
                ------------------------------------------------
                EXAMPLE Directory for the TINKER Program Package
                ------------------------------------------------

          This directory contains several examples illustrating the
          use of some of the programs in the TINKER package:

          (1) ANION       estimation of the free energy of hydration
                          of Cl- anion vs. Br- anion via a 2 picosecond
                          simulation on a "hybrid" anion in a box of
                          water, followed by free energy perturbation

          (2) ARGON       minimization followed by 6 picoseconds
                          of a molecular dynamics run on a periodic
                          box containing 150 argon atoms

          (3) CLUSTER     performs a set of 10 Gaussian density
                          annealing trials on a cluster of 13 argon
                          atoms in an attempt to locate the "global"
                          minimum energy structure

          (4) CRAMBIN     generation of a TINKER file from a PDB
                          file, followed by a single point energy
                          computation and determination of the
                          molecular volume and surface area

          (5) CYCLOHEX    location of the transition state between
                          chair and boat cyclohexane, refinement
                          of the transition state and vibrational
                          analysis to show one negative frequency

          (6) ENKEPHALIN  generation of coordinates from the
                          amino acid sequence and phi/psi angles,
                          followed by energy minimization and
                          determination of the lowest frequency
                          normal mode

          (7) FORMAMIDE   generation of unit cell from fractional
                          coordinates, followed by full crystal
                          energy minimization and determination of
                          optimal carbonyl oxygen energy parameters
                          from a fit to lattice energy and structure

          (8) HELIX       rigid-body optimization of the packing of
                          two idealized polyalanine helices using
                          only van der Waals interactions

          (9) SALT        convert sodium chloride asymmetric unit to
                          the unit cell, then a crystal minimization
                          starting from the diffraction structure
                          using Ewald summation for electrostatics

          For example, the argon.run file contains the commands to run
          the first example on a Unix machine. The resulting output is
          found in the file argon.log.

          The clean.make script will remove any output files generated
          during the example runs and should be used prior to trying
          to validate TINKER executables against the provided log files.

