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Entry Level Molecular Dynamics Simulation Jobs (NOW HIRING)

1910

Computational Theoretical Chemist II

Boston, MA

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulation are changing the way we develop new drugs. At 1910 , we put computation at the heart ...

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Entry Level Molecular Dynamics Simulation information

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How much do entry level molecular dynamics simulation jobs pay per year?

As of Aug 25, 2026, the average yearly pay for entry level molecular dynamics simulation in the United States is $123,399.00, according to ZipRecruiter salary data. Most workers in this role earn between $92,000.00 and $146,500.00 per year, depending on experience, location, and employer.

What is an entry level molecular dynamics simulation?

Entry level molecular dynamics simulation jobs involve using computational methods to model the physical movements of atoms and molecules. These positions are typically suitable for recent graduates or those new to the field, and may include tasks such as setting up simulations, analyzing data, and assisting with research projects in fields like chemistry, biology, or materials science. Entry level roles often require a background in a relevant scientific discipline, familiarity with simulation software, and basic programming skills. These jobs provide a foundation for gaining expertise in computational research and can lead to more advanced positions in academia or industry.

What does an entry level molecular dynamics simulation professional do?

In an entry-level molecular dynamics simulation position, you can expect to spend much of your day setting up and running computational experiments, analyzing simulation data, and troubleshooting issues with simulation software. You'll likely collaborate closely with more senior researchers, computational scientists, and sometimes experimentalists to ensure your simulations align with project goals. Documentation and reporting of your findings are also important, as is staying updated on new methodologies and tools in the field. Over time, you'll gain opportunities to contribute to research publications and take on more complex simulation projects.

What are the key skills and qualifications needed to thrive as an entry level molecular dynamics simulation professional?

To thrive as an Entry Level Molecular Dynamics Simulation professional, you need a solid background in physics, chemistry, or materials science, often supported by a relevant bachelor's or master's degree. Familiarity with simulation software such as GROMACS, LAMMPS, or AMBER, as well as proficiency in programming languages like Python or C++, is typically required. Analytical thinking, attention to detail, and strong problem-solving abilities are crucial soft skills that set candidates apart. These combined skills ensure accurate simulation results, effective troubleshooting, and meaningful scientific insights in research or industrial applications.

What is the difference between Entry Level Molecular Dynamics Simulation vs Entry Level Computational Chemist?

AspectEntry Level Molecular Dynamics SimulationEntry Level Computational Chemist
Required CredentialsBachelor's in Chemistry, Physics, or related field; basic knowledge of simulation softwareBachelor's in Chemistry, Chemical Engineering, or related; familiarity with computational tools
Work EnvironmentResearch labs, academic institutions, industry R&DResearch labs, pharmaceutical companies, academic settings
Industry UsageMaterial science, biochemistry, pharmaceuticalsDrug discovery, materials research, chemical analysis

Both roles involve computational work in chemistry-related fields, but Molecular Dynamics Simulation focuses specifically on simulating molecular interactions over time, while Computational Chemists may perform a broader range of modeling and analysis tasks. The choice depends on your interest in dynamic simulations versus general computational chemistry applications.

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Entry Level Molecular Dynamics Simulation jobs near you
Infographic showing various Entry Level Molecular Dynamics Simulation job openings in the United States as of August 2026, with employment types broken down into 50% Full Time, and 50% Contract. Highlights an 100% In-person job distribution, with an average salary of $123,399 per year, or $59.3 per hour.

ML & Molecular Simulation Scientist

San Mateo, CA • On-site

Genesis Molecular AI
See more jobs at Genesis Molecular AIexternal

Full-time

Re-posted 13 days ago

Job description

Job Summary:
Genesis Molecular AI is pioneering foundation models for molecular AI to unlock a new era of drug design and development. They are seeking a ML & Molecular Simulation Scientist to develop and apply methods at the intersection of 3D molecular simulation and machine learning, contributing to impactful drug discovery programs.
Responsibilities:
• Build and apply ML models informed by 3D structural data, including geometric deep learning, equivariant neural networks, and diffusion-based generative models for molecular design and property prediction
• Integrate physics-based and ML + data-driven approaches, combining force field methods, quantum chemistry, and structure-based design with modern ML to improve accuracy and throughput
• Develop and apply simulation methods spanning molecular dynamics, enhanced sampling (metadynamics, replica exchange, umbrella sampling), and free energy calculations (FEP/TI) to support active drug discovery programs
• Contribute to the GEMS platform, improving our generative AI and scoring capabilities, focusing on 3D methods; strengthen ML and physics-based scoring functions (and their intersection), build next-gen force fields
• Work directly with CADD and discovery scientists to apply computational methods across the drug discovery pipeline, from target structure analysis through lead optimization
• Stay current with the field, implementing and adapting methods from the latest literature in geometric ML, biomolecular simulation, and computational drug design
• Communicate scientific results clearly to multidisciplinary teams, including experimental chemists and biologists
Qualifications:
Required:
• Practical experience with 3D machine learning – geometric deep learning, graph neural networks, equivariant architectures (e.g., SE(3)/E(3) networks), or diffusion models applied to molecular data
• PhD (preferred) in computer science, machine learning, chemical engineering, biophysics, physics, or a closely related field; postdoctoral or industry experience is a plus
• Deep, hands-on expertise in molecular simulation, including MD, enhanced sampling, and/or free energy methods using tools such as GROMACS, AMBER, OpenMM, or NAMD
• Familiarity with structure-based drug design workflows: docking, binding site analysis, protein-ligand interaction modeling using tools such as MOE, or PyMOL
• Proficiency in Python and scientific computing libraries (PyTorch, JAX, NumPy, MDAnalysis, RDKit); comfort with HPC environments and scripting for large-scale simulation workflows
• A track record of applying computational methods to real scientific problems, demonstrated through publications, open-source contributions, or industry impact
• Collaborative, curious, and able to move between rigorous method development and fast-paced discovery work
Preferred:
• Familiarity with cheminformatics and ADMET property prediction
• Contributions to open-source simulation or ML tooling
Company:
Genesis Therapeutics unifies AI and biotech to accelerate the discovery of new medicines. Founded in 2019, the company is headquartered in South San Francisco, USA, with a team of 51-200 employees. The company is currently Growth Stage.

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