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Molecular Simulation Jobs (NOW HIRING)

Achira

CADD / Application Scientist

New York, NY · On-site

We are developing physics-grounded models for molecular simulation that can make the chemical and biological systems behind drug discovery more learnable, predictable, and designable. You will be ...

Xenon7

Research Advisor, Computational Chemistry

Perform molecular dynamics simulations of chemically modified oligonucleotide duplexes and single-stranded species to characterize the structural and thermodynamic consequences of sugar, backbone ...

ChampionX

Chemical Data Scientist

Sugar Land, TX

Proficiency with molecular simulation software (examples like Biovia Materials Studio). * Strong foundation in computational chemistry: DFT, MD, Monte Carlo. * Force field selection/parameterization;

ChampionX

Chemical Data Scientist

Sugar Land, TX · On-site

Proficiency with molecular simulation software (examples like Biovia Materials Studio). * Strong foundation in computational chemistry: DFT, MD, Monte Carlo. * Force field selection/parameterization;

GSK

Principal Scientist

Upper Providence, PA · On-site

Expertise with molecular simulation, enhanced sampling and/or statistical analysis * Ability to present data in team meetings and participate in writing abstracts and publications * Independently ...

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How much do molecular simulation jobs pay per year?

As of May 31, 2026, the average yearly pay for molecular simulation 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 a Molecular Simulation job?

A Molecular Simulation job involves using computational techniques to model and analyze molecular systems at the atomic level. Professionals in this field apply physics-based algorithms and software to study material properties, chemical reactions, and biological processes. They work in industries such as pharmaceuticals, materials science, and energy to optimize product development and research. Strong skills in computational chemistry, physics, and programming are essential for this role.

What are the key skills and qualifications needed to thrive in the Molecular Simulation position, and why are they important?

To thrive in Molecular Simulation, you need a solid background in chemistry, physics, or computational science, often at the graduate level, with expertise in molecular modeling and statistical mechanics. Familiarity with industry-standard simulation software (such as GROMACS, AMBER, or CHARMM), programming languages (like Python or C++), and high-performance computing platforms is essential. Strong analytical thinking, attention to detail, and effective communication are valuable soft skills in this role. These competencies are crucial for accurately modeling molecular systems, interpreting results, and collaborating with multidisciplinary teams in research or industry settings.

What are some common challenges faced by professionals in molecular simulation roles?

Professionals in molecular simulation often encounter challenges such as optimizing computational workloads, troubleshooting simulation errors, and interpreting complex data outputs. Balancing the accuracy of simulations with computational efficiency can also be demanding, especially when working with large biomolecular systems or advanced algorithms. Additionally, staying abreast of rapidly evolving software tools and scientific methodologies requires ongoing learning and adaptation. Being able to collaborate with experimental scientists and clearly communicate results is important for integrating simulation findings into broader research projects.
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Molecular Simulation jobs near you
Infographic showing various Molecular Simulation job openings in the United States as of May 2026, with employment types broken down into 76% Full Time, 22% Part Time, and 2% Contract. Highlights an 91% Physical, and 9% Remote job distribution, with an average salary of $80,687 per year, or $38.8 per hour.

CADD / Application Scientist

Achira

New York, NY • On-site

Full-time

Posted 3 days ago

Job description

Why Achira
At Achira, you will join a team of scientists, ML researchers, and engineers working together to move beyond the beaten path in drug discovery. We are developing physics-grounded models for molecular simulation that can make the chemical and biological systems behind drug discovery more learnable, predictable, and designable.
You will be part of the journey from our first protein-ligand applications in potency and lead optimization toward a broader vision: bringing more of the wet lab in silico, from selectivity and ADMET to eventual de novo molecular design.
You will work at the frontier of AI x chemistry in a well-funded, talent-dense organization that values rigor, speed, execution, ownership, and the shared urgency required to turn ambitious models into real scientific tools.
About the Role
We are looking for CADD / Application Scientists who want to help define the next generation of computational drug discovery tools, not just operate the current one.
You will be a scientific design partner for our model and training teams, bringing real discovery program experience into what we train on, what model behaviors matter, and which applications are worth building toward. As the models mature, you will also help bring these tools to pharma and biotech partners, shaping collaborations around problems where better molecular simulation could change real program decisions.
What You'll Do
  • Shape training data strategy for our models: identify which experimental, structural, partner-accessible, and synthetic data sources are likely to improve affinity prediction, selectivity, generalization, and downstream drug discovery utility.
  • Own data and structure curation for high-value protein-ligand systems end-to-end: connect affinity measurements to assay context, prepare structures, assign protein and ligand states, review or generate poses, and label assumptions and uncertainty.
  • Work with model and training teams to interpret model successes and failures, separating data problems, setup problems, and model limitations.
  • Help decide which applications are worth pursuing, from lead optimization and selectivity to pose assessment, scaffold transfer, affinity prediction, hit rescoring, and future extensions beyond potency.
  • Shape partner programs with BD and leadership, translating model capabilities into scientifically credible collaborations with pharma and biotech teams.

About You
  • You have significant experience in CADD, structure-based drug design, computational chemistry, medicinal chemistry collaboration, or related work in drug discovery.
  • You have experience supporting, or leading external collaborations with pharma, biotech, or discovery partners.
  • You have strong intuition for protein-ligand binding, ligand poses, assay artifacts, protonation / tautomer states, waters, cofactors, ligand strain, and where modeling workflows quietly go wrong.
  • You are comfortable making expert judgments from imperfect data and can tell which benchmarks, application ideas, or partner case studies would matter to a real discovery team.
  • You are excited to work closely with ML researchers, simulation scientists, and platform teams.

Nice to Have
Even if you hit none of these bonus features, we encourage you to apply.
  • Experience curating and running protein-ligand affinity or FEP benchmarks, including OpenFE or related evaluation efforts.
  • Experience across the full discovery arc from target identification through hit finding, hit-to-lead, and lead optimization.
  • Experience designing scientific case studies, technical reports, or partner-facing demonstrations for new computational methods.
  • Familiarity with ML-assisted drug discovery, active learning, synthetic data generation, or model evaluation for molecular systems.

Apply