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