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Molecular Simulation Jobs in Colorado (NOW HIRING)

Quantinuum

Atomic Source Physicist - 869

Broomfield, CO · On-site

$135K - $180K/yr

... or molecular beams, and other cold atom techniques * Experience working with trapped ions * Experience working with quantum computing hardware * Experience performing simulation and modeling to ...

Watchmaker Genomics

IT Systems Engineer

Boulder, CO · On-site

... molecular diagnostics, and personalized medicine. Position Summary Watchmaker Genomics is inviting ... Conduct regular DR testing and simulations to validate the effectiveness of recovery plans ...

Watchmaker Genomics

IT Systems Engineer

Boulder, CO

... molecular diagnostics, and personalized medicine. Position Summary Watchmaker Genomics is inviting ... Conduct regular DR testing and simulations to validate the effectiveness of recovery plans ...

Tolmar

Microbiologist I (Onsite)

Fort Collins, CO · On-site

$28 - $29/hr

... simulations. * Perform routine quality control product testing on pharmaceutical items under GMP ... Experience with routine culture/molecular techniques, microbial identification procedures ...

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All JobsMolecular Simulation JobsMolecular Simulation Jobs in Colorado

Molecular Simulation information

See Colorado salary details

$11.6K

$84.8K

$108.8K

How much do molecular simulation jobs pay per year?

As of Jul 28, 2026, the average yearly pay for molecular simulation in Colorado is $84,843.00, according to ZipRecruiter salary data. Most workers in this role earn between $72,600.00 and $103,600.00 per year, depending on experience, location, and employer.

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 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 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.

What are the most commonly searched types of Molecular Simulation jobs in Colorado? The most popular types of Molecular Simulation jobs in Colorado are:
What are popular job titles related to Molecular Simulation jobs in Colorado? For Molecular Simulation jobs in Colorado, the most frequently searched job titles are:
What job categories do people searching Molecular Simulation jobs in Colorado look for? The top searched job categories for Molecular Simulation jobs in Colorado are:
What cities in Colorado are hiring for Molecular Simulation jobs? Cities in Colorado with the most Molecular Simulation job openings:
Molecular Simulation jobs near you
Infographic showing various Molecular Simulation job openings in Colorado as of July 2026, with employment types broken down into 67% Full Time, 30% Part Time, 1% Temporary, and 2% Contract. Highlights an 71% Physical, 1% Hybrid, and 28% Remote job distribution, with an average salary of $84,843 per year, or $40.8 per hour.
Principal Scientist, Computational Chemistry

Principal Scientist, Computational Chemistry

Cogent Biosciences

Boulder, CO • On-site

Full-time

Medical, Dental, Vision, Retirement, PTO

Posted 12 days ago

Job description

Who We Are:
Cogent Biosciences is a publicly traded biotechnology company focused on developing novel precision therapies to treat a broad range of patients with unmet medical needs. Cogent's lead program, bezuclastinib, is designed to selectively and potently inhibit exon 17 mutations found within the KIT receptor tyrosine kinase, including KIT D816V. KIT D816V is responsible for driving a rare and serious condition called Systemic Mastocytosis, and exon 17 mutations are also found in patients with gastrointestinal stromal tumors (GIST), a type of cancer with strong dependence on oncogenic KIT signaling. Bezuclastinib has exhibited promising initial data across all three trials: APEX in AdvSM, SUMMIT in NonAdvSM, and PEAK in GIST, including an encouraging safety profile across 600+ patients in single-agent and combination dosing.
The Role:
We are seeking an Experienced Computational Chemist who thrives at the intersection of molecular modeling, data-driven decision making, and innovative drug design. In this role, you will directly influence discovery programs by generating actionable structure-based insights, developing predictive models, and partnering with multidisciplinary teams to guide molecular design from hits to optimized leads. This is a full-time, on-site position based at our R&D facility in Boulder, Colorado.
Responsibilities:
  • Apply structure-based and ligand-based drug design methods-including docking, protein modeling, and a range of computational techniques-to support projects from hit discovery through lead optimization.
  • Collaborate with project team members, engaging them in iterative structure-based drug design cycles to generate hypotheses, evaluate targets, triage hits, and guide SAR exploration.
  • Present modeling insights clearly and effectively to cross-functional project teams, ensuring data is interpreted in the right context.
  • Develop, refine, and maintain robust computational workflows on HPC Linux environments, enabling scalable execution of large-scale simulations.
  • Train and mentor colleagues on computational chemistry tools, cheminformatics standards, data formats, and key workflow practices.

Qualifications:
  • Ph.D. in Computational Chemistry or a related field, with 3+ years of relevant industrial experience.
  • Expertise in structure-based design, docking, virtual screening, pharmacophore modeling, and other computational approaches for lead optimization.
  • Expertise in MOE modeling software, with working knowledge of other commercial and open-source computational chemistry platforms preferred.
  • Strong hands-on experience with cheminformatics platforms and tools, including Spotfire.
  • Strong programming skills with experience in building custom scripts or automated pipelines, is a plus.
  • Proficiency in Linux/UNIX, shell scripting, and HPC frameworks (e.g., SLURM, LSF, PBS/Torque).
  • Experience optimizing large computational workloads on cluster or cloud infrastructure.
  • Familiarity with molecular representations and cheminformatics standards (SMILES, SDF, descriptors, fragment-based encodings).
  • A solid publication record and excellent scientific communication skills.
  • Proven effectiveness working within cross-functional, data-driven scientific teams.

Salary Range:
$165k - 190k USD
Target Bonus: 15%
Exact compensation will vary based on skills, experience, and location.
Our Locations
Waltham, MA: Our headquarters is located in the Greater Boston life sciences community, with an open, collaborative office environment designed to support teamwork and connection. Employees benefit from convenient on-site amenities, including free on-site parking and gym facilities in the building.
Boulder, CO: Our Boulder location is home to Cogent's discovery research organization and a key scientific hub with strong leadership based on site. Situated in the greater Denver-Boulder biopharmaceutical corridor, this office plays a central role in advancing our discovery efforts and pipeline.
Our Offer To You
At Cogent Biosciences, we offer a competitive salary, bonus, and ongoing stock awards, alongside a benefits package that sets us apart. We cover 100% of medical, dental, and vision premiums for you and your family, and help reduce out-of-pocket costs by funding up to 75% of in-network deductibles. Our benefits also include a 401(k) match with immediate vesting, generous paid time off, 12 weeks of fully paid parental leave, paid family and medical leave for all employees regardless of location, and company-paid short-term disability coverage for up to 20 weeks. Additional perks like wellness programs, tuition reimbursement, and inclusive family-forming support help you thrive at work and beyond.
We are proud to be an Equal Opportunity Employer. Our goal is to have a diverse workforce. We do not discriminate on the basis of race, age, color, religion, national origin, gender, sexual orientation, gender identity or expression, veteran status or disability, or any other status protected under federal, state, or local law. All employment is decided on the basis of qualifications, merit, and business need.

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