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Title: ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences (PLS) Directorate
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Computing Directorate
  3. IBM, Yorktown Heights, NY (United States). Thomas J. Watson Research Center
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); National Institutes of Health (NIH)
OSTI Identifier:
1669229
Alternate Identifier(s):
OSTI ID: 1642324
Report Number(s):
LLNL-JRNL-810343
Journal ID: ISSN 0021-9606; 1016751
Grant/Contract Number:  
AC52-07NA27344; JDACS4C
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 153; Journal Issue: 4; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
supercomputer; molecular dynamics software; proteins; MARTINI force field; lipid bilayer; graphics processing units

Citation Formats

Zhang, Xiaohua, Sundram, Shiv, Oppelstrup, Tomas, Kokkila-Schumacher, Sara L., Carpenter, Timothy S., Ingólfsson, Helgi I., Streitz, Frederick H., Lightstone, Felice C., and Glosli, James N. ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. United States: N. p., 2020. Web. doi:10.1063/5.0014500.
Zhang, Xiaohua, Sundram, Shiv, Oppelstrup, Tomas, Kokkila-Schumacher, Sara L., Carpenter, Timothy S., Ingólfsson, Helgi I., Streitz, Frederick H., Lightstone, Felice C., & Glosli, James N. ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. United States. doi:10.1063/5.0014500.
Zhang, Xiaohua, Sundram, Shiv, Oppelstrup, Tomas, Kokkila-Schumacher, Sara L., Carpenter, Timothy S., Ingólfsson, Helgi I., Streitz, Frederick H., Lightstone, Felice C., and Glosli, James N. Thu . "ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field". United States. doi:10.1063/5.0014500. https://www.osti.gov/servlets/purl/1669229.
@article{osti_1669229,
title = {ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field},
author = {Zhang, Xiaohua and Sundram, Shiv and Oppelstrup, Tomas and Kokkila-Schumacher, Sara L. and Carpenter, Timothy S. and Ingólfsson, Helgi I. and Streitz, Frederick H. and Lightstone, Felice C. and Glosli, James N.},
abstractNote = {},
doi = {10.1063/5.0014500},
journal = {Journal of Chemical Physics},
number = 4,
volume = 153,
place = {United States},
year = {2020},
month = {7}
}

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Works referenced in this record:

Perspective on the Martini model
journal, January 2013

  • Marrink, Siewert J.; Tieleman, D. Peter
  • Chemical Society Reviews, Vol. 42, Issue 16
  • DOI: 10.1039/c3cs60093a

The CORAL Supercomputer Systems
journal, January 2019


Kokkos: Enabling manycore performance portability through polymorphic memory access patterns
journal, December 2014

  • Carter Edwards, H.; Trott, Christian R.; Sunderland, Daniel
  • Journal of Parallel and Distributed Computing, Vol. 74, Issue 12
  • DOI: 10.1016/j.jpdc.2014.07.003

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
journal, January 1996

  • Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian
  • Journal of the American Chemical Society, Vol. 118, Issue 45
  • DOI: 10.1021/ja9621760

Canonical sampling through velocity rescaling
journal, January 2007

  • Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
  • The Journal of Chemical Physics, Vol. 126, Issue 1
  • DOI: 10.1063/1.2408420

Martini Coarse-Grained Force Field: Extension to RNA
journal, July 2017

  • Uusitalo, Jaakko J.; Ingólfsson, Helgi I.; Marrink, Siewert J.
  • Biophysical Journal, Vol. 113, Issue 2
  • DOI: 10.1016/j.bpj.2017.05.043

Parameters for Martini sterols and hopanoids based on a virtual-site description
journal, December 2015

  • Melo, M. N.; Ingólfsson, H. I.; Marrink, S. J.
  • The Journal of Chemical Physics, Vol. 143, Issue 24
  • DOI: 10.1063/1.4937783

The ras protein family: evolutionary tree and role of conserved amino acids
journal, May 1991

  • Valencia, Alfonso; Chardin, Pierre; Wittinghofer, Alfred
  • Biochemistry, Vol. 30, Issue 19
  • DOI: 10.1021/bi00233a001

Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions
journal, December 2012

  • Fattebert, J. -L.; Richards, D. F.; Glosli, J. N.
  • Computer Physics Communications, Vol. 183, Issue 12
  • DOI: 10.1016/j.cpc.2012.07.013

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes
journal, December 2011


Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes
journal, March 2018

  • Brandner, Astrid; Schüller, Andreas; Melo, Francisco
  • Biochemical and Biophysical Research Communications, Vol. 498, Issue 2
  • DOI: 10.1016/j.bbrc.2017.09.086

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
conference, January 2016


A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
journal, January 2004

  • Oostenbrink, Chris; Villa, Alessandra; Mark, Alan E.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20090

More bang for your buck: Improved use of GPU nodes for GROMACS 2018
journal, July 2019

  • Kutzner, Carsten; Páll, Szilárd; Fechner, Martin
  • Journal of Computational Chemistry, Vol. 40, Issue 27
  • DOI: 10.1002/jcc.26011

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
journal, August 2015

  • Kutzner, Carsten; Páll, Szilárd; Fechner, Martin
  • Journal of Computational Chemistry, Vol. 36, Issue 26
  • DOI: 10.1002/jcc.24030

Scalable molecular dynamics with NAMD on the Summit system
journal, November 2018

  • Acun, B.; Hardy, D. J.; Kale, L. V.
  • IBM Journal of Research and Development, Vol. 62, Issue 6
  • DOI: 10.1147/jrd.2018.2888986

Monte Carlo studies of the dielectric properties of water-like models
journal, September 1973


The power of coarse graining in biomolecular simulations: The power of coarse graining in biomolecular simulations
journal, August 2013

  • Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3
  • DOI: 10.1002/wcms.1169

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
journal, February 2009

  • Deng, Yuqing; Roux, Benoît
  • The Journal of Physical Chemistry B, Vol. 113, Issue 8
  • DOI: 10.1021/jp807701h

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters
journal, January 1982

  • Swope, William C.; Andersen, Hans C.; Berens, Peter H.
  • The Journal of Chemical Physics, Vol. 76, Issue 1
  • DOI: 10.1063/1.442716

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
journal, August 2013

  • Salomon-Ferrer, Romelia; Götz, Andreas W.; Poole, Duncan
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 9
  • DOI: 10.1021/ct400314y

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

  • Parrinello, M.; Rahman, A.
  • Journal of Applied Physics, Vol. 52, Issue 12
  • DOI: 10.1063/1.328693

Beyond Finite-Size Scaling in Solidification Simulations
journal, June 2006


The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008

  • Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 5
  • DOI: 10.1021/ct700324x

RAJA: Portable Performance for Large-Scale Scientific Applications
conference, November 2019

  • Beckingsale, David A.; Scogland, Thomas RW; Burmark, Jason
  • 2019 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC)
  • DOI: 10.1109/P3HPC49587.2019.00012

Martini straight: Boosting performance using a shorter cutoff and GPUs
journal, February 2016

  • de Jong, Djurre H.; Baoukina, Svetlana; Ingólfsson, Helgi I.
  • Computer Physics Communications, Vol. 199
  • DOI: 10.1016/j.cpc.2015.09.014

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
journal, September 2015


The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

  • Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
  • The Journal of Physical Chemistry B, Vol. 111, Issue 27
  • DOI: 10.1021/jp071097f

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
journal, April 2012

  • Götz, Andreas W.; Williamson, Mark J.; Xu, Dong
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 5
  • DOI: 10.1021/ct200909j

SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics
journal, January 2015

  • Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 2
  • DOI: 10.1021/ct5007746

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
journal, April 2011

  • Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B.
  • Journal of Computational Chemistry, Vol. 32, Issue 10
  • DOI: 10.1002/jcc.21787

CHARMM: The biomolecular simulation program
journal, July 2009

  • Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
  • Journal of Computational Chemistry, Vol. 30, Issue 10
  • DOI: 10.1002/jcc.21287

Martini Coarse-Grained Force Field: Extension to DNA
journal, July 2015

  • Uusitalo, Jaakko J.; Ingólfsson, Helgi I.; Akhshi, Parisa
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 8
  • DOI: 10.1021/acs.jctc.5b00286

CODATA Recommended Values of the Fundamental Physical Constants: 2014
journal, December 2016

  • Mohr, Peter J.; Newell, David B.; Taylor, Barry N.
  • Journal of Physical and Chemical Reference Data, Vol. 45, Issue 4
  • DOI: 10.1063/1.4954402

Computational Modeling of Realistic Cell Membranes
journal, January 2019


Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
journal, October 1983


LINCS: A linear constraint solver for molecular simulations
journal, September 1997


Empirical force fields for biological macromolecules: Overview and issues
journal, January 2004

  • Mackerell, Alexander D.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20082

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
journal, July 2017


Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations
journal, April 2015

  • Wassenaar, Tsjerk A.; Ingólfsson, Helgi I.; Böckmann, Rainer A.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 5
  • DOI: 10.1021/acs.jctc.5b00209