Molecular modeling on GPUs

Molecular modeling on GPU is the technique of using a graphics

processing unit (GPU) for molecular simulations.[1]

In 2007, Nvidia introduced video cards that could be used not only to
show graphics but also for scientific calculations. These cards include
many arithmetic units (as of 2016, up to 3,584 in Tesla P100) working in
parallel. Long before this event, the computational power of video cards
was purely used to accelerate graphics calculations. What was new is
that Nvidia made it possible to develop parallel programs in a high-level Ionic liquid simulation on
application programming interface (API) named CUDA. This GPU (Abalone)
technology substantially simplified programming by enabling programs
to be written in C/C++. More recently, OpenCL allows cross-platform
GPU acceleration.

Quantum chemistry calculations[2][3][4][5][6][7] and molecular mechanics simulations[8][9][10] (molecular

modeling in terms of classical mechanics) are among beneficial applications of this technology. The video
cards can accelerate the calculations tens of times, so a PC with such a card has the power similar to that
of a cluster of workstations based on common processors.

GPU accelerated molecular modelling software

Programs
Abalone – Molecular Dynamics (Benchmark (http://www.biomolecular-modeling.com/Abalon
e/Benchmarking.html))
ACEMD on GPUs since 2009 (https://pubs.acs.org/doi/10.1021/ct9000685) Benchmark (http
s://www.acellera.com/products/molecular-dynamics-software-gpu-acemd/)
AMBER on GPUs version (http://ambermd.org/gpus/)
Ascalaph (http://www.biomolecular-modeling.com/Products.html) on GPUs version –
Ascalaph Liquid GPU (http://www.biomolecular-modeling.com/Ascalaph/Ascalaph-Liquid.ht
ml)
AutoDock – Molecular docking
BigDFT Ab initio program based on wavelet
BrianQC (http://www.brianqc.com) Quantum chemistry (HF and DFT) and molecular
mechanics
Blaze (http://www.cresset-group.com/blaze/) ligand-based virtual screening
CHARMM – Molecular dynamics [1] (https://www.academiccharmm.org/)
CP2K Ab initio molecular dynamics
Desmond (software) on GPUs, workstations, and clusters
Firefly (formerly PC GAMESS)
FastROCS (http://www.eyesopen.com/fastrocs)
 GOMC (http://gomc.eng.wayne.edu/) – GPU Optimized Monte Carlo simulation engine
GPIUTMD (http://gpiutmd.iut.ac.ir/) – Graphical processors for Many-Particle Dynamics
GPU4PySCF (https://github.com/pyscf/gpu4pyscf) – GPU accelerated plugin package for
PySCF (https://github.com/pyscf/pyscf)
GPUMD (https://gpumd.org/) - A light weight general-purpose molecular dynamics code
GROMACS on GPUs [11]
HALMD (http://halmd.org/) – Highly Accelerated Large-scale MD package
HOOMD-blue (https://glotzerlab.engin.umich.edu/hoomd-blue/) Archived (https://web.archiv
e.org/web/20111111003320/http://codeblue.umich.edu/hoomd-blue/index.html) 2011-11-11
at the Wayback Machine – Highly Optimized Object-oriented Many-particle Dynamics—Blue
Edition
LAMMPS on GPUs version – lammps for accelerators (http://lammps.sandia.gov/doc/Sectio
n_accelerate.html)
LIO (https://github.com/MALBECC/lio) DFT-Based GPU optimized code - [2] (https://github.c
om/MALBECC/lio)
Octopus has support for OpenCL.
oxDNA (http://dna.physics.ox.ac.uk/) – DNA and RNA coarse-grained simulations on GPUs
PWmat (https://web.archive.org/web/20160121101500/http://www.pwmat.com/pwmat) –
Plane-Wave Density Functional Theory simulations
RUMD (http://rumd.org) - Roskilde University Molecular Dynamics[12]
TeraChem – Quantum chemistry and ab initio Molecular Dynamics
TINKER on GPUs.[13]
VMD & NAMD on GPUs versions (http://www.ks.uiuc.edu/Research/gpu/)
YASARA runs MD simulations on all GPUs using OpenCL.

API
BrianQC (http://brianqc.com) – has an open C level API for quantum chemistry simulations
on GPUs, provides GPU-accelerated version of Q-Chem and PSI
OpenMM (http://simtk.org/home/openmm/) – an API for accelerating molecular dynamics on
GPUs, v1.0 provides GPU-accelerated version of GROMACS
mdcore (http://mdcore.sourceforge.net) – an open-source platform-independent library for
molecular dynamics simulations on modern shared-memory parallel architectures.

Distributed computing projects

GPUGRID (http://www.gpugrid.net/) distributed supercomputing infrastructure
Folding@home distributed computing project
Exscalate4Cov large-scale virtual screening experiment

See also
GPU
GPU cluster
GPGPU
Molecular design software
 List of quantum chemistry and solid state physics software
Comparison of software for molecular mechanics modeling
Comparison of nucleic acid simulation software
Molecule editor
Folding@home
Simulated reality

References
1. Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K (December 2007).
"Accelerating molecular modeling applications with graphics processors". Journal of
Computational Chemistry. 28 (16): 2618–2640. CiteSeerX 10.1.1.466.3823 (https://citeseer
x.ist.psu.edu/viewdoc/summary?doi=10.1.1.466.3823). doi:10.1002/jcc.20829 (https://doi.or
g/10.1002%2Fjcc.20829). PMID 17894371 (https://pubmed.ncbi.nlm.nih.gov/17894371).
S2CID 15313533 (https://api.semanticscholar.org/CorpusID:15313533).
2. Yasuda K (August 2008). "Accelerating Density Functional Calculations with Graphics
Processing Unit". Journal of Chemical Theory and Computation. 4 (8): 1230–1236.
doi:10.1021/ct8001046 (https://doi.org/10.1021%2Fct8001046). PMID 26631699 (https://pu
bmed.ncbi.nlm.nih.gov/26631699).
3. Yasuda K (February 2008). "Two-electron integral evaluation on the graphics processor
unit". Journal of Computational Chemistry. 29 (3): 334–342. CiteSeerX 10.1.1.498.364 (http
s://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.498.364). doi:10.1002/jcc.20779 (http
s://doi.org/10.1002%2Fjcc.20779). PMID 17614340 (https://pubmed.ncbi.nlm.nih.gov/17614
340). S2CID 8078401 (https://api.semanticscholar.org/CorpusID:8078401).
4. Vogt L, Olivares-Amaya R, Kermes S, Shao Y, Amador-Bedolla C, Aspuru-Guzik A (March
2008). "Accelerating resolution-of-the-identity second-order Møller-Plesset quantum
chemistry calculations with graphical processing units" (http://nrs.harvard.edu/urn-3:HUL.Ins
tRepos:5344183). The Journal of Physical Chemistry A. 112 (10): 2049–2057.
Bibcode:2008JPCA..112.2049V (https://ui.adsabs.harvard.edu/abs/2008JPCA..112.2049V).
doi:10.1021/jp0776762 (https://doi.org/10.1021%2Fjp0776762). PMID 18229900 (https://pu
bmed.ncbi.nlm.nih.gov/18229900). S2CID 4566211 (https://api.semanticscholar.org/CorpusI
D:4566211).
5. Ufimtsev IS, Martínez TJ (February 2008). "Quantum Chemistry on Graphical Processing
Units. 1. Strategies for Two-Electron Integral Evaluation". Journal of Chemical Theory and
Computation. 4 (2): 222–231. doi:10.1021/ct700268q (https://doi.org/10.1021%2Fct700268
q). PMID 26620654 (https://pubmed.ncbi.nlm.nih.gov/26620654).
6. Ivan S. Ufimtsev & Todd J. Martinez (2008). "Graphical Processing Units for Quantum
Chemistry". Computing in Science & Engineering. 10 (6): 26–34.
Bibcode:2008CSE....10f..26U (https://ui.adsabs.harvard.edu/abs/2008CSE....10f..26U).
doi:10.1109/MCSE.2008.148 (https://doi.org/10.1109%2FMCSE.2008.148).
S2CID 10225262 (https://api.semanticscholar.org/CorpusID:10225262).
7. Tornai GJ, Ladjánszki I, Rák Á, Kis G, Cserey G (October 2019). "Calculation of Quantum
Chemical Two-Electron Integrals by Applying Compiler Technology on GPU". Journal of
Chemical Theory and Computation. 15 (10): 5319–5331. doi:10.1021/acs.jctc.9b00560 (http
s://doi.org/10.1021%2Facs.jctc.9b00560). PMID 31503475 (https://pubmed.ncbi.nlm.nih.go
v/31503475). S2CID 202555796 (https://api.semanticscholar.org/CorpusID:202555796).
 8. Joshua A. Anderson; Chris D. Lorenz; A. Travesset (2008). "General Purpose Molecular
Dynamics Simulations Fully Implemented on Graphics Processing Units". Journal of
Computational Physics. 227 (10): 5342–5359. Bibcode:2008JCoPh.227.5342A (https://ui.ad
sabs.harvard.edu/abs/2008JCoPh.227.5342A). CiteSeerX 10.1.1.552.2883 (https://citeseer
x.ist.psu.edu/viewdoc/summary?doi=10.1.1.552.2883). doi:10.1016/j.jcp.2008.01.047 (http
s://doi.org/10.1016%2Fj.jcp.2008.01.047).
9. Christopher I. Rodrigues; David J. Hardy; John E. Stone; Klaus Schulten & Wen-Mei W.
Hwu. (2008). "GPU acceleration of cutoff pair potentials for molecular modeling
applications". In CF'08: Proceedings of the 2008 Conference on Computing Frontiers, New
York, NY, USA: 273–282.
10. Peter H. Colberg; Felix Höfling (2011). "Highly accelerated simulations of glassy dynamics
using GPUs: Caveats on limited floating-point precision". Comput. Phys. Commun. 182 (5):
1120–1129. arXiv:0912.3824 (https://arxiv.org/abs/0912.3824).
Bibcode:2011CoPhC.182.1120C (https://ui.adsabs.harvard.edu/abs/2011CoPhC.182.1120
C). doi:10.1016/j.cpc.2011.01.009 (https://doi.org/10.1016%2Fj.cpc.2011.01.009).
S2CID 7173093 (https://api.semanticscholar.org/CorpusID:7173093).
11. Yousif RH (2020). "Exploring the Molecular Interactions between Neoculin and the Human
Sweet Taste Receptors through Computational Approaches" (http://www.ukm.my/jsm/pdf_fil
es/SM-PDF-49-3-2020/ARTIKEL%206.pdf) (PDF). Sains Malaysiana. 49 (3): 517–525.
doi:10.17576/jsm-2020-4903-06 (https://doi.org/10.17576%2Fjsm-2020-4903-06).
12. Bailey N, Ingebrigtsen T, Hansen JS, Veldhorst A, Bøhling L, Lemarchand C, et al. (2017-12-
14). "RUMD: A general purpose molecular dynamics package optimized to utilize GPU
hardware down to a few thousand particles" (https://doi.org/10.21468%2FSciPostPhys.3.6.0
38). SciPost Physics. 3 (6): 038. arXiv:1506.05094 (https://arxiv.org/abs/1506.05094).
Bibcode:2017ScPP....3...38B (https://ui.adsabs.harvard.edu/abs/2017ScPP....3...38B).
doi:10.21468/SciPostPhys.3.6.038 (https://doi.org/10.21468%2FSciPostPhys.3.6.038).
ISSN 2542-4653 (https://search.worldcat.org/issn/2542-4653). S2CID 43964588 (https://api.
semanticscholar.org/CorpusID:43964588).
13. Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, et al. (September 2017).
"Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539969). Journal of Computational
Chemistry. 38 (23): 2047–2055. doi:10.1002/jcc.24853 (https://doi.org/10.1002%2Fjcc.2485
3). PMC 5539969 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539969).
PMID 28600826 (https://pubmed.ncbi.nlm.nih.gov/28600826).

External links
More links for classical and quantum сhemistry on GPUs (http://www.nvidia.com/object/verti
cal_solutions.html)

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