2018/05/31 by Iain Bethune, Ralf Banisch, Elena Breitmoser +10
Chemistry · Computer Science · Physics and Astronomy · #Advanced Data Storage Technologies #Chemistry #Computational chemistry #Computational science #Computer science #Fortran #Integrator #Interface (matter) #Mass Spectrometry Techniques and Applications #Message Passing Interface #Message passing #Molecular dynamics #Parallel Computing and Optimization Techniques #Parallel computing #Programming language #physics.comp-ph
paper · pdf · doi:10.1016/j.cpc.2018.10.006
Pre-print accepted for Computer Physics Communications
openalex created_date 2018/06/01 · arxiv created 2018/10/08 · openalex publication_date 2018/10/17 · arxiv updated 2018/10/19 · openalex updated_date 2026/08/05
We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract in- terface to common molecular dynamics codes, enabling rapid and portable development of new integration schemes for molecular dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS and Amber, and includes several standard integration schemes, a constraint solver, tem- perature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and For- tran APIs which can be used to interface additional MD codes to MIST. We show, for a range of test systems, that MIST introduces negligible overheads for serial, shared-memory parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself. As a demonstration of the capabilities of MIST, we describe a simulated tempering simulation used to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions.