This Winter School class is dedicated to the functionalities and the usage of the Tinker modeling package. The Tinker package comes with several programs to run molecular simulations, from system preparation to molecular dynamics up to analysis of the results of such simulations. It has a particular focus on the use of advanced polarizable multipolar force fields such as AMOEBA whose electrostatic interactions include a polarization term modelling the induction response of atomic electron clouds to a fluctuating environment. This higher-resolution description of the molecular interactions comes with a higher computational cost, which is why High-Performance implementations such as Tinker-HP (for CPUs and GPUs) have been introduced. These implementations share the structures of their inputs and outputs and many of their core functionalities. Therefore, this school has a particular focus on Tinker-HP (https://tinker-hp.org/ and https://github.com/TinkerTools/tinker-hp).
The goal here is not to review all of the (many) functionalities of the Tinker programs but to focus on the most basic ones such as system preparation, energy analysis, standard molecular dynamics and simple enhanced sampling simulations. For a more complete description of all these possibilities, one can look at the Tinker user guide available on Jay Ponder’s web page dedicated to Tinker. For the more complex case of the parametrization of a new system with AMOEBA, one can look at the poltype2 program that can handle this procedure systematically.
Video is available only for registered users.