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.
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28 January 2023
Research Article|
January 25 2023
TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model
Vinícius Wilian D. Cruzeiro
;
Vinícius Wilian D. Cruzeiro
(Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing)
1
Department of Chemistry and The PULSE Institute, Stanford University
, Stanford, California 94305, USA
2
SLAC National Accelerator Laboratory
, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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Yuanheng Wang
;
Yuanheng Wang
(Conceptualization, Methodology, Software, Validation, Writing – original draft, Writing – review & editing)
1
Department of Chemistry and The PULSE Institute, Stanford University
, Stanford, California 94305, USA
2
SLAC National Accelerator Laboratory
, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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Elisa Pieri
;
Elisa Pieri
(Conceptualization, Methodology, Validation, Writing – original draft, Writing – review & editing)
1
Department of Chemistry and The PULSE Institute, Stanford University
, Stanford, California 94305, USA
2
SLAC National Accelerator Laboratory
, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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Edward G. Hohenstein
;
Edward G. Hohenstein
(Conceptualization, Software, Supervision)
1
Department of Chemistry and The PULSE Institute, Stanford University
, Stanford, California 94305, USA
2
SLAC National Accelerator Laboratory
, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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Todd J. Martínez
Todd J. Martínez
a)
(Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing)
1
Department of Chemistry and The PULSE Institute, Stanford University
, Stanford, California 94305, USA
2
SLAC National Accelerator Laboratory
, 2575 Sand Hill Road, Menlo Park, California 94025, USA
a)Author to whom correspondence should be addressed: toddjmartinez@gmail.com
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a)Author to whom correspondence should be addressed: toddjmartinez@gmail.com
J. Chem. Phys. 158, 044801 (2023)
Article history
Received:
October 15 2022
Accepted:
January 04 2023
Citation
Vinícius Wilian D. Cruzeiro, Yuanheng Wang, Elisa Pieri, Edward G. Hohenstein, Todd J. Martínez; TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model. J. Chem. Phys. 28 January 2023; 158 (4): 044801. https://doi.org/10.1063/5.0130886
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