Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_energy - writes energies to xvg files and displays averagesVERSION4.6.5

**SYNOPSIS**

g_energy-fener.edr-f2ener.edr-stopol.tpr-oenergy.xvg-violviolaver.xvg-pairspairs.xvg-oraorienta.xvg-ortorientt.xvg-odaorideva.xvg-odroridevr.xvg-odtoridevt.xvg-otenoriten.xvg-correnecorr.xvg-visvisco.xvg-ravgrunavgdf.xvg-odhdhdl.xvg-[no]h-[no]version-niceint-btime-etime-[no]w-xvgenum-[no]fee-fetempreal-zeroreal-[no]sum-[no]dp-nbminint-nbmaxint-[no]mutot-skipint-[no]aver-nmolint-[no]fluct_props-[no]driftcorr-[no]fluc-[no]orinst-[no]ovec-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

**DESCRIPTION**

g_energyextracts 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-nbminand-nbmax.Notethat 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 theg_energystatistics output more accurate than the.xvgoutput. 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_propsis 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 donotinclude any corrections for quantum effects. Use theg_dosprogram if you need that (and you do). When the-violoption 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-pairsoption. Options-ora,-ort,-oda,-odrand-odtare 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-odrplots the RMS deviation as a function of restraint. When the run used time or ensemble averaged orientation restraints, option-orinstcan be used to analyse the instantaneous, not ensemble-averaged orientations and deviations instead of the time and ensemble averages. Option-otenplots the eigenvalues of the molecular order tensor for each orientation restraint experiment. With option-ovecalso the eigenvectors are plotted. Option-odhextracts and plots the free energy data (Hamiltoian differences and/or the Hamiltonian derivative dhdl) from theener.edrfile. With-feean 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-fetempand 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.Notethat the energies must both be calculated from the same trajectory.

**FILES**

-fener.edrInputEnergy file-f2ener.edrInput,Opt.Energy file-stopol.tprInput,Opt.Run input file: tpr tpb tpa-oenergy.xvgOutputxvgr/xmgr file-violviolaver.xvgOutput,Opt.xvgr/xmgr file-pairspairs.xvgOutput,Opt.xvgr/xmgr file-oraorienta.xvgOutput,Opt.xvgr/xmgr file-ortorientt.xvgOutput,Opt.xvgr/xmgr file-odaorideva.xvgOutput,Opt.xvgr/xmgr file-odroridevr.xvgOutput,Opt.xvgr/xmgr file-odtoridevt.xvgOutput,Opt.xvgr/xmgr file-otenoriten.xvgOutput,Opt.xvgr/xmgr file-correnecorr.xvgOutput,Opt.xvgr/xmgr file-visvisco.xvgOutput,Opt.xvgr/xmgr file-ravgrunavgdf.xvgOutput,Opt.xvgr/xmgr file-odhdhdl.xvgOutput,Opt.xvgr/xmgr file

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-[no]wnoView output.xvg,.xpm,.epsand.pdbfiles-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-[no]feenoDo a free energy estimate-fetempreal300Reference temperature for free energy calculation-zeroreal0Subtract a zero-point energy-[no]sumnoSum the energy terms selected rather than display them all-[no]dpnoPrint energies in high precision-nbminint5Minimum number of blocks for error estimate-nbmaxint5Maximum number of blocks for error estimate-[no]mutotnoCompute the total dipole moment from the components-skipint0Skip number of frames between data points-[no]avernoAlso print the exact average and rmsd stored in the energy frames (only when 1 term is requested)-nmolint1Number of molecules in your sample: the energies are divided by this number-[no]fluct_propsnoCompute properties based on energy fluctuations, like heat capacity-[no]driftcorrnoUseful only for calculations of fluctuation properties. The drift in the observables will be subtracted before computing the fluctuation properties.-[no]flucnoCalculate autocorrelation of energy fluctuations rather than energy itself-[no]orinstnoAnalyse instantaneous orientation data-[no]ovecnoAlso plot the eigenvectors with-oten-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7,exp9orerffit-ncskipint0Skip this many points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time where to end the exponential fit of the correlation function, -1 is until the end

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_energy(1)