
                     #####################################
                     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 flexible SPC water,
                      followed by free energy perturbation

    (2) ARGON         Performs an initial energy minimization on a periodic
                      box containing 150 argon atoms, then performs 25
                      picoseconds of molecular dynamics simulation, on a
                      box with 150 argon atoms

    (3) CATION        Computes the hydration free energy difference for
                      Rb+ vs. Cs+ cation via a 10 picosecond simulation of
                      each cation in a box of AMOEBA water, followed by a
                      BAR free energy calculation

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

    (5) CRAMBIN       Generates 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   Locates 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          Runs 10 steps of molecular dynamics on an equilibrated
                      system of DHFR protein in water using the AMOEBA force
                      field; note this is the so-called Joint Amber-CHARMM
                      "JAC" benchmark containing 23558 total atoms

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

    (9) ENKEPHALIN    Builds coordinates for Met-enkephalin from amino acid
                      sequence and phi/psi angles, followed by truncated
                      Newton energy minimization and determination of the
                      lowest frequency normal mode

    (10) ETHANOL      Fits torsional parameter values for the ethanol C-C-O-H
                      bond based on relative quantum mechanical energies from
                      Gaussian for rotating the C-O bond

    (11) FORMAMIDE    Generates 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         Finds the lowest-frequency bacteriorhodopsin normal
                      mode using a sliding block iterative diagonalization;
                      alter the 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        Performs rigid-body optimization of the packing of two
                      ideal polyalanine helices using only van der Waals
                      interactions

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

    (15) IFABP        Generates three distance geometry structures for
                      intestinal fatty acid binding protein from a set of
                      NOE distance restraints and torsional restraints

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

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

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

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

    (20) PYRIDINE     Converts a simple XYZ file for pyridine to Tinker XYZ
                      format using the BASIC force field, and computes the
                      molecular mechanics energy

    (21) SALT         Converts a sodium chloride asymmetric unit to the
                      corresponding unit cell, then minimizes the crystal
                      starting from the diffraction structure using Ewald
                      summation to model long-range electrostatics

    (22) SCORPION     Converts a multi-model RCSB PDBx/mmCIF for scorpion
                      toxin (1CHL) to Tinker XYZ and evaluates energies,
                      then converts the XYZ to legacy PDB format and back
                      to Tinker XYZ, and finally evaluates energies of the
                      new XYZ file to compare with the prior values

    (23) TIP4P        Minimizes the energy to a small gradient and enforces
                      holonomic constraints for a cubic box of 1000 TIP4P
                      water molecules, then runs a short MD simulation under
                      NVT at 298K

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

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

