.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_energy - writes energies to xvg files and displays averages .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_energy\fP .BI "\-f" " ener.edr " .BI "\-f2" " ener.edr " .BI "\-s" " topol.tpr " .BI "\-o" " energy.xvg " .BI "\-viol" " violaver.xvg " .BI "\-pairs" " pairs.xvg " .BI "\-ora" " orienta.xvg " .BI "\-ort" " orientt.xvg " .BI "\-oda" " orideva.xvg " .BI "\-odr" " oridevr.xvg " .BI "\-odt" " oridevt.xvg " .BI "\-oten" " oriten.xvg " .BI "\-corr" " enecorr.xvg " .BI "\-vis" " visco.xvg " .BI "\-ravg" " runavgdf.xvg " .BI "\-odh" " dhdl.xvg " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-b" " time " .BI "\-e" " time " .BI "\-[no]w" "" .BI "\-xvg" " enum " .BI "\-[no]fee" "" .BI "\-fetemp" " real " .BI "\-zero" " real " .BI "\-[no]sum" "" .BI "\-[no]dp" "" .BI "\-nbmin" " int " .BI "\-nbmax" " int " .BI "\-[no]mutot" "" .BI "\-skip" " int " .BI "\-[no]aver" "" .BI "\-nmol" " int " .BI "\-[no]fluc" "" .BI "\-[no]orinst" "" .BI "\-[no]ovec" "" .BI "\-acflen" " int " .BI "\-[no]normalize" "" .BI "\-P" " enum " .BI "\-fitfn" " enum " .BI "\-ncskip" " int " .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION \&\fB g_energy\fR extracts 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 \&\fB \-nbmin\fR and \fB \-nbmax\fR. \&\fB Note\fR 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 \fB g_energy\fR statistics output more accurate \&than the \fB .xvg\fR 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. \&When the \fB \-viol\fR 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 \fB \-pairs\fR option. \&Options \fB \-ora\fR, \fB \-ort\fR, \fB \-oda\fR, \fB \-odr\fR and \&\fB \-odt\fR 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 \fB \-odr\fR plots the RMS \&deviation as a function of restraint. \&When the run used time or ensemble averaged orientation restraints, \&option \fB \-orinst\fR can be used to analyse the instantaneous, \¬ ensemble\-averaged orientations and deviations instead of \&the time and ensemble averages. \&Option \fB \-oten\fR plots the eigenvalues of the molecular order \&tensor for each orientation restraint experiment. With option \&\fB \-ovec\fR also the eigenvectors are plotted. \&Option \fB \-odh\fR extracts and plots the free energy data \&(Hamiltoian differences and/or the Hamiltonian derivative dhdl) \&from the \fB ener.edr\fR file. \&With \fB \-fee\fR 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 \fB \-fetemp\fR 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_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 (\fB \-f2\fR), 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. The running average \&of the free energy difference is printed to a file specified by \fB \-ravg\fR. \&\fB Note\fR that the energies must both be calculated from the same trajectory. .SH FILES .BI "\-f" " ener.edr" .B Input Energy file .BI "\-f2" " ener.edr" .B Input, Opt. Energy file .BI "\-s" " topol.tpr" .B Input, Opt. Run input file: tpr tpb tpa .BI "\-o" " energy.xvg" .B Output xvgr/xmgr file .BI "\-viol" " violaver.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-pairs" " pairs.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ora" " orienta.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ort" " orientt.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-oda" " orideva.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-odr" " oridevr.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-odt" " oridevt.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-oten" " oriten.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-corr" " enecorr.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-vis" " visco.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ravg" " runavgdf.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-odh" " dhdl.xvg" .B Output, Opt. xvgr/xmgr file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 19" Set the nicelevel .BI "\-b" " time" " 0 " First frame (ps) to read from trajectory .BI "\-e" " time" " 0 " Last frame (ps) to read from trajectory .BI "\-[no]w" "no " View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]fee" "no " Do a free energy estimate .BI "\-fetemp" " real" " 300 " Reference temperature for free energy calculation .BI "\-zero" " real" " 0 " Subtract a zero\-point energy .BI "\-[no]sum" "no " Sum the energy terms selected rather than display them all .BI "\-[no]dp" "no " Print energies in high precision .BI "\-nbmin" " int" " 5" Minimum number of blocks for error estimate .BI "\-nbmax" " int" " 5" Maximum number of blocks for error estimate .BI "\-[no]mutot" "no " Compute the total dipole moment from the components .BI "\-skip" " int" " 0" Skip number of frames between data points .BI "\-[no]aver" "no " Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested) .BI "\-nmol" " int" " 1" Number of molecules in your sample: the energies are divided by this number .BI "\-[no]fluc" "no " Calculate autocorrelation of energy fluctuations rather than energy itself .BI "\-[no]orinst" "no " Analyse instantaneous orientation data .BI "\-[no]ovec" "no " Also plot the eigenvectors with \fB \-oten\fR .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames .BI "\-[no]normalize" "yes " Normalize ACF .BI "\-P" " enum" " 0" Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions .BI "\-beginfit" " real" " 0 " Time where to begin the exponential fit of the correlation function .BI "\-endfit" " real" " \-1 " Time where to end the exponential fit of the correlation function, \-1 is until the end .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.