g_energy Main Table of Contents

VERSION 3.2.0 Sun 25 Jan 2004

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.

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.

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

Other options