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Molecular Dynamics Jobs (NOW HIRING)

Menlo Ventures

ML & Molecular Simulation Scientist

San Mateo, CA · On-site

$110 - $150/hr

  • Medical

  • Dental

  • Vision

  • Retirement

  • PTO

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 ...

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Molecular Dynamics information

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$11K

$80.7K

$103.5K

How much do molecular dynamics jobs pay per year?

As of Aug 19, 2026, the average yearly pay for molecular dynamics in the United States is $80,687.00, according to ZipRecruiter salary data. Most workers in this role earn between $69,000.00 and $98,500.00 per year, depending on experience, location, and employer.

What is molecular dynamics?

A Molecular Dynamics job typically involves using computational simulations to study the physical movements of atoms and molecules. Professionals in this field use specialized software and high-performance computing to analyze molecular interactions in fields like drug discovery, materials science, and biophysics. They may work in academia, pharmaceuticals, or research labs to model molecular behavior and predict system properties. Strong backgrounds in physics, chemistry, and programming are often required.

What does someone working in molecular dynamics do?

Professionals in Molecular Dynamics frequently work on computational research projects that involve simulating the behavior of molecules to gain insights into physical, chemical, or biological processes. Daily tasks often include designing simulation experiments, running large-scale computations, analyzing simulation results, and preparing reports or publications. Collaboration with multidisciplinary teams—such as chemists, biologists, and materials scientists—is common to ensure projects address real-world scientific questions. This role may also involve presenting findings at meetings or conferences and staying current with advancements in simulation techniques. Being part of a collaborative research environment offers continuous learning and the opportunity to contribute to innovative discoveries.

What are the key skills and qualifications needed to thrive in molecular dynamics?

To excel in a Molecular Dynamics role, a strong background in physics, chemistry, computational modeling, and a relevant advanced degree (often a Ph.D.) are essential. Experience using molecular simulation software such as GROMACS, AMBER, or LAMMPS, as well as proficiency in programming languages like Python, C++, or Fortran, is typically required. Strong analytical thinking, meticulous attention to detail, and effective communication skills are valuable soft skills in this field. These qualifications are critical for accurately modeling molecular systems, interpreting complex data, and collaborating effectively with interdisciplinary research teams.

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Molecular Dynamics jobs near you
Infographic showing various Molecular Dynamics job openings in the United States as of August 2026, with employment types broken down into 85% Full Time, 14% Part Time, and 1% Contract. Highlights an 78% Physical, 4% Hybrid, and 18% Remote job distribution, with an average salary of $80,687 per year, or $38.8 per hour.

ML Research Scientist - Computational Biophysics

Merge Labs

San Francisco, CA • On-site

$200K - $270K/yr

Full-time

Re-posted 28 days ago

Job description

Merge Labs is a frontier research lab with the mission of bridging biological and artificial intelligence to maximize human ability, agency and experience. We're pursuing this goal by developingfundamentally new approaches to brain-computer interfaces that interact with the brain at high bandwidth, integrate with advanced AI, and are ultimately safe and accessible for anyone to use.
About the team:
Our Bio team designs, builds, and characterizes the biotechnologies that form the foundation of next-generation brain-computer interfaces. We combine molecular engineering, synthetic biology, neuroscience and advanced physical methods such as ultrasound to establish less invasive, high-bandwidth connections with neurons. The Bio team develops our core molecular technologies, validates their performance in vitro and in vivo, and demonstrates their advanced capabilities in animal models. We build custom experimental setups and pipelines and collaborate closely with engineers and data scientists. We work across disciplines to come up with creative ideas and solve some of the most challenging problems in biotechnology.
About the role:
We're hiring a Senior / Principal ML Biophysicist to lead the development of scalable molecular dynamics pipelines and integrate physics-based models with machine learning frameworks. Starting from first principles, you'll architect the company's molecular modeling foundations-establishing tools and workflows for simulating, analyzing, and interpreting biomolecular dynamics to function relationships. Over time, you'll help translate these into predictive frameworks that accelerate molecular engineering, inform experimental campaigns, and enable the discovery of highly functional molecules.
In this role, you will:
  • Build the scientific and engineering scaffolding for protein structure modeling, molecular dynamics, and integrations with downstream ML frameworks.
  • Collaborate with wet-lab scientists to define tractable optimization objectives and encode domain specific priors and constraints.
  • Prototype modeling frameworks using internal and public datasets; benchmark and validate performance.
  • Serve to non-domain experts for democratization of first-principles analysis
  • Drive the development of ML frameworks that explicitly incorporate first-principles priors.
  • Stay up-to-date with the latest research in deep-learning, molecular dynamics, and protein structure modeling and prototype novel algorithms that can be deployed to improve the company's discovery or development workflows.
  • Contribute to the long-term research roadmap and serve as a thought-leader for scientists.

You might thrive in this role if you have:
  • Strong grounding in deep-learning, protein-structure modeling, and molecular dynamics.
  • Working knowledge of transfer-learning strategies
  • Proficiency in Python / PyTorch / Jax and comfort writing clean, reproducible production grade code.
  • Experience bridging machine learning and experimental science-working with sparse, noisy, and or high-cost data.
  • A collaborative, systems-level mindset.

Nice to haves
  • Familiarity with neuroscience.
  • Familiarity with language / state-space models.

If you're excited about this role but don't meet every qualification, please apply. As we build, we're hiring for complementary strengths to form a high-impact team.
For more information about hiring at Merge, please visit our Hiring FAQ
Merge Labs does not discriminate on the basis of race, color, religion, national origin, age, sex, sexual orientation, gender, gender identity, gender expression, marital status, physical or mental disability, medical condition, genetic information, family status, ancestry, citizenship, U.S. military (state and federal) and veteran status, or any other legally protected status. It is our intention that all applicants be given equal opportunity and that selection decisions are based on job related factors. We are an equal opportunity employer.
Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.
We are committed to providing reasonable accommodations to applicants with disabilities, and requests can be made by emailing accommodations@merge.io.

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