
                     #####################################
                     TEST Directory for the Tinker Package
                     #####################################

    This directory contains some test casess illustrating use of several
    of the programs in the Tinker package.

    For example, the argon.run file contains commands to run the first
    test case. The resulting output is found in the file argon.log.

    The clean.make script will remove any output files generated during
    these test runs, and should be invoked prior to validating Tinker
    executables against the provided log files.

    (1) ANION         estimates the hydration free energy difference for
                      Cl- vs. Br- anion via a 10 picosecond simulation
                      of a "hybrid" anion in a box of water, followed by
                      free energy perturbation

    (2) ARGON         minimize, then perform 25 picoseconds of molecular
                      dynamics simulation, on a box with 150 argon atoms

    (3) CATION        estimates the hydration free energy difference for
                      Rb+ vs. Cs+ cation via a 2 picosecond simulation
                      of each cation in a box of water, followed by a BAR
                      free energy calculation

    (4) CLUSTER       performs 10 Gaussian density annealing trials on a
                      cluster of 13 argon atoms to find the global minimum
                      energy structure

    (5) CRAMBIN       generate a Tinker XYZ file from a PDB file, followed
                      by single point energy computation and determination
                      of the molecular volume and surface area

    (6) CYCLOHEXANE   locate the transition state between chair and boat
                      cyclohexane via two methods: the Muller-Brown saddle
                      point method, and path sampling using the Elber
                      algorithm; vibrational analysis of the results shows
                      the same TS with one negative frequency

    (7) DHFR          run 10 molecular dynamics steps on pre-equilibrated
                      DHFR protein in water using the AMOEBA force field
                      (the so-called Joint Amber-CHARMM benchmark)

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

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

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

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

    (12) GPCR         find the lowest-frequency bacteriorhodopsin normal
                      mode using a sliding block iterative diagonalization
                      (alter gpcr.run script to save the file gpcr.001 if
                      you want to view the mode; this example can require
                      up to an hour to complete)

    (13) HELIX        optimize rigid-body packing of two ideal polyalanine
                      helices using only van der Waals interactions

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

    (15) IFABP        generate distance geometry structures for intestinal
                      fatty acid binding protein from NOE distances and
                      torsional restraints

    (16) LIQUID       print the system setup and compute the force field
                      energy components for three small liquid water boxes
                      using the AMOEBA, AMOEBA+ and HIPPO force fields

    (17) METHANOL     process distributed multipole analysis (DMA) output
                      to extract coordinates and permanent multipoles, set
                      local frames and polarization groups, modify the
                      intramolecular polarization, and average equivalent
                      atomic sites

    (18) NITROGEN     calculate the self-diffusion constant and N-N radial
                      distribution function for a liquid nitrogen box via
                      analysis of a 50ps MD trajectory

    (19) POLYALA      generate an extended conformation of capped alanine
                      octapeptide, then use Monte Carlo Minimization with
                      torsion moves to find the 3/10 helix global minimum

    (20) SALT         convert sodium chloride asymmetric unit to the unit
                      cell, then minimize the crystal from the diffraction
                      structure using Ewald summation electrostatics

    (21) VASOPRESSIN  compare analytical and finite difference numerical
                      gradient over Cartesian and internal coordinates for
                      vasopressin using the AMOEBA force field model

    (22) WATER        fit the electrostatic potential for TIP3P, AMOEBA
                      and HIPPO water models to a QM-derived potential
                      at MP2/aug-cc-pVTZ on a grid of points outside the
                      molecular surface

