MOL-SPEC:  Specify a molecular system.

MOL-spec creates a log file with recording the specifications for a
molecular system, or displays the specifications in an existing log
file.

Usage:

   mol-spec log-file dim scale width [ maxpe ] "NVT" N length 

or:

   mol-spec log-file dim scale width [ maxpe ] "NPT" N pressure [ inv-temp ]

or:

   mol-spec log-file

When called with arguments after the log file name, mol-spec creates a
log file of that name (wiping out the contents of any previous file
with that name), and stores in it the following specifications:

   dim       Dimensionality of the space, either 1, 2, or 3
   scale     Overall scale factor for the pair potential
   width     Width parameter of the pair potential (divides distance)
   maxpe     Maximum value for a pair potential (default is infinite)

   N         Number of molecules
   length    Length of each dimension of space (for NVT ensemble)
   pressure  Pressure (for NPT ensemble)

   inv-temp  The inverse temperature to use for the "infinite temperature"
             distribution of volume, needed when using annealed importance 
             sample, Hamiltonian importance sampline, and Metropolis 
             importance sampling.  Has to be finite and non-zero to make
             actual sampling possible.  May be specified directly, or as 
             /T, where T is the temperature.  (For NPT ensemble only.)

See mol.doc for the formula for the pair potential.  The "NVT" or
"NPT" argument (which are one or the other of these strings, no quotes
needed) determines whether the NVT ensemble is used, in which the
length of each dimension is fixed (to the given length), or whether
instead the NPT ensemble is used, in which length is variable but the
pressure is fixed (to the given pressure).

When called with only a log file name as an argument, mol-spec reads
the specification record from that log file and displays the values
stored, from the previous mol-spec command.  It also displays the
density implied by N and length (for NVT ensemble), and the density
(for NVT ensemble), pressure (for NPT ensemble), and temperature in
"reduced" units, accounting for the width and scale chosen.

The specifications are stored in the log file as a single record of
type 'M' and index -1,

            Copyright (c) 1995-2004 by Radford M. Neal