GROMACS software development Professors and Supervisors

Erik LindahlView profile

Professor

University of YorkUnited Kingdom

Erik Lindahl is a Professor at Stockholm University with a co-affiliation at KTH Royal Institute of Technology. He leads a research group at SciLifeLab focused on membrane proteins, particularly ion channels and pumps that transport ions for nervous system functioning. His work bridges computational and experimental approaches in biophysics. Dr. Lindahl's research spans multiple disciplines within biophysics and computational biology. His team uses bioinformatics to build models of human receptors based on bacterial structures, biomolecular simulations to understand molecular-level interactions, and experimental techniques like electrophysiology and spectroscopy. Key research areas include voltage-gated ion channels, ligand-gated ion channels, ATPase pumps, and allosteric modulation. His group has made significant contributions to understanding how these molecular machines function at the atomic level. The recent publications reveal a strong focus on the structural and functional mechanisms of ion channels and membrane proteins. His work combines molecular dynamics simulations with experimental validation, particularly in the areas of voltage sensing, alcohol modulation of receptors, and ion pump mechanisms. The publications demonstrate expertise in both computational methodology development and biological application. Dr. Lindahl leads a substantial research group with multiple PhD students, postdocs, and researchers. His team collaborates extensively, as evidenced by the multi-institutional authorship on his publications. He also contributes to major methodological developments in computational biophysics, most notably through his involvement with the GROMACS molecular simulation package. The research group operates at the intersection of several laboratories and facilities, leveraging both computational resources and experimental setups for electrophysiology and structural biology. This integrated approach allows the team to tackle complex questions about membrane protein function from multiple angles, combining theoretical modeling with empirical validation.

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Alessandra VillaView profile

Researcher

KTH Royal Institute of TechnologySweden

Alessandra Villa is a researcher at KTH Royal Institute of Technology, affiliated with the PDC Center for High Performance Computing. She contributes to the European Center of Excellence BioExcel and participates in the GROMACS user-driven development. Her work spans multiple institutions in Germany (Goethe University, MPI for Polymer Science) and Sweden (Karolinska Institute, Molecular Biophysics Stockholm). University of Milano - Degree in Chemistry (1995) University of Milano - PhD in Physical Chemistry (2000) Karolinska Institute - Docent in Biochemistry (2015) Her research focuses on elucidating molecular interactions governing cellular processes through multiscale biomolecular simulations . She specializes in atomistic and coarse-grained molecular modeling , particularly for nucleic acids and axonal membrane systems , combining experimental data with computational approaches. Recent publications highlight her work in molecular dynamics simulations of tRNA-enzyme interactions (2024), axonal injury mechanisms (2023), and nucleic acid structural studies (2017-2019). Key trends include biomolecular force field development , RNA conformational analysis , and lipid membrane mechanical behavior . Marie Curie Fellowship Docent in Biochemistry (Karolinska Institute, 2015) She actively develops GROMACS training materials , contributes to the Competency Hub, and manages the GROMACS forum. Her projects include multiscale modeling of axonal components and density-guided simulations combining cryo-EM data .

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Viet Hoang ManView profile

Researcher

University of PittsburghUnited States

Dr. Viet Hoang Man is a Researcher at the School of Pharmacy, University of Pittsburgh. He holds a PhD in Biophysics from the Institute of Physics, Polish Academy of Sciences (Poland), and completed postdoctoral training at the Department of Physics, North Carolina State University. His expertise spans Cryolab techniques, solid-state physics, and biophysics, with a focus on molecular dynamics simulations, protein-ligand binding affinity calculations, and amyloid aggregation studies. He actively contributes to AMBER and GROMACS software development for molecular dynamics. Education: Bachelor's and Master's in Physics from Hanoi University of Science, Vietnam PhD in Biophysics from Institute of Physics, Polish Academy of Sciences Research Focus: Neurodegenerative diseases, drug design, and computational methods for protein aggregation. Affiliations: Computational Genomics Screening Center His research bridges biophysics and pharmaceutical sciences, emphasizing computational approaches to address protein aggregation mechanisms and drug development.

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Sarath Chandra DantuView profile

Lecturer

Brunel University LondonUnited Kingdom

Sarath Chandra Dantu is a Lecturer in the Department of Computer Science at Brunel University London. He holds a PhD in Biology from the University of Göttingen (2012) and an M.Res in Bioinformatics from the University of Glasgow (2008). His research focuses on computational models for rational biomolecular design. Education: PhD in Biology (2012), University of Göttingen M.Res Bioinformatics (2008), University of Glasgow Dantu's work integrates molecular dynamics simulations (using GROMACS/AMBER) with residue-residue coevolution analysis to advance protein engineering and drug design. He leads the development of PyCoM , a Python library and database for coevolutionary analysis, and DyNoPy , a pipeline for dynamic coupling analysis. His research leverages high-performance computing facilities like ARCHER2 and MMM Young. Key collaborations include Dr. Dalia Chakrabarty (University of York), Dr. James Garnett (KCL), Professor Shozeb Haider (UCL), and international partners at IIT Bombay, UT Dallas, and CNRS Lille. Selected publications reveal trends in protein coevolution analysis, molecular dynamics profiling, and computational drug discovery. Notably, his 2024 work on PyCoM provides a framework for large-scale residue-residue coevolution studies, while his 2025 paper explores graph-based methods for identifying functionally critical residues. Key Software Contributions: PyCoM - Open-source coevolution matrix database DyNoPy - Dynamic coupling computational pipeline

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Cathrine BerghView profile

Researcher

KTH Royal Institute of TechnologySweden

Cathrine Bergh is a postdoctoral researcher at the PDC Center for High-Performance Computing, KTH Royal Institute of Technology. Her work focuses on computational biophysics, particularly the simulation and analysis of biomolecular systems like ion channels in the nervous system. She develops physics-based and AI-driven methods to compute free energy landscapes and predict protein behavior under genetic or chemical perturbations. Education: Engineering Physics, KTH Royal Institute of Technology (2018) Ph.D., Theoretical Biophysics, KTH Royal Institute of Technology (2023) Her research integrates molecular dynamics (MD) simulations, elastic network models, and Markov state modeling to study conformational transitions in biological macromolecules. She specializes in high-performance computing to optimize large-scale simulations and contributes to software like GROMACS. Recent publications highlight her expertise in lipid binding sites, pH-dependent state transitions, and computational methods for protein dynamics. Her work bridges structural biology, computational modeling, and neuroscience.

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Yihan ShaoView profile

Associate Professor

University of OklahomaUnited States

Yihan Shao is an Associate Professor in the Department of Chemistry and Biochemistry at the University of Oklahoma. He holds a B.S. from Nanjing University (1993) and a Ph.D. from UC Berkeley (2002). Prior to OU, he served as a Principal Scientist at Q-Chem Inc. (2002–2016). His research focuses on computational chemistry applications, theory, and software development, particularly in enzyme reactions, photochemical processes, and polariton chemistry. Key areas include free energy simulations, quantum mechanical phenomena in complex environments, and molecular modeling using QM/MM approaches. Shao leads a research group producing impactful work in Enzyme catalysis mechanisms (e.g., CRISPR-Cas9) Photochemical reactions in photon cavities Development of machine learning potentials His work has been supported by grants such as the NIH R35 and NSF awards. Shao has advised numerous students and collaborators, including notable achievements like Xiaoliang Pan’s 2019 PCCP HOT Article and Junjie Yang’s 2021 JCP Editor’s Pick. His lab also contributes to software advancements, including the Q-Chem package and CHARMMing interface. Current projects include polariton chemistry simulations and enzyme reaction modeling. Scientific awards include the 2018 Ralph E. Powe Junior Faculty Enhancement Award and grants for spin-crossing reactions and polariton chemistry. Shao’s research bridges theory and application, addressing challenges in quantum processes and chemical systems.

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Ilpo Tapio VattulainenView profile

Professor

University of HelsinkiFinland

Ilpo Tapio Vattulainen is a Professor of Physics at the University of Helsinki, leading the Biological Physics group. He serves as the supervisor for multiple doctoral programs including Biomedicine, Chemistry and Molecular Sciences, Integrative Life Science, and Materials Research and Nanosciences. His research focuses on computational biophysics, multi-scale simulations, and AI/ML applications to study membrane receptors, lipids, protein function, and disease mechanisms such as viral infections, cancers, and dry eye syndrome. Key research areas include lipid-protein interactions, viral entry mechanisms, and drug delivery systems. Recent projects include investigating E-cigarette additive effects on pulmonary surfactants and developing scalable simulation tools for biomolecular systems. He leads several funded projects, including the Jusélius/Vattulainen 2024-27 initiative and the Academy of Finland's BarrierForce program. Vattulainen also serves on editorial boards and actively participates in international conferences and peer-review activities. His lab is part of the Biological Physics and Soft Matter research group, emphasizing interdisciplinary approaches to bridge computational and experimental studies.

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Noora AhoView profile

Researcher

Saarland UniversityGermany

Noora Aho is a Postdoctoral Researcher at Saarland University, Germany, working in Professor Jochen Hub's Computational Biophysics group since July 2023. She specializes in molecular modeling of biological systems using GROMACS, with expertise in constant pH molecular dynamics (CpHMD) for membrane-protein complexes and photoacids, alongside SAXS-MD integration for structural validation. Her educational background includes: Postdoc in Computational Biophysics, Saarland University (2023–present) PhD in Computational Chemistry, University of Jyväskylä, Finland (2018–2023), supervised by Prof. Gerrit Groenhof Teacher’s Pedagogical Studies, University of Jyväskylä (2020–2022) MSc in Physics, University of Helsinki, Finland (2015–2018), thesis with Prof. Ilpo Vattulainen BSc in Physics, University of Jyväskylä, Finland (2012–2015) Dr. Aho's research centers on pH-dependent biomolecular simulations, developing CpHMD methodologies for GROMACS and coupling MD with experimental SAXS data. Her work targets membrane-embedded systems where protonation dynamics govern function, enabling accurate modeling of biological processes like proton transport. Her 2022–2023 publications reveal a focused trajectory in computational methodology: advancing CpHMD implementation (JCTC 2022), establishing best practices (ChemRXiv 2023), and applying these to proton diffusion in membranes (JCTC 2022). These contributions strengthen the toolkit for simulating pH-sensitive biomolecules, particularly membrane proteins. No scientific awards or fellowships were documented in the source material. As a recent postdoc, Dr. Aho has no advisory roles or grant leadership mentioned; her contributions center on collaborative research within Hub's group. She actively engages with the GROMACS community through GitLab, troubleshooting forcefield updates and simulation protocols for CpHMD. She operates within Saarland University's Computational Biophysics group, which develops advanced simulation techniques for biomolecular systems. The team emphasizes open-source tool development (e.g., GROMACS-SWAXS) and interdisciplinary approaches bridging computation with biophysical experiments.

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Bernhard ReuterView profile

Researcher

University of TübingenGermany

Bernhard Reuter is a researcher at the University of Tübingen in the Department of Computer Science , focusing on machine learning methods for biomedical data . He develops tools for drug-resistance prediction in tuberculosis and HIV, and created the Generalized Perron Cluster Cluster Analysis (G-PCCA) for modeling non-equilibrium systems. Education Dr. rer. nat. in Theoretical Physics (2018), University of Kassel Dipl.-Phys. in Physics (2013), University of Kassel Research Highlights : His work bridges machine learning with biomolecular dynamics , particularly in drug resistance prediction and non-equilibrium system modeling . Publications in Nature Methods and Journal of Chemical Physics demonstrate his technical contributions. Awards GDCH travel scholarships (2014, 2016) CINSAT poster award (2013) Doctoral scholarship (2013) Studienstiftung scholarship (2006) He has contributed to open-source software projects like pyGPCCA and COmic , and collaborated with institutions including the Max Planck Institute for Biological Cybernetics .

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Erik LindahlView profile

Professor

Stockholm UniversitySweden

Erik Lindahl is a Professor of Theoretical Chemistry at the Department of Biochemistry and Biophysics, Stockholm University. His research group is primarily located at the Science for Life Laboratory, a joint research environment for Stockholm University, KTH Royal Institute of Technology, and Karolinska Institutet. Lindahl serves as deputy director of the Swedish e-Science Research Center (SeRC), sits on the steering committee for the national program in Data-driven Life Sciences at SciLifeLab, and is program manager for Stockholm University's part of a joint master's program in molecular techniques for the life sciences. He also serves as vice section dean for chemistry and is involved in creating a Swedish node within CECAM. Lindahl's research focuses on understanding the structure and function of ligand-gated ion channels, particularly in the human nervous system. His group combines experimental and computational approaches, including bioinformatics for building receptor models, molecular dynamics simulations to understand molecular interactions, and experimental techniques like electrophysiology and spectroscopy. They have made significant contributions to understanding how voltage-gated and ligand-gated ion channels function, including determining molecular mechanisms of channel opening and identifying binding sites for molecules that modulate neural signaling. The group is also a leader in developing computational tools for life sciences, particularly the widely used GROMACS software package for molecular dynamics simulations and methods for cryo-electron microscopy data analysis through the RELION program. Analysis of Lindahl's recent publications reveals a strong focus on structural biology of membrane proteins, particularly ligand-gated ion channels. His work integrates cutting-edge computational methods like molecular dynamics simulations, AlphaFold predictions, and cryo-EM data analysis to understand protein conformational dynamics and ligand binding. Key research themes include the structural basis of ion channel function, lipid-protein interactions that stabilize membrane proteins, and computational methods for biomolecular simulation and structural biology. His publications demonstrate a consistent interdisciplinary approach that bridges computational chemistry, structural biology, and neuroscience. Lindahl leads an active research group with multiple postdocs, researchers, and PhD students working on various aspects of membrane protein structure and function. His research is supported by diverse funding sources including the Swedish Research Council, European Research Council, Knut and Alice Wallenberg Foundation, and several EU programs. He plays significant leadership roles in major computational infrastructure initiatives including BioExcel (an EU-funded center of excellence for computational biomolecular research), PRACE (the European computing infrastructure), and EuroHPC. The Lindahl research group operates primarily at the Science for Life Laboratory, where they have access to advanced computational resources and experimental facilities for structural biology. The group collaborates extensively with researchers across Stockholm University, KTH, Karolinska Institutet, and international partners through EU-funded projects. They are particularly active in developing and maintaining open-source software tools that are widely used in the computational biology community.

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Bert de GrootView profile

Professor

Max Planck Institute for Molecular BiomedicineGermany

Bert de Groot is an apl. Professor leading the Computational Biomolecular Dynamics group at the Max Planck Institute for Multidisciplinary Sciences in Göttingen, Germany. His research employs advanced computational methods to study biomolecular dynamics, with a focus on atomic-level simulations of protein function and membrane processes. His primary research interests include computational biomolecular dynamics, molecular dynamics simulations, protein structure-function relationships, membrane transport mechanisms, and allosteric regulation. He investigates how collective protein motions enable biological functions, particularly in water channel proteins like aquaporin and signaling molecules like ubiquitin. Analysis of his publications reveals consistent expertise in simulating biomolecular systems to uncover mechanistic insights, with recent work emphasizing allosteric communication pathways and membrane transport dynamics. His research bridges computational physics with structural biology to explain experimental observations at atomic resolution. No scientific awards were mentioned in the provided text. No information regarding student advising or research grants was provided in the source material. He directs the Computational Biomolecular Dynamics group which develops specialized software including Concoord for protein structure generation from distance constraints, Maptools for processing experimental 3D maps (X-ray/EM), and contributes essential dynamics modules to the Gromacs molecular dynamics package.

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Luis Carlos Pardo SotoView profile

Associate Professor

Polytechnic University of CataloniaSpain

Luis Carlos Pardo Soto is an Associate Professor in the Department of Physics at the Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC). He is a core member of the Group of Characterization of Materials (GCM), the Multiscale Science and Engineering Research Center (CCEM), and the Phase Transitions, Polymorphism, Glasses and Dynamics of Metastability (PTP-GlaDyM) research group. His research focuses on disordered systems including molecular liquids, plastic crystal phases, and their glassy states. He investigates the structural and dynamic properties of these systems using experimental techniques such as neutron and X-ray diffraction, dielectric spectroscopy, and high-pressure devices, complemented by molecular dynamics simulations using GROMACS. His work particularly examines water structure and its interactions with biologically relevant molecules. Pardo Soto has developed specialized software tools including ANGULA for orientational order analysis in disordered systems and FABADA for Bayesian analysis of experimental data. His research outputs include numerous indexed journal articles, book chapters, and conference presentations, with significant contributions in the fields of glass formation, molecular dynamics, and disordered materials characterization. He is actively involved in scientific outreach through FISIDABO VISIONS (STEAM-FORUM and STEAM-ANELLA initiatives) and maintains a YouTube channel for disseminating scientific content. His teaching responsibilities focus on disordered systems and related physics concepts.

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