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] [-[no]aver] [-nmol <int>]


           [-[no]fluct_props] [-[no]driftcorr] [-[no]fluc]


           [-[no]orinst] [-[no]ovec] [-einstein_restarts <int>]


           [-acflen <int>] [-[no]normalize] [-P <enum>]


           [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]

DESCRIPTION¶

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:

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 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.

For liquids, viscosities can be calculated by integrating the auto-correlation function of, or by using the Einstein formula for, the off-diagonal pressure elements. The option -vis turns calculation of the shear and bulk viscosity through integration of the auto-correlation function. For accurate results, this requires extremely frequent computation and output of the pressure tensor. The Einstein formula does not require frequent output and is therefore more convenient. Note that frequent pressure calculation (nstcalcenergy mdp parameter) is still needed. Option -evicso gives this shear viscosity estimate and option -eviscoi the integral. Using one of these two options also triggers the other. The viscosity is computed from integrals averaged over -einstein_restarts starting points uniformly distributed over the first quarter of the trajectory.

OPTIONS¶

Options to specify input files:

Options to specify output files:

Other options:

SEE ALSO¶

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT¶

2024, GROMACS development team