TINKER

TINKER is a comprehensive software package that is specifically designed for molecular mechanics and dynamics, offering a range of features for biopolymers. The software has the ability to utilize different parameter sets, including popular sets like Amber, CHARMM, Allinger MM, OPLS, and more. In addition, the software incorporates novel algorithms, such as a new distance geometry metrization method, Elber's reaction path methods, and various potential smoothing and search methods for global optimization.

Other key features of TINKER include an efficient potential surface scanning procedure, atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments, normal mode analysis, and minimization in Cartesian, torsional or rigid body space. The software also offers velocity Verlet stochastic dynamics, an improved spherical energy cutoff method, Particle Mesh Ewald summation for partial charges, and regular Ewald for polarizable multipoles.

TINKER boasts additional options such as novel reaction field treatment of electrostatics and many more. The software is constantly expanding with sets for other standard force fields like GROMOS, UFF, ENCAD, and MM4 under consideration for future releases. The inclusion of AMOEBA polarizable atomic multipole force field and Liam Dang's polarizable potentials offer users a range of options to choose from.

Overall, TINKER is a versatile software package, with features that enable chemists and molecular biologists to accomplish a variety of tasks. The multitude of options available combined with the constantly evolving set of algorithms, make it an extremely valuable tool for any research group interested in molecular modeling.