Treffer: GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.
Title:
GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.
Authors:
Moe S; Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States., Chipot C; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019, Université de Lorraine, 54506 Vandœuvre-les-Nancy Cedex, France.; Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States., Roux B; Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States.
Source:
Journal of chemical information and modeling [J Chem Inf Model] 2025 Dec 22; Vol. 65 (24), pp. 13338-13345. Date of Electronic Publication: 2025 Dec 09.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE
Imprint Name(s):
Original Publication: Washington, D.C. : American Chemical Society, c2005-
MeSH Terms:
References:
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J Chem Theory Comput. 2015 Aug 11;11(8):3919-31. (PMID: 26300709)
Nat Methods. 2017 Jan;14(1):71-73. (PMID: 27819658)
J Mol Biol. 2001 Jan 26;305(4):839-49. (PMID: 11162096)
Biophys J. 1994 Apr;66(4):1180-4. (PMID: 8038389)
Proteins. 2004 Sep 1;56(4):738-52. (PMID: 15281127)
Biochemistry. 2006 Aug 8;45(31):9363-73. (PMID: 16878971)
J Chem Phys. 2015 Jan 14;142(2):024101. (PMID: 25591332)
Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12224-9. (PMID: 19592512)
Science. 1995 May 26;268(5214):1144-9. (PMID: 7761829)
Proteins. 2009 Nov 15;77(3):570-88. (PMID: 19533744)
J Phys Chem B. 2012 Aug 2;116(30):8805-11. (PMID: 22694266)
Biochemistry. 1995 Apr 11;34(14):4714-23. (PMID: 7718577)
Biochim Biophys Acta. 1983 Feb 15;742(3):576-85. (PMID: 6838890)
Curr Pharm Des. 2013;19(23):4182-90. (PMID: 23170880)
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):E1009-18. (PMID: 22025687)
Proteins. 2011 Dec;79(12):3420-36. (PMID: 22002801)
J Chem Theory Comput. 2010 Apr 13;6(4):1401-1412. (PMID: 20514364)
Curr Opin Struct Biol. 2022 Dec;77:102498. (PMID: 36410222)
J Mol Biol. 2010 Oct 22;403(2):313-27. (PMID: 20816989)
J Phys Chem B. 2025 Aug 14;129(32):8144-8155. (PMID: 40758407)
J Chem Theory Comput. 2022 Dec 13;18(12):7510-7527. (PMID: 36377980)
J Mol Biol. 2005 Oct 21;353(2):427-46. (PMID: 16168437)
J Chem Theory Comput. 2011 Sep 13;7(9):2728-2739. (PMID: 22125476)
J Chem Inf Model. 2020 Jun 22;60(6):3030-3042. (PMID: 32348143)
Langmuir. 2005 Jul 5;21(14):6210-9. (PMID: 15982022)
J Chem Phys. 2014 Sep 21;141(11):114107. (PMID: 25240345)
J Chem Theory Comput. 2015 Apr 14;11(4):1864-74. (PMID: 26574392)
J Biol Chem. 1967 Oct 25;242(20):4731-5. (PMID: 6061418)
Nature. 2005 Feb 10;433(7026):633-8. (PMID: 15660107)
J Chem Theory Comput. 2016 Nov 8;12(11):5411-5421. (PMID: 27709966)
Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11337-42. (PMID: 23798426)
Nat Struct Mol Biol. 2006 Apr;13(4):311-8. (PMID: 16532009)
J Chem Theory Comput. 2017 Dec 12;13(12):5933-5944. (PMID: 29111720)
Biochemistry. 1998 Jun 16;37(24):8643-52. (PMID: 9628726)
Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):522-46. (PMID: 9761848)
J Chem Phys. 2020 Jul 28;153(4):044130. (PMID: 32752662)
J Phys Chem B. 1998 Apr 30;102(18):3586-616. (PMID: 24889800)
J Phys Chem B. 2020 Jul 30;124(30):6520-6528. (PMID: 32628482)
Proteins. 2002 Jun 1;47(4):469-80. (PMID: 12001225)
J Comput Chem. 2016 Sep 15;37(24):2171-80. (PMID: 27405884)
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Sep;60(3):2721-6. (PMID: 11970075)
J Biol Chem. 2021 Jan-Jun;296:100718. (PMID: 33989634)
Science. 1989 Jun 2;244(4908):1069-72. (PMID: 2727695)
J Chem Phys. 2007 Apr 28;126(16):164112. (PMID: 17477594)
Biochemistry. 1998 Mar 10;37(10):3229-36. (PMID: 9536962)
J Chem Inf Model. 2020 Nov 23;60(11):5301-5307. (PMID: 32805108)
J Am Chem Soc. 2019 Aug 28;141(34):13421-13433. (PMID: 31382734)
Biophys J. 2022 Apr 5;121(7):1336-1347. (PMID: 35151630)
Biophys J. 2009 Jul 8;97(1):50-8. (PMID: 19580743)
J Chem Theory Comput. 2010 Feb 9;6(2):560-568. (PMID: 20148176)
J Phys Chem B. 2018 May 31;122(21):5466-5486. (PMID: 29649876)
Nat Struct Biol. 1997 Mar;4(3):180-4. (PMID: 9164455)
Nature. 2010 Jul 8;466(7303):272-5. (PMID: 20613845)
Biophys J. 1997 May;72(5):2075-93. (PMID: 9129810)
J Mol Biol. 2009 Apr 10;387(4):986-92. (PMID: 19136007)
Mol Simul. 2014 Jan 1;40(10-11):830-838. (PMID: 25309035)
Proteins. 1997 Apr;27(4):523-44. (PMID: 9141133)
Proteins. 2014 Jul;82(7):1319-31. (PMID: 24375620)
J Am Chem Soc. 2015 Aug 5;137(30):9543-6. (PMID: 26186663)
J Chem Theory Comput. 2025 Feb 25;21(4):1762-1786. (PMID: 39919102)
J Chem Theory Comput. 2011 Jun 14;7(6):1962-1978. (PMID: 21687785)
J Comput Chem. 2004 Dec;25(16):2038-48. (PMID: 15481090)
J Biol Chem. 2007 May 18;282(20):15179-86. (PMID: 17360718)
Proteins. 2011 Mar;79(3):685-702. (PMID: 21287606)
J Phys Chem Lett. 2024 Apr 11;15(14):3796-3804. (PMID: 38557030)
J Chem Theory Comput. 2022 Oct 11;18(10):6148-6160. (PMID: 36128977)
J Phys Chem B. 2022 Sep 15;126(36):6868-6877. (PMID: 36049129)
J Chem Theory Comput. 2014 Mar 11;10(3):1341-1352. (PMID: 24803862)
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273. (PMID: 23341755)
Q Rev Biophys. 2013 May;46(2):181-209. (PMID: 23889892)
Biochemistry. 1993 Aug 10;32(31):8045-56. (PMID: 8347606)
Biophys J. 2010 Mar 3;98(5):872-80. (PMID: 20197041)
J Chem Theory Comput. 2015 Aug 11;11(8):3919-31. (PMID: 26300709)
Nat Methods. 2017 Jan;14(1):71-73. (PMID: 27819658)
J Mol Biol. 2001 Jan 26;305(4):839-49. (PMID: 11162096)
Biophys J. 1994 Apr;66(4):1180-4. (PMID: 8038389)
Proteins. 2004 Sep 1;56(4):738-52. (PMID: 15281127)
Biochemistry. 2006 Aug 8;45(31):9363-73. (PMID: 16878971)
J Chem Phys. 2015 Jan 14;142(2):024101. (PMID: 25591332)
Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12224-9. (PMID: 19592512)
Science. 1995 May 26;268(5214):1144-9. (PMID: 7761829)
Proteins. 2009 Nov 15;77(3):570-88. (PMID: 19533744)
J Phys Chem B. 2012 Aug 2;116(30):8805-11. (PMID: 22694266)
Grant Information:
R35 GM152124 United States GM NIGMS NIH HHS; S10 OD028655 United States OD NIH HHS
Substance Nomenclature:
0 (Protons)
Entry Date(s):
Date Created: 20251209 Date Completed: 20251222 Latest Revision: 20260103
Update Code:
20260103
PubMed Central ID:
PMC12756948
DOI:
10.1021/acs.jcim.5c02162
PMID:
41364919
Database:
MEDLINE
Weitere Informationen
We introduce a GPU-based implementation of the hybrid nonequilibrium molecular dynamics-Monte Carlo constant-pH simulation method within the NAMD package. Benchmark results demonstrate that the new implementation achieves a substantial speedup over its CPU-based counterpart, while preserving the same level of accuracy. This performance gain expands the practical applicability of pH-controlled, all-atom simulations across a wide range of biomolecular systems. Although exhaustive enumeration of all possible protonation-state combinations remains a major challenge within conventional molecular dynamics frameworks, the ability to simulate at a defined pH─combined with GPU-acceleration─offers a powerful and efficient means for investigating dynamic protonation profiles of biomolecules.