Molecular Dynamics

I previously used to work on TINKER while working at the Center for Computational Biology at Wash U. Tinker is developed by Jay Ponder, in the Department of Biochemistry and Molecular Biophysics. I continue to work on this application part-time, specifically for parallelizing the application for multi-core SMP systems. Parallelization work is covered in part by a grant from the National Science Foundation (Award Number: 1152522).

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, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.