
                 ---------------------------------------------
                 TEST Directory for the TINKER Program Package
                 ---------------------------------------------

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

         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.

         (01) 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

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

         (03) CLUSTER     perform 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

         (04) 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

         (05) CYCLOHEX    location of the transition state between
                          chair and boat cyclohexane via two methods:
                          refinement of the transition state using
                          Muller-Brown saddle point algorithm, then
                          path sampling using the Elber algorithm;
                          vibrational analysis of both results shows
                          the same TS with one negative frequency

         (06) DHFR        performs 10 steps of molecular dynamics on
                          a pre-equilibrated system of DHFR protein
                          in a box or water using the AMOEBA force
                          field (this is the so-called Joint Amber-
                          CHARMM benchmark with 23558 total atoms)

         (07) DIALANINE   find all the local minima of alanine
                          dipeptide via a potential energy surface
                          scan using torsional modes to jump between
                          the minima

         (08) 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

         (09) ETHANOL     fitting of torsional parameter values for
                          the C-C-O-H bond based on relative quantum
                          mechanical (G09) energies for rotating the
                          C-O bond

         (10) 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

         (11) GPCR        finds the lowest-frequency normal mode
                          of bacteriorhodopsin using vibrational
                          analysis via a sliding block iterative
                          matrix diagonalization (Alter gpcr.run
                          script to save the file gpcr.001 if you
                          want to view the modes. Note this example
                          requires about an hour to complete.)

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

         (13) ICE         short MD simulation of the monoclinic ice V
                          crystal form using the iAMOEBA water model,
                          neighbor lists and PME electrostatics

         (14) IFABP       generation of distance geometry structures
                          for intestinal fatty acid binding protein
                          from NOE distance and torsional restraints

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

         (16) TETRAALA    generate capped alanine tetrapeptide in an
                          extended conformation, then use Monte Carlo
                          Minimization with random torsional moves to
                          find the global minimum energy structure

         (17) WATER       fit the electrostatic potential around an
                          AMOEBA water molecule to the QM-derived
                          potential (MP2/aug-cc-pVTZ) on a grid of
                          points outside the molecular surface.

