TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model
Abstract
The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ∼250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI−)—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 25, 2023
- Source ID
- 10.1063/5.0130886
Entities
People
- Edward G Hohenstein
- Elisa Pieri
- Todd Martinez
- Vinícius Wilian D. Cruzeiro
- Yuanheng Wang
Organizations
- Office of Naval Research
- SLAC National Accelerator Laboratory
- Stanford University