ACS Publications. Most Trusted. Most Cited. Most Read

OR SEARCH CITATIONS

My Activity
Publications
CONTENT TYPES

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Theory Comput. 2008, 4, 3, 435-447
RETURN TO ISSUEPREVArticleNEXT

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

View Author Information
Max-Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
Department of Theoretical and Computational Biophysics, Max-Planck-Institute of Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden
Cite this: J. Chem. Theory Comput. 2008, 4, 3, 435–447
Publication Date (Web):February 2, 2008
https://doi.org/10.1021/ct700301q
Copyright © 2008 American Chemical Society
Request reuse permissions

    Article Views

    36657

    Altmetric

    -

    Citations

    12941
    LEARN ABOUT THESE METRICS
    Other access options
    Get e-Alerts
    SUBJECTS:

    Abstract

    Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    *

    In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.

    Cited By

    This article is cited by 12941 publications.

    1. Fabian Schuhmann, Jessica L. Ramsay, Daniel R. Kattnig, Ilia A. Solov’yov. Structural Rearrangements of Pigeon Cryptochrome 4 Undergoing a Complete Redox Cycle. The Journal of Physical Chemistry B 2024, 128 (16) , 3844-3855. https://doi.org/10.1021/acs.jpcb.4c00424
    2. Paulina Jesionek, Barbara Hachuła, Karolina Jurkiewicz, Patryk Włodarczyk, Marek Hreczka, Kamil Kamiński, Ewa Kamińska. Variation of Activation Volume as an Indicator of the Difference in Clusterization Phenomenon Induced by H-Bonding and F−Π Stacking Interactions in Enantiomers and a Racemate of Flurbiprofen. The Journal of Physical Chemistry B 2024, 128 (16) , 4021-4032. https://doi.org/10.1021/acs.jpcb.4c00582
    3. Mi Zhou, Wenyu Zhou, Hong Yang, Luoxia Cao, Ming Li, Ping Yin, Yang Zhou. Molecular Modeling of Shockwave-Mediated Blood-Brain Barrier Opening for Targeted Drug Delivery. ACS Applied Materials & Interfaces 2024, 16 (16) , 20212-20220. https://doi.org/10.1021/acsami.4c00812
    4. Lalita Mohan Behera, Pulkit Kr. Gupta, Manaswini Ghosh, Sucharita Shadangi, Soumendra Rana. A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2. The Journal of Physical Chemistry B 2024, Article ASAP.
    5. Ander Francisco Pereira, Leandro Martínez. Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. Journal of Chemical Information and Modeling 2024, 64 (8) , 3350-3359. https://doi.org/10.1021/acs.jcim.3c01822
    6. Tian Hua Wang, Hai Ping Shao, Bing Qiang Zhao, Hong Lin Zhai. Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. Journal of Chemical Information and Modeling 2024, 64 (8) , 3503-3523. https://doi.org/10.1021/acs.jcim.3c01730
    7. Chuanbo Zheng, Hongqiong Liang, Liqiang Dai, Jin Yu, Chunhong Long. Dissecting the CRISPR Cas1-Cas2 Protospacer Binding and Selection Mechanism by Using Molecular Dynamics Simulations. The Journal of Physical Chemistry B 2024, 128 (15) , 3563-3574. https://doi.org/10.1021/acs.jpcb.3c07320
    8. Fahmi Bedoui, Mehdi Sahihi, Andres Jaramillo-Botero, William A. Goddard, III. Enhancing Multifunctionality: Optimal Properties of Iron-Oxide-Reinforced Polyvinylidene Difluoride Unveiled Through Full Atom Molecular Dynamics Simulations. Langmuir 2024, 40 (15) , 8067-8073. https://doi.org/10.1021/acs.langmuir.3c04011
    9. Fernando Bruno da Silva, Boštjan Gabrovšek, Marta Korpacz, Kamil Luczkiewicz, Szymon Niewieczerzal, Maciej Sikora, Joanna I. Sulkowska. Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks. Macromolecules 2024, Article ASAP.
    10. Yikai Liu, Tushar K. Ghosh, Guang Lin, Ming Chen. Unbiasing Enhanced Sampling on a High-Dimensional Free Energy Surface with a Deep Generative Model. The Journal of Physical Chemistry Letters 2024, 15 (14) , 3938-3945. https://doi.org/10.1021/acs.jpclett.3c03515
    11. Miriam Nnadili, Andrew N. Okafor, Teslim Olayiwola, David Akinpelu, Revati Kumar, Jose A. Romagnoli. Surfactant-Specific AI-Driven Molecular Design: Integrating Generative Models, Predictive Modeling, and Reinforcement Learning for Tailored Surfactant Synthesis. Industrial & Engineering Chemistry Research 2024, 63 (14) , 6313-6324. https://doi.org/10.1021/acs.iecr.4c00401
    12. Mansureh Kialashaki, Javad Sayyad Amin, Sohrab Zendehboudi. Further Molecular Insights into Formation of Tetra-n-Butyl Bromide Semi-Clathrate Hydrates. Industrial & Engineering Chemistry Research 2024, 63 (14) , 6411-6423. https://doi.org/10.1021/acs.iecr.3c04670
    13. Chenchen Wang, Yueyue Ji, Xingyu Huo, Xiaodan Li, Wenjia Lu, Zhaoran Zhang, Wenqi Dong, Xiangru Wang, Huanchun Chen, Chen Tan. Discovery of Salifungin as a Repurposed Antibiotic against Methicillin-Resistant Staphylococcus aureus with Limited Resistance Development. ACS Infectious Diseases 2024, Article ASAP.
    14. Liqun Liang, Yuqi Zhang, Yanyan Zhu, Juxia Bai, Yangyang Ni, Junfeng Wan, Haiyan Yue, Qingjie Zhao, Huiyu Li. Structures and Dynamics of β-Rich Oligomers of ATTR (105–115) Assembly. ACS Chemical Neuroscience 2024, 15 (7) , 1356-1365. https://doi.org/10.1021/acschemneuro.3c00574
    15. Geeta Verma, Jacob Hostert, Alex A. Summerville, Alicia S. Robang, Ricardo Garcia Carcamo, Anant K. Paravastu, Rachel B. Getman, Christine E. Duval, Julie Renner. Investigation of Rare Earth Element Binding to a Surface-Bound Affinity Peptide Derived from EF-Hand Loop I of Lanmodulin. ACS Applied Materials & Interfaces 2024, 16 (13) , 16912-16926. https://doi.org/10.1021/acsami.3c17565
    16. Mi Zhou, Liu Liu, Wenyu Zhou, Hong Yang, Ming Li, Ping Yin, Yang Zhou. How Microbubble-Enhanced Shock Waves Promote the Delivery of Lipid-siRNA across Neuronal Plasma Membrane: A Computational Study. The Journal of Physical Chemistry B 2024, 128 (12) , 2897-2904. https://doi.org/10.1021/acs.jpcb.3c07556
    17. Zhongqing Wen, Zhoukang Zhuang, Huiming Liu, Zilong Wang, Xueqiong Feng, Xiangcheng Zhu, Xiaohui Yan, Yanwen Duan, Yong Huang. DNA Interaction and Cleavage Modes of Anthraquinone-Fused Enediynes: A Study on Tiancimycins, Yangpumicins, and Their Semisynthetic Analogues. Journal of Medicinal Chemistry 2024, 67 (6) , 4624-4640. https://doi.org/10.1021/acs.jmedchem.3c02049
    18. Yu Fan, Yuxin Chen, Wangxin Ge, Lei Dong, Yanbin Qi, Cheng Lian, Xiaodong Zhou, Honglai Liu, Zhen Liu, Hongliang Jiang, Chunzhong Li. Mechanistic Insights into Surfactant-Modulated Electrode–Electrolyte Interface for Steering H2O2 Electrosynthesis. Journal of the American Chemical Society 2024, 146 (11) , 7575-7583. https://doi.org/10.1021/jacs.3c13660
    19. Fengyi Mi, Zhongjin He, Guosheng Jiang, Fulong Ning. Effect of Glucose on CH4 Hydrate Formation in Clay Nanopores and Bulk Solution: Insights from Microsecond Molecular Dynamics Simulations. ACS Sustainable Chemistry & Engineering 2024, 12 (11) , 4644-4654. https://doi.org/10.1021/acssuschemeng.3c08280
    20. Diego J. Obiol, María J. Amundarain, Fernando Zamarreño, Agustín Vietri, Silvia S. Antollini, Marcelo D. Costabel. Oleic Acid Could Act as a Channel Blocker in the Inhibition of nAChR: Insights from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 2024, 128 (10) , 2398-2411. https://doi.org/10.1021/acs.jpcb.3c07067
    21. Sara Gómez, Matteo Ambrosetti, Tommaso Giovannini, Chiara Cappelli. Close-Up Look at Electronic Spectroscopic Signatures of Common Pharmaceuticals in Solution. The Journal of Physical Chemistry B 2024, 128 (10) , 2432-2446. https://doi.org/10.1021/acs.jpcb.3c07795
    22. Jingjing Dong, Yuxiang Bai, Qin Wang, Qiuming Chen, Xiaoxiao Li, Yanli Wang, Hangyan Ji, Xiangfeng Meng, Tjaard Pijning, Birte Svensson, Lubbert Dijkhuizen, Maher Abou Hachem, Zhengyu Jin. Insights into the Structure–Function Relationship of GH70 GtfB α-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme. Journal of Agricultural and Food Chemistry 2024, 72 (10) , 5391-5402. https://doi.org/10.1021/acs.jafc.4c00104
    23. Shuang Li, Xinke Zhang, Jiaye Su. Enhanced Rectification Performance in Bipolar Janus Graphene Oxide Channels by Lateral Electric Fields. Langmuir 2024, 40 (10) , 5488-5498. https://doi.org/10.1021/acs.langmuir.4c00021
    24. Isaure Sergent, Thibault Schutz, Laurence Oswald, Georgette Obeid, Jean-François Lutz, Laurence Charles. Using Nitroxides To Model the Ion Mobility Behavior of Nitroxide-Ended Oligomers: A Bottom-up Approach To Predict Mobility Separation. Journal of the American Society for Mass Spectrometry 2024, 35 (3) , 534-541. https://doi.org/10.1021/jasms.3c00393
    25. Xiaoya Su, Zhangmin Wan, Yi Lu, Orlando Rojas. Control of the Colloidal and Adsorption Behaviors of Chitin Nanocrystals and an Oppositely Charged Surfactant at Solid, Liquid, and Gas Interfaces. Langmuir 2024, 40 (9) , 4881-4892. https://doi.org/10.1021/acs.langmuir.3c03787
    26. Taiping Hu, Yuan Guo, Guangchao Han, Yuanping Yi. Selectively Controlling the Guest–Host Contacts to Improve the Horizontal Orientation of Thermally Activated Delayed Fluorescence Emitters. The Journal of Physical Chemistry C 2024, 128 (8) , 3148-3154. https://doi.org/10.1021/acs.jpcc.3c08248
    27. Gül H. Zerze. Optimizing the Martini 3 Force Field Reveals the Effects of the Intricate Balance between Protein–Water Interaction Strength and Salt Concentration on Biomolecular Condensate Formation. Journal of Chemical Theory and Computation 2024, 20 (4) , 1646-1655. https://doi.org/10.1021/acs.jctc.2c01273
    28. Sibali Debnath, Amar H. Flood, Krishnan Raghavachari. Solvent-Dependent Folding Behavior of a Helix-Forming Aryl-Triazole Foldamer. The Journal of Physical Chemistry B 2024, 128 (7) , 1586-1594. https://doi.org/10.1021/acs.jpcb.3c04907
    29. Maurice Karrenbrock, Valerio Rizzi, Piero Procacci, Francesco Luigi Gervasio. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. The Journal of Physical Chemistry B 2024, 128 (7) , 1595-1605. https://doi.org/10.1021/acs.jpcb.3c06516
    30. Torsten John, Aldo Rampioni, David Poger, Alan E. Mark. Molecular Insights into the Dynamics of Amyloid Fibril Growth: Elongation and Lateral Assembly of GNNQQNY Protofibrils. ACS Chemical Neuroscience 2024, 15 (4) , 716-723. https://doi.org/10.1021/acschemneuro.3c00754
    31. Katsumi Hagita, Takashi Yamamoto, Hiromu Saito, Eiji Abe. Chain-Level Analysis of Reinforced Polyethylene through Stretch-Induced Crystallization. ACS Macro Letters 2024, 13 (2) , 247-251. https://doi.org/10.1021/acsmacrolett.3c00554
    32. Amal Vijay, Venkata Sai Sreyas Adury, Arnab Mukherjee. Targeting RdRp of SARS-CoV-2 with De Novo Molecule Generation. ACS Applied Bio Materials 2024, 7 (2) , 609-616. https://doi.org/10.1021/acsabm.3c00339
    33. Fangchen Hu, Yiqiu Wang, Juan Zeng, Xianming Deng, Fei Xia, Xin Xu. Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations. The Journal of Physical Chemistry B 2024, 128 (6) , 1418-1427. https://doi.org/10.1021/acs.jpcb.3c07666
    34. Chunlong Xue, Deluo Ji, Yutong Wen, Ye Zhang, Meng Zhang, Yifei Zhao, Ying Li. Critical Contribution of Water in Hybrid CO2/Water Enhanced Shale Oil Recovery: Insights from Molecular Dynamics. Energy & Fuels 2024, 38 (4) , 3066-3076. https://doi.org/10.1021/acs.energyfuels.3c04592
    35. Raquel López-Rios de Castro, Robert M. Ziolek, Martin B. Ulmschneider, Christian D. Lorenz. Therapeutic Peptides Are Preferentially Solubilized in Specific Microenvironments within PEG–PLGA Polymer Nanoparticles. Nano Letters 2024, 24 (6) , 2011-2017. https://doi.org/10.1021/acs.nanolett.3c04558
    36. Michael J. Bakker, Henrik V. Sørensen, Marie Skepö. Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation. Journal of Chemical Theory and Computation 2024, 20 (3) , 1423-1433. https://doi.org/10.1021/acs.jctc.3c00971
    37. Pravin Kumar Ramalingam, Manikandan Chandrasekaran, Poonam Gupta, Vinod Nelamangala Umesh, Tharun Bharadwaj, Naveen Banchallihundi Krishna, Roopa Lalitha, Gladstone Sigamani Gunaseelan. In Silico Screening of Chlorogenic Acids from Plant Sources against Human Translocase-I to Identify Competitive Inhibitors to Treat Diabetes. ACS Omega 2024, 9 (6) , 6561-6568. https://doi.org/10.1021/acsomega.3c07267
    38. Haihong Jia, Yan-Fang Zhang, Shixuan Du. Atomistic Insight into the Growth of Chiral Gold Clusters: A Theoretical Study. The Journal of Physical Chemistry C 2024, 128 (5) , 2037-2042. https://doi.org/10.1021/acs.jpcc.3c07492
    39. Shoaib Manzoor, Moustafa T. Gabr, Mohamed S. Nafie, Md Kausar Raza, Ashma Khan, Shahid M. Nayeem, Reem K. Arafa, Nasimul Hoda. Discovery of Quinolinone Hybrids as Dual Inhibitors of Acetylcholinesterase and Aβ Aggregation for Alzheimer’s Disease Therapy. ACS Chemical Neuroscience 2024, 15 (3) , 539-559. https://doi.org/10.1021/acschemneuro.3c00588
    40. Yue Zhao, Zhengcai Zhang. Molecular Insights into the Influence of Major Marine Ions on Carbon Dioxide Hydrate Growth. Crystal Growth & Design 2024, 24 (3) , 1380-1388. https://doi.org/10.1021/acs.cgd.3c01354
    41. Shasha Liu, Yawen Yuan, Lin Wang, Shideng Yuan, Shiling Yuan. Molecular Dynamics Study on the Effect of Polyacrylamide on Electric Field Demulsification of Oil-in-Water Emulsion. Langmuir 2024, 40 (5) , 2698-2707. https://doi.org/10.1021/acs.langmuir.3c03267
    42. Yuling Zhao, Xingyi Wang, Zhiyong Li, Huiyong Wang, Yang Zhao, Jikuan Qiu. Understanding the Positive Role of Ionic Liquids in CO2 Capture by Poly(ethylenimine). The Journal of Physical Chemistry B 2024, 128 (4) , 1079-1090. https://doi.org/10.1021/acs.jpcb.3c06510
    43. Johanna Busch, Dietmar Paschek. Computing Accurate True Self-Diffusion Coefficients and Shear Viscosities Using the OrthoBoXY Approach. The Journal of Physical Chemistry B 2024, 128 (4) , 1040-1052. https://doi.org/10.1021/acs.jpcb.3c07540
    44. Anurag Prakash Sunda, Anuj Kumar Sharma. Molecular Insights into Cu/Zn Metal Response to the Amyloid β-Peptide (1–42). ACS Physical Chemistry Au 2024, 4 (1) , 57-66. https://doi.org/10.1021/acsphyschemau.3c00041
    45. Amanda C. Macke, Jacob E. Stump, Maria S. Kelly, Jamie Rowley, Vageesha Herath, Sarah Mullen, Ruxandra I. Dima. Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. Journal of Chemical Information and Modeling 2024, 64 (2) , 470-482. https://doi.org/10.1021/acs.jcim.3c01511
    46. Xiangyuan Li, Lei Fu, Shan Zhang, Yi Dong, Lianghui Gao. Relationship between Protein-Induced Membrane Curvature and Membrane Thermal Undulation. The Journal of Physical Chemistry B 2024, 128 (2) , 515-525. https://doi.org/10.1021/acs.jpcb.3c06775
    47. Shuang Li, Xinke Zhang, Jiaye Su. Desalination Performance in Janus Graphene Oxide Channels: Geometric Asymmetry vs Charge Polarity. ACS Applied Materials & Interfaces 2024, 16 (2) , 2659-2671. https://doi.org/10.1021/acsami.3c16592
    48. Meng Chen, Yuhang Li, Runliang Zhu, Jianxi Zhu, Hongping He. Kinetics of Oriented Attachment of Mica Crystals. Inorganic Chemistry 2024, 63 (2) , 1367-1377. https://doi.org/10.1021/acs.inorgchem.3c03892
    49. Congwen Qin, Yonglei Wang, Hongshuai Gao, Xue Liu, Yi Nie, Xiaoyan Ji. Insight into the Keratin Ratio Effect of the Keratin/Cellulose Composite Fiber. ACS Applied Polymer Materials 2024, 6 (1) , 265-276. https://doi.org/10.1021/acsapm.3c01912
    50. Barbara Hachuła, Patryk Włodarczyk, Karolina Jurkiewicz, Joanna Grelska, Demetrio Scelta, Samuele Fanetti, Marian Paluch, Sebastian Pawlus, Kamil Kamiński. Pressure-Induced Aggregation of Associating Liquids as a Driving Force Enhancing Hydrogen Bond Cooperativity. The Journal of Physical Chemistry Letters 2024, 15 (1) , 127-135. https://doi.org/10.1021/acs.jpclett.3c03037
    51. Liting Fei, Meiling Wang, Mengdan Qiao, Yu Zhang, Ao Wang, Yingying Zhao, Jie Liu, Shizhao Wang, Xiaofu Guo, Jing Wang, Jingtao Bi, Panpan Zhang, Zhiyuan Guo, Yajun Yue, Junsheng Yuan, Devis Di Tommaso, Fei Li, Zhiyong Ji. Comparative Investigation of the Microstructure of MgCl2 Aqueous Solutions Using Different X-ray Scattering Sources, Raman Spectroscopy, and Atomistic Simulations. The Journal of Physical Chemistry B 2024, 128 (1) , 208-221. https://doi.org/10.1021/acs.jpcb.3c05763
    52. Chaofu Wu. Temperature-Transferable Coarse-Grained Models for Volumetric Properties of Poly(lactic Acid). The Journal of Physical Chemistry B 2024, 128 (1) , 358-370. https://doi.org/10.1021/acs.jpcb.3c07026
    53. Zhen Zhao, Lu Zhang, Hao Zhang, Guoqiang Lu, Tong Meng, Hongguo Hao, Yongmin Zhang, Jun Li, Hui Yan. Computational Insights into a CO2-Responsive Emulsion Prepared Using the Superamphiphile Assembled by Electrostatic Interactions. Langmuir 2024, 40 (1) , 938-949. https://doi.org/10.1021/acs.langmuir.3c03140
    54. Yunpeng Liu, Ren Zou, Zhongxin Chen, Wenguang Tu, Ruidong Xia, Emmanuel Iheanyichukwu Iwuoha, Xinwen Peng. Engineering a Hydrophobic–Hydrophilic Diphase in a Bi2WO6–C3N4 Heterojunction for Solar-Powered CO2 Reduction. ACS Catalysis 2024, 14 (1) , 138-147. https://doi.org/10.1021/acscatal.3c03983
    55. Xun Niu, Zhangmin Wan, Sameer E. Mhatre, Yuhang Ye, Yi Lu, Guang Gao, Long Bai, Orlando J. Rojas. Structured Emulgels by Interfacial Assembly of Terpenes and Nanochitin. ACS Nano 2023, 17 (24) , 25542-25551. https://doi.org/10.1021/acsnano.3c09533
    56. Robert M. Raddi, Vincent A. Voelz. Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding. The Journal of Physical Chemistry B 2023, 127 (50) , 10682-10690. https://doi.org/10.1021/acs.jpcb.3c04775
    57. Abhishek Acharya, Kalyanashis Jana, Ulrich Kleinekathöfer. Antibiotic Charge Profile Determines the Extent of L3 Dynamics in OmpF: An Expedited Passage for Molecules with a Positive Charge. The Journal of Physical Chemistry B 2023, 127 (50) , 10766-10777. https://doi.org/10.1021/acs.jpcb.3c04557
    58. Ravi Malik, Abhilash Chandra, Banshi Das, Amalendu Chandra. Theoretical Study of the Two-Dimensional Vibrational Sum Frequency Generation Spectroscopy of the Air–Water Interface at Varying Temperature and Its Connections to the Interfacial Structure and Dynamics. The Journal of Physical Chemistry B 2023, 127 (50) , 10880-10895. https://doi.org/10.1021/acs.jpcb.3c03205
    59. Xikun Liu, Shuya Duan, Yingying Jin, Ethan Walker, Michelle Tsao, Joshua H. Jang, Ziying Chen, Ambuj K. Singh, Kristi Lazar Cantrell, Helgi I. Ingolfsson, Steven K. Buratto, Michael T. Bowers. Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43307–319 Aggregation. ACS Chemical Neuroscience 2023, 14 (24) , 4395-4408. https://doi.org/10.1021/acschemneuro.3c00582
    60. Kris Strunge, Tucker Burgin, Thaddeus W. Golbek, Steven J. Roeters, Jim Pfaendtner, Tobias Weidner. Umbrella-like Helical Structure of α-Synuclein at the Air–Water Interface Observed with Experimental and Theoretical Sum Frequency Generation Spectroscopy. The Journal of Physical Chemistry Letters 2023, 14 (49) , 11030-11035. https://doi.org/10.1021/acs.jpclett.3c02543
    61. Yonghui Li, Xujun Pu, Kun Ge, Lunzhao Yi, Dabing Ren, Ying Gu, Shuo Wang. Engineering an Antifouling Electrochemical Sensing Platform Based on an All-in-One Peptide and a Hierarchical β-Bi2O3–Au Microsphere for Vancomycin Detection in Food. Journal of Agricultural and Food Chemistry 2023, 71 (49) , 19866-19878. https://doi.org/10.1021/acs.jafc.3c07570
    62. Si Zheng, Yufan Ji, Nanxing Li, Lin Zhang. Biomimetic Design of Peptide Inhibitor to Block CD47/SIRPα Interactions. Langmuir 2023, 39 (49) , 18101-18112. https://doi.org/10.1021/acs.langmuir.3c02898
    63. Hyuntae Kim, Balázs Fábián, Gerhard Hummer. Neighbor List Artifacts in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2023, 19 (23) , 8919-8929. https://doi.org/10.1021/acs.jctc.3c00777
    64. Shitong Zhang, Yanjing He, Shengtang Liu, Zhengqing Zhang, Chongli Zhong. Metal–Organic Framework Membrane Constructor: A Tool for High-Throughput Construction of Metal–Organic Framework Membrane Models. Journal of Chemical Information and Modeling 2023, 63 (23) , 7476-7486. https://doi.org/10.1021/acs.jcim.3c01678
    65. Akshay Malik, Hemant K. Kashyap. Solvation Shell Anatomy of H2S and CO Dissolved in Reline and Ethaline Deep Eutectic Solvents. The Journal of Physical Chemistry B 2023, 127 (48) , 10392-10403. https://doi.org/10.1021/acs.jpcb.3c03411
    66. Safwat Abdel-Azeim, Ahmed Al-Yaseri, Kion Norrman, Pramod Patil, Abdulaziz Qasim, Ali Yousef. Wettability of Caprock–H2–Water: Insights from Molecular Dynamic Simulations and Sessile-Drop Experiment. Energy & Fuels 2023, 37 (23) , 19348-19356. https://doi.org/10.1021/acs.energyfuels.3c03198
    67. Asim Bisoi, Sunipa Sarkar, Prashant Chandra Singh. Hydrophobic Interaction-Induced Topology-Independent Destabilization of G-Quadruplex. Biochemistry 2023, 62 (23) , 3430-3439. https://doi.org/10.1021/acs.biochem.3c00585
    68. Jeffrey D. Tamucci, Nathan N. Alder, Eric R. May. Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations. Molecular Pharmaceutics 2023, 20 (12) , 6114-6129. https://doi.org/10.1021/acs.molpharmaceut.3c00480
    69. Kennet J. Rueda Espinosa, Alexei A. Kananenka, Alexander A. Rusakov. Novel Computational Chemistry Infrastructure for Simulating Astatide in Water: From Basis Sets to Force Fields Using Particle Swarm Optimization. Journal of Chemical Theory and Computation 2023, 19 (22) , 7998-8012. https://doi.org/10.1021/acs.jctc.3c00826
    70. Leonard P. Heinz, Helmut Grubmüller. Why Solvent Response Contributions to Solvation Free Energies Are Compatible with Ben-Naim’s Theorem. Journal of Chemical Theory and Computation 2023, 19 (22) , 8013-8019. https://doi.org/10.1021/acs.jctc.3c00655
    71. Andreas Steinhoff, Alexandra Höltzel, Ulrich Tallarek. The Solvation Shell of Small Solutes in Aqueous–Organic Solvent Mixtures and Its Implications for Reversed-Phase Liquid Chromatography. The Journal of Physical Chemistry B 2023, 127 (46) , 10052-10066. https://doi.org/10.1021/acs.jpcb.3c05492
    72. Luise Jacobsen, Laura Lydersen, Himanshu Khandelia. ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations. The Journal of Physical Chemistry B 2023, 127 (45) , 9685-9696. https://doi.org/10.1021/acs.jpcb.3c03473
    73. Almaz Khabibrakhmanov, Dmitry V. Fedorov, Alexandre Tkatchenko. Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators. Journal of Chemical Theory and Computation 2023, 19 (21) , 7895-7907. https://doi.org/10.1021/acs.jctc.3c00797
    74. Francini Fonseca Lopez, Jiayuan Miao, Jovan Damjanovic, Luca Bischof, Michael B. Braun, Yingjie Ling, Marcus D. Hartmann, Yu-Shan Lin, Joshua A. Kritzer. Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. Journal of Chemical Information and Modeling 2023, 63 (21) , 6925-6937. https://doi.org/10.1021/acs.jcim.3c01337
    75. Yan Xiang, Yu-Hang Tang, Zheng Gong, Hongyi Liu, Liang Wu, Guang Lin, Huai Sun. Efficient Exploration of Chemical Compound Space Using Active Learning for Prediction of Thermodynamic Properties of Alkane Molecules. Journal of Chemical Information and Modeling 2023, 63 (21) , 6515-6524. https://doi.org/10.1021/acs.jcim.3c01430
    76. Subinoy Adhikari, Jagannath Mondal. Machine Learning Subtle Conformational Change due to Phosphorylation in Intrinsically Disordered Proteins. The Journal of Physical Chemistry B 2023, 127 (44) , 9433-9449. https://doi.org/10.1021/acs.jpcb.3c05136
    77. Chunlei Zhang, Haihong Jia, Yan-Fang Zhang, Shixuan Du. Capping Layer Determined Self-assembly of Au–Ag Bimetallic Janus Nanoparticles at An Oil/Water Interface by Molecular Dynamics Simulations. The Journal of Physical Chemistry B 2023, 127 (44) , 9543-9549. https://doi.org/10.1021/acs.jpcb.3c04600
    78. Darren T. Gass, Michael S. Cordes, Sebastian N. Alberti, H. Jamie Kim, Elyssia S. Gallagher. Evidence of H/D Exchange within Metal-Adducted Carbohydrates after Ion/Ion-Dissociation Reactions. Journal of the American Chemical Society 2023, 145 (44) , 23972-23985. https://doi.org/10.1021/jacs.3c05793
    79. Tangming Mo, Jianguo Zhou, Haoyu He, Bingzheng Zhu. Oscillation Charging Dynamics in Nanopore Supercapacitors with Organic Electrolyte. ACS Applied Materials & Interfaces 2023, 15 (44) , 51274-51280. https://doi.org/10.1021/acsami.3c12913
    80. Rudolf G. Abdelmessih, Jiaming Xu, Francisco R. Hung, Debra T. Auguste. Integration of an LPAR1 Antagonist into Liposomes Enhances Their Internalization and Tumor Accumulation in an Animal Model of Human Metastatic Breast Cancer. Molecular Pharmaceutics 2023, 20 (11) , 5500-5514. https://doi.org/10.1021/acs.molpharmaceut.3c00348
    81. Yue Zhao, Fansen Zeng, Dachuan Zhao, Lei Lin, Zhengcai Zhang. Molecular Study on Carbon Dioxide Hydrate Formation in Salty Water. Crystal Growth & Design 2023, 23 (11) , 8361-8369. https://doi.org/10.1021/acs.cgd.3c01018
    82. Ping Gao, Fei Zhang, Xingchao Wang, Miaomiao Wu, Qian Xiang, Aikai Yang, Ying Sun, Jixi Guo, Yudai Huang. Ultrastable Dendrite-Free Potassium Metal Batteries Enabled by Weakly-Solvated Electrolyte. ACS Nano 2023, 17 (20) , 20325-20333. https://doi.org/10.1021/acsnano.3c06368
    83. Vera Truttmann, Adea Loxha, Rareş Banu, Ernst Pittenauer, Sami Malola, María Francisca Matus, Yuchen Wang, Elizabeth A. Ploetz, Günther Rupprechter, Thomas Bürgi, Hannu Häkkinen, Christine Aikens, Noelia Barrabés. Directing Intrinsic Chirality in Gold Nanoclusters: Preferential Formation of Stable Enantiopure Clusters in High Yield and Experimentally Unveiling the “Super” Chirality of Au144. ACS Nano 2023, 17 (20) , 20376-20386. https://doi.org/10.1021/acsnano.3c06568
    84. Raphael V. R. Dias, Renan P. Pedro, Murilo N. Sanches, Giovana C. Moreira, Vitor B. P. Leite, Icaro P. Caruso, Fernando A. de Melo, Leandro C. de Oliveira. Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding. Journal of Chemical Information and Modeling 2023, 63 (20) , 6344-6353. https://doi.org/10.1021/acs.jcim.3c00955
    85. Luc Bondaz, Anshaj Ronghe, Shaoxian Li, Kristia̅ns Čerņevičs, Jian Hao, Oleg V. Yazyev, K. Ganapathy Ayappa, Kumar Varoon Agrawal. Selective Photonic Gasification of Strained Oxygen Clusters on Graphene for Tuning Pore Size in the Å Regime. JACS Au 2023, 3 (10) , 2844-2854. https://doi.org/10.1021/jacsau.3c00395
    86. João T. S. Coimbra, Pedro A. Fernandes, Maria J. Ramos. Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 2023, 63 (20) , 6354-6365. https://doi.org/10.1021/acs.jcim.3c00962
    87. Roxanne Vasquez, Leonardo Batista, Teobaldo Cuya. Computational Study on the Enzyme–Ligand Relationship between Cannabis Phytochemicals and Human Acetylcholinesterase: Implications in Alzheimer’s Disease. The Journal of Physical Chemistry B 2023, 127 (41) , 8780-8795. https://doi.org/10.1021/acs.jpcb.3c04315
    88. Junfang Zhang, Michael B. Clennell, David N. Dewhurst. Transport Properties of NaCl in Aqueous Solution and Hydrogen Solubility in Brine. The Journal of Physical Chemistry B 2023, 127 (41) , 8900-8915. https://doi.org/10.1021/acs.jpcb.3c03863
    89. Wenchuan Liu, Dengwei Jing. Droplet Rolling Transport on Hydrophobic Surfaces Under Rotating Electric Fields: A Molecular Dynamics Study. Langmuir 2023, 39 (41) , 14660-14669. https://doi.org/10.1021/acs.langmuir.3c01989
    90. Nikhil Maroli. Riding the Wave: Unveiling the Conformational Waves from RBD of SARS-CoV-2 Spike Protein to ACE2. The Journal of Physical Chemistry B 2023, 127 (40) , 8525-8536. https://doi.org/10.1021/acs.jpcb.3c04366
    91. Mikhail Ivanov, Maksim Posysoev, Alexander P. Lyubartsev. Coarse-Grained Modeling Using Neural Networks Trained on Structural Data. Journal of Chemical Theory and Computation 2023, 19 (19) , 6704-6717. https://doi.org/10.1021/acs.jctc.3c00516
    92. Weiwei He, Xiangyun Qiu, Serdal Kirmizialtin. Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA–DNA Interactions. Journal of Chemical Theory and Computation 2023, 19 (19) , 6827-6838. https://doi.org/10.1021/acs.jctc.3c00520
    93. Yamiao Zhang, Jianlong Xiu, Lina Yi, Guangzhi Liao, Li Yu, Lixin Huang. Simulation Study on Molecular Behavior of Rhamnolipids and Biobased Zwitterionic Surfactants at the Oil/Water Interface: Effect of Rhamnose Moiety Structures. ACS Omega 2023, 8 (40) , 36655-36661. https://doi.org/10.1021/acsomega.3c02253
    94. Rongrong Chu, Shuang Hao, Wenxiong Shi, Yunxia Hu. Quantitatively Unveiling the Structure–Activity Relationship of Polyamide Nanofiltration Membranes with Complex Structures. Langmuir 2023, 39 (38) , 13503-13511. https://doi.org/10.1021/acs.langmuir.3c01440
    95. Kun Gao, Shidi Ju, Shuning Li, Shaohua Zhang, Jiajia Liu, Tian Yang, Jinsheng Lv, Wenjing Yu, Zhipan Zhang. Decoupling Electrochromism and Energy Storage for Flexible Quasi-Solid-State Aqueous Electrochromic Batteries with High Energy Density. ACS Nano 2023, 17 (18) , 18359-18371. https://doi.org/10.1021/acsnano.3c05702
    96. Fei Liu, Jin Wang. ATP Acts as a Hydrotrope to Regulate the Phase Separation of NBDY Clusters. JACS Au 2023, 3 (9) , 2578-2585. https://doi.org/10.1021/jacsau.3c00391
    97. Poonam Pandey, Alexander D. MacKerell, Jr.. Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. Journal of Chemical Information and Modeling 2023, 63 (18) , 5903-5915. https://doi.org/10.1021/acs.jcim.3c00514
    98. Zheng Xu, Yunpo Sun, Jian Xie, Shuangyu Liu, Yang Nie, Xiongwen Xu, Jian Tu, Fang Chen, Tiejun Zhu, Xinbing Zhao. Nonflammable Organics/H2O Hybrid Electrolyte with a High Organics Ratio toward Safe and Sustainable Aqueous Na/Zn Hybrid Batteries. ACS Sustainable Chemistry & Engineering 2023, 11 (38) , 14176-14185. https://doi.org/10.1021/acssuschemeng.3c03936
    99. Hyeyeon Kim, Rakesh Parida, Kounghwa Youn, Sang Chul Shin, Gyochang Keum, Jin Yong Lee, Eun-Kyoung Bang, Soyeon Yoo. Amyloid β Aggregate-Sensitive Red Fluorescent Dipolar Probes. ACS Applied Optical Materials 2023, 1 (9) , 1513-1526. https://doi.org/10.1021/acsaom.3c00159
    100. Johanna Busch, Dietmar Paschek. OrthoBoXY: A Simple Way to Compute True Self-Diffusion Coefficients from MD Simulations with Periodic Boundary Conditions without Prior Knowledge of the Viscosity. The Journal of Physical Chemistry B 2023, 127 (37) , 7983-7987. https://doi.org/10.1021/acs.jpcb.3c04492
    Load more citations
    Download PDF

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect