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   examples using the TINKER package


12. Examples using the TINKER Package

This section contains some comments on the five sample calculations found in the EXAMPLE subdirectory of the TINKER distribution. These examples exercise several of the current TINKER programs and provide a flavor of the capabilities of the package.

ANION Example
Computes an 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 a free energy perturbation calculation

ARGON Example
Performs a minimization followed by 6 picoseconds of a molecular dynamics run on a periodic box containing 150 argon atoms

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

Generates a TINKER file from a PDB file, followed by a single point energy computation and determination of the molecular volume and surface area

Locates the transition state between chair and boat cyclohexane, with subsequent refinement of the transition state and vibrational analysis to show one negative frequency

Produces coordinates from the amino acid sequence and phi/psi angles, followed by energy minimization and determination of the lowest frequency normal mode

Converts to a 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

HELIX Example
Performs a rigid-body optimization of the packing of two idealized polyalanine helices using only van der Waals interactions

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