MOL-QUANTITIES: Quantities from log files relating to molecular systems. These quantities relating to molecular systems can be obtained from log files (eg, for use in mol-plt). The generic quantities documented in quantities.doc, and the Markov chain quantities documented in mc-quantities.doc, are defined as well. The quantities specific to molecular systems are listed below. x, y, z Arrays of coordinates of molecules - eg, x@0:3 means the x coordinates of the first four molecules. The values are wrapped to lie in [0,len), where len is the length of a dimension of space, from mol-spec. x1, y1, z1 Like x, y, z except that half the length of a dimension is added before wrapping. Useful when looking at structures that would otherwise be split by the arbitrary wrapping boundary. dn Array of distances of other molecules from molecule n, where n is the index of a molecule, starting with zero. n As an array, the distances from each molecule to its nearest neighbor. As a scalar, the smallest distance between any two molecules. N As an array, the distances from each molecule to the molecule farthest from it. As a scalar, the largest distance between any two molecules. U Potential energy (for molecular interactions only, not volume for NPT ensemble) divided by the scale factor in the Lennard-Jones potential (from mol-spec). This is the form of the potential energy that is appropriate if the scale is set to something other than one to mimic a temperature other than one. u U divided by the number of molecules in the system. W The volume. This is a constant if the NVT ensemble is being used. w The length of each dimension. This is a constant if the NVT ensemble is being used. Note that W = w^D, where D is the number of dimensions. O The density, equal to the number of molecules divided by W. This will be constant if the NVT ensemble is being used. o The reduced density, equal to O times the width parameter of the Lennard-Jones potential raised to the dimensionality. V The "virial", equal to the sum over all pairs of distinct molecules of the force pushing the pair apart (which may be negative) times their distance. v V divided by the scale factor in the Lennard-Jones potential. P The pressure, equal to V plus the number of molecules, divided by the volume. This assumes that the temperature is one. Note that this is a variable quantity, computed from the current state and the current volume, even if the NPT ensemble is being used. p P divided by the scale factor in the Lennard-Jones potential and multiplied by the width factor in the potential raised to the dimensionality. This is the appropriate measure of pressure if the scale factor is set to something other than one to mimic a temperature other than one. The adjustment according to the width parameter give the pressure in "reduced" units. Copyright (c) 1995-2004 by Radford M. Neal