Pittsburgh Supercomputing Center 

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TINKER

TINKER is a molecular modeling package for molecular mechanics and dynamics.  The TINKER website says:

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009) polarizable atomic multipole force field. Parameter sets for other widely-used force fields are under consideration for future releases.

The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, our potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, and more....

Installed on blacklight.

Usage

To run a TINKER using OpenMP, you must

  1. Create a batch job containing commands to
    1. Set up the module command
    2. Load the TINKER module
      module load tinker
    3. Define OMP_NUM_THREADS to be the number of cpus requested in the job
      setenv OMP_NUM_THREADS $PBS_NCPUS
    4. Execute TINKER with a command like
      omplace -nt $OMP_NUM_THREADS tinker-program input-file input-parameters
  2. Submit the job with the qsub command.

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