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.

1.
M.
Williams
,
R.
Forbes
,
H.
Weir
,
K.
Veyrinas
,
R. J.
MacDonell
,
A. E.
Boguslavskiy
,
M. S.
Schuurman
,
A.
Stolow
, and
T. J.
Martinez
, “
Unmasking the cis-stilbene phantom state via vacuum ultraviolet time-resolved photoelectron spectroscopy and ab initio multiple spawning
,”
J. Phys. Chem. Lett.
12
,
6363
6369
(
2021
).
2.
V. W. D.
Cruzeiro
,
A.
Wildman
,
X.
Li
, and
F.
Paesani
, “
Relationship between hydrogen-bonding motifs and the 1b1 splitting in the x-ray emission spectrum of liquid water
,”
J. Phys. Chem. Lett.
12
,
3996
4002
(
2021
).
3.
S.
Seritan
,
K.
Thompson
, and
T. J.
Martínez
, “
TeraChem Cloud: A high-performance computing service for scalable distributed GPU-accelerated electronic structure calculations
,”
J. Chem. Inf. Model.
60
,
2126
2137
(
2020
).
4.
L.-P.
Wang
,
A.
Titov
,
R.
McGibbon
,
F.
Liu
,
V. S.
Pande
, and
T. J.
Martínez
, “
Discovering chemistry with an ab initio nanoreactor
,”
Nat. Chem.
6
,
1044
1048
(
2014
).
5.
E.
Pieri
,
D.
Lahana
,
A. M.
Chang
,
C. R.
Aldaz
,
K. C.
Thompson
, and
T. J.
Martínez
, “
The non-adiabatic nanoreactor: Towards the automated discovery of photochemistry
,”
Chem. Sci.
12
,
7294
7307
(
2021
).
6.
B. F. E.
Curchod
and
T. J.
Martínez
, “
Ab initio nonadiabatic quantum molecular dynamics
,”
Chem. Rev.
118
,
3305
3336
(
2018
).
7.
S.
Seritan
,
C.
Bannwarth
,
B. S.
Fales
,
E. G.
Hohenstein
,
S. I. L.
Kokkila-Schumacher
,
N.
Luehr
,
J. W.
Snyder
,
C.
Song
,
A. V.
Titov
,
I. S.
Ufimtsev
, and
T. J.
Martínez
, “
TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units
,”
J. Chem. Phys.
152
,
224110
(
2020
).
8.
I. S.
Ufimtsev
and
T. J.
Martinez
, “
Quantum chemistry on graphical processing units. 2. Direct self-consistent-field implementation
,”
J. Chem. Theory Comput.
5
,
1004
1015
(
2009
).
9.
I. S.
Ufimtsev
and
T. J.
Martínez
, “
Quantum chemistry on graphical processing units. 1. Strategies for two-electron integral evaluation
,”
J. Chem. Theory Comput.
4
,
222
231
(
2008
).
10.
I. S.
Ufimtsev
and
T. J.
Martinez
, “
Quantum chemistry on graphical processing units. 3. Analytical energy gradients, geometry optimization, and first principles molecular dynamics
,”
J. Chem. Theory Comput.
5
,
2619
2628
(
2009
).
11.
F.
Liu
,
D. M.
Sanchez
,
H. J.
Kulik
, and
T. J.
Martínez
, “
Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models
,”
Int. J. Quantum Chem.
119
,
e25760
(
2019
).
12.
A. V.
Titov
,
I. S.
Ufimtsev
,
N.
Luehr
, and
T. J.
Martinez
, “
Generating efficient quantum chemistry codes for novel architectures
,”
J. Chem. Theory Comput.
9
,
213
221
(
2012
).
13.
I. S.
Ufimtsev
and
T. J.
Martínez
, “
Graphical processing units for quantum chemistry
,”
Comput. Sci. Eng.
10
,
26
34
(
2008
).
14.
C.
Bergonzo
,
A. J.
Campbell
,
R. C.
Walker
, and
C.
Simmerling
, “
A partial nudged elastic band implementation for use with large or explicitly solvated systems
,”
Int. J. Quantum Chem.
109
,
3781
3790
(
2009
).
15.
D.
Ghoreishi
,
D. S.
Cerutti
,
Z.
Fallon
,
C.
Simmerling
, and
A. E.
Roitberg
, “
Fast implementation of the nudged elastic band method in AMBER
,”
J. Chem. Theory Comput.
15
,
4699
4707
(
2019
).
16.
J.
Kästner
, “
Umbrella sampling
,”
WIREs: Comput. Mol. Sci.
1
,
932
942
(
2011
).
17.
D. A.
Case
,
K.
Belfon
,
I. Y.
Ben-Shalom
,
S. R.
Brozell
,
D. S.
Cerutti
,
T. E.
Cheatham
 III
,
V. W. D.
Cruzeiro
,
T. A.
Darden
,
R. E.
Duke
,
G.
Giambasu
,
M. K.
Gilson
,
H.
Gohlke
,
A. W.
Goetz
,
R.
Harris
,
S.
Izadi
,
S. A.
Izmailov
,
K.
Kasavajhala
,
A.
Kovalenko
,
R.
Krasny
,
T.
Kurtzman
,
T. S.
Lee
,
S.
LeGrand
,
P.
Li
,
C.
Lin
,
J.
Liu
,
T.
Luchko
,
R.
Luo
,
V.
Man
,
K. M.
Merz
,
Y.
Miao
,
O.
Mikhailovskii
,
G.
Monard
,
H.
Nguyen
,
A.
Onufriev
,
F.
Pan
,
S.
Pantano
,
R.
Qi
,
D. R.
Roe
,
A.
Roitberg
,
C.
Sagui
,
S.
Schott-Verdugo
,
J.
Shen
,
C.
Simmerling
,
N. R.
Skrynnikov
,
J.
Smith
,
J.
Swails
,
R. C.
Walker
,
J.
Wang
,
L.
Wilson
,
R. M.
Wolf
,
X.
Wu
,
Y.
Xiong
,
Y.
Xue
,
D. M.
York
, and
P. A.
Kollman
,
AMBER 2020
(
University of California
,
San Francisco
,
2020
).
18.
A. P.
Thompson
,
H. M.
Aktulga
,
R.
Berger
,
D. S.
Bolintineanu
,
W. M.
Brown
,
P. S.
Crozier
,
P. J.
in ’t Veld
,
A.
Kohlmeyer
,
S. G.
Moore
,
T. D.
Nguyen
,
R.
Shan
,
M. J.
Stevens
,
J.
Tranchida
,
C.
Trott
, and
S. J.
Plimpton
, “
LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
,”
Comput. Phys. Commun.
271
,
108171
(
2022
).
19.
V.
Kapil
,
M.
Rossi
,
O.
Marsalek
,
R.
Petraglia
,
Y.
Litman
,
T.
Spura
,
B.
Cheng
,
A.
Cuzzocrea
,
R. H.
Meißner
,
D. M.
Wilkins
,
B. A.
Helfrecht
,
P.
Juda
,
S. P.
Bienvenue
,
W.
Fang
,
J.
Kessler
,
I.
Poltavsky
,
S.
Vandenbrande
,
J.
Wieme
,
C.
Corminboeuf
,
T. D.
Kühne
,
D. E.
Manolopoulos
,
T. E.
Markland
,
J. O.
Richardson
,
A.
Tkatchenko
,
G. A.
Tribello
,
V.
Van Speybroeck
, and
M.
Ceriotti
, “
i-PI 2.0: A universal force engine for advanced molecular simulations
,”
Comput. Phys. Commun.
236
,
214
223
(
2019
).
20.
P.
Eastman
,
J.
Swails
,
J. D.
Chodera
,
R. T.
McGibbon
,
Y.
Zhao
,
K. A.
Beauchamp
,
L.-P.
Wang
,
A. C.
Simmonett
,
M. P.
Harrigan
,
C. D.
Stern
,
R. P.
Wiewiora
,
B. R.
Brooks
, and
V. S.
Pande
, “
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
,”
PLoS Comput. Biol.
13
,
e1005659
(
2017
).
21.
C. M.
Isborn
,
N.
Luehr
,
I. S.
Ufimtsev
, and
T. J.
Martínez
, “
Excited-state electronic structure with configuration interaction singles and Tamm–Dancoff time-dependent density functional theory on graphical processing units
,”
J. Chem. Theory Comput.
7
,
1814
1823
(
2011
).
22.
B. S.
Fales
and
B. G.
Levine
, “
Nanoscale multireference quantum chemistry: Full configuration interaction on graphical processing units
,”
J. Chem. Theory Comput.
11
,
4708
4716
(
2015
).
23.
P.
Slavíček
and
T. J.
Martínez
, “
Ab initio floating occupation molecular orbital-complete active space configuration interaction: An efficient approximation to CASSCF
,”
J. Chem. Phys.
132
,
234102
(
2010
).
24.
E. G.
Hohenstein
,
M. E. F.
Bouduban
,
C.
Song
,
N.
Luehr
,
I. S.
Ufimtsev
, and
T. J.
Martínez
, “
Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units
,”
J. Chem. Phys.
143
,
014111
(
2015
).
25.
E. G.
Hohenstein
, “
Analytic formulation of derivative coupling vectors for complete active space configuration interaction wavefunctions with floating occupation molecular orbitals
,”
J. Chem. Phys.
145
,
174110
(
2016
).
26.
D.
Hollas
,
L.
Šištík
,
E. G.
Hohenstein
,
T. J.
Martínez
, and
P.
Slavíček
, “
Nonadiabatic ab initio molecular dynamics with the floating occupation molecular orbital-complete active space configuration interaction method
,”
J. Chem. Theory Comput.
14
,
339
350
(
2017
).
27.
Protocol Buffers Documentation, https://developers.google.com/protocol-buffers/docs (accessed 29 April 2022).
28.
S.
Ahmadi
,
L.
Barrios Herrera
,
M.
Chehelamirani
,
J.
Hostaš
,
S.
Jalife
, and
D. R.
Salahub
, “
Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD: A tutorial review
,”
Int. J. Quantum Chem.
118
,
e25558
(
2018
).
29.
M. G.
Quesne
,
T.
Borowski
, and
S. P.
de
Visser
, “
Quantum mechanics/molecular mechanics modeling of enzymatic processes: Caveats and breakthroughs
,”
Chem. Eur. J.
22
,
2562
2581
(
2016
).
30.
U. N.
Morzan
,
D. J.
Alonso de Armiño
,
N. O.
Foglia
,
F.
Ramírez
,
M. C.
González Lebrero
,
D. A.
Scherlis
, and
D. A.
Estrin
, “
Spectroscopy in complex environments from QM-MM simulations
,”
Chem. Rev.
118
,
4071
4113
(
2018
).
31.
H.
Lin
and
D. G.
Truhlar
, “
QM/MM: What have we learned, where are we, and where do we go from here?
,”
Theor. Chem. Acc.
117
,
185
199
(
2007
).
32.
H. M.
Senn
and
W.
Thiel
, “
QM/MM methods for biomolecular systems
,”
Angew. Chem., Int. Ed. Engl.
48
,
1198
1229
(
2009
).
33.
T. S.
Hofer
and
S. P.
de Visser
, “
Editorial: Quantum mechanical/molecular mechanical approaches for the investigation of chemical systems–recent developments and advanced applications
,”
Front. Chem.
6
,
357
(
2018
).
34.
C. M.
Isborn
,
A. W.
Götz
,
M. A.
Clark
,
R. C.
Walker
, and
T. J.
Martínez
, “
Electronic absorption spectra from MM and ab initio QM/MM molecular dynamics: Environmental effects on the absorption spectrum of photoactive yellow protein
,”
J. Chem. Theory Comput.
8
,
5092
5106
(
2012
).
35.
L. J.
Nåbo
,
J. M. H.
Olsen
,
T. J.
Martínez
, and
J.
Kongsted
, “
The quality of the embedding potential is decisive for minimal quantum region size in embedding calculations: The case of the green fluorescent protein
,”
J. Chem. Theory Comput.
13
,
6230
6236
(
2017
).
36.
V. W. D.
Cruzeiro
,
M.
Manathunga
,
K. M.
Merz
, and
A. W.
Götz
, “
Open-source multi-GPU-accelerated QM/MM simulations with AMBER and QUICK
,”
J. Chem. Inf. Model.
61
,
2109
2115
(
2021
).
37.
A. W.
Götz
,
M. A.
Clark
, and
R. C.
Walker
, “
An extensible interface for QM/MM molecular dynamics simulations with AMBER
,”
J. Comput. Chem.
35
,
95
108
(
2014
).
38.
A. O.
Dohn
, “
Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review
,”
Int. J. Quantum Chem.
120
,
e26343
(
2020
).
39.
C.
McLaughlin
,
M.
Assmann
,
M. A.
Parkes
,
J. L.
Woodhouse
,
R.
Lewin
,
H. C.
Hailes
,
G. A.
Worth
, and
H. H.
Fielding
, “
Ortho and para chromophores of green fluorescent protein: Controlling electron emission and internal conversion
,”
Chem. Sci.
8
,
1621
1630
(
2017
).
40.
S.
Kojima
,
H.
Ohkawa
,
T.
Hirano
,
S.
Maki
,
H.
Niwa
,
M.
Ohashi
,
S.
Inouye
, and
F. I.
Tsuji
, “
Fluorescent properties of model chromophores of tyrosine-66 substituted mutants of Aequorea green fluorescent protein (GEP)
,”
Tetrahedron Lett.
39
,
5239
5242
(
1998
).
41.
O.
Shimomura
,
F. H.
Johnson
, and
Y.
Saiga
, “
Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea
,”
J. Cell. Comp. Physiol.
59
,
223
239
(
1962
).
42.
M.
Chalfie
,
Y.
Tu
,
G.
Euskirchen
,
W. W.
Ward
, and
D. C.
Prasher
, “
Green fluorescent protein as a marker for gene expression
,”
Science
263
,
802
805
(
1994
).
43.
B. J.
Feilmeier
,
G.
Iseminger
,
D.
Schroeder
,
H.
Webber
, and
G. J.
Phillips
, “
Green fluorescent protein functions as a reporter for protein localization in Escherichia coli
,”
J. Bacteriol.
182
,
4068
4076
(
2000
).
44.
J.
Lippincott-Schwartz
,
E.
Snapp
, and
A.
Kenworthy
, “
Studying protein dynamics in living cells
,”
Nat. Rev. Mol. Cell Biol.
2
,
444
456
(
2001
).
45.
R. Y.
Tsien
, “
The green fluorescent protein
,”
Annu. Rev. Biochem.
67
,
509
544
(
1998
).
46.
C. M.
Jones
,
N. H.
List
, and
T. J.
Martínez
, “
Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water
,”
Chem. Sci.
12
,
11347
11363
(
2021
).
47.
H.
Fukunishi
,
O.
Watanabe
, and
S.
Takada
, “
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
,”
J. Chem. Phys.
116
,
9058
9067
(
2002
).
48.
C.
Bergonzo
,
N. M.
Henriksen
,
D. R.
Roe
,
J. M.
Swails
,
A. E.
Roitberg
, and
T. E.
Cheatham
, “
Multidimensional replica exchange molecular dynamics yields a converged ensemble of an RNA tetranucleotide
,”
J. Chem. Theory Comput.
10
,
492
499
(
2014
).
49.
Y.
Wu
,
H. L.
Tepper
, and
G. A.
Voth
, “
Flexible simple point-charge water model with improved liquid-state properties
,”
J. Chem. Phys.
124
,
024503
(
2006
).
50.
A.
Grossfield
, WHAM: An implementation of the weighted histogram analysis method, version 2.0.11, http://membrane.urmc.rochester.edu/content/wham/ (accessed 29 April 2022).
51.
M. E.
Martin
,
F.
Negri
, and
M.
Olivucci
, “
Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution
,”
J. Am. Chem. Soc.
126
,
5452
5464
(
2004
).
52.
A.
Toniolo
,
S.
Olsen
,
L.
Manohar
, and
T. J.
Martínez
, “
Conical intersection dynamics in solution: The chromophore of Green Fluorescent Protein
,”
Faraday Discuss.
127
,
149
163
(
2004
).
53.
T. J.
Giese
and
D. M.
York
, “
Ambient-potential composite Ewald method for ab initio quantum mechanical/molecular mechanical molecular dynamics simulation
,”
J. Chem. Theory Comput.
12
,
2611
2632
(
2016
).

Supplementary Material

You do not currently have access to this content.