Tinker 8: Software Tools for Molecular Design

Abstract

The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.

Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]

“…Here, it is the code for Tinker-HP and the 2DECOMP library. 2. the Non-User Code (NUC), which comprises all the code executed by the process because of library calls from the UC, system calls done on behalf of the UC or code introduced implicitly by the compiler.…”

“…Even if we do not use OpenMP* [18] in the dynamic simulation engine, other parts of the Tinkertools suite (Tinker 8 [2]) use OpenMP directives. So, object files are linked with the flags shown in listing 2 where :…”

“…This means the process makes many system calls and performs many memory operations. 2. the vector usage percentage is strictly 0.00 for all the computation subroutines.…”

“…This way, the quantities calculated can be kept in arrays and vector operations can be executed on them. 2. Cope with the way the compiler works on loops.…”

“…Depending on the setup, we used ehal1(vec) or elj1(vec). 2. time_elec, which is the time taken by electrostatic calculations.…”