g_energy_d (1) Linux Manual Page

g_energy – writes energies to xvg files and displays averages

VERSION 4.0.1

Synopsis

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

Description

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 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 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.

Files

-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 

Other Options

-[no]hno
 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

-[no]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]feeno
 Do a free energy estimate

-fetemp real 300
 Reference temperature for free energy calculation

-zero real 0
 Subtract a zero-point energy

-[no]sumno
 Sum the energy terms selected rather than display them all

-[no]dpno
 Print energies in high precision

-[no]mutotno
 Compute the total dipole moment from the components

-[no]uniyes
 Skip non-uniformly spaced frames

-skip int 0
 Skip number of frames between data points

-[no]averno
 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 number

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

-[no]flucno
 Calculate autocorrelation of energy fluctuations rather than energy itself

-[no]orinstno
 Analyse instantaneous orientation data

-[no]ovecno
 Also plot the eigenvectors with -oten

-acflen int -1
 Length of the ACF, default is half the number of frames

-[no]normalizeyes
 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 or  exp9

-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

See Also

gromacs(7)

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