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Entry Level Molecular Dynamics Simulation Jobs (NOW HIRING)

RFA Engineering

Vehicle Dynamics Engineer

Waterloo, IA · On-site

... simulation software (i.e. Ansys Motion, GT-Suite - GT-3DMBD Vehicle Dynamics) is preferred * Ideal candidate will have 1-3 years of related work experience, but entry level being considered. Visa ...

Deep Origin

Senior Scientific Developer

Familiarity with molecular simulation ecosystems: force fields, system preparation, alchemical free ... molecular dynamics, cheminformatics, and related computational biology workflows. * Build and ...

NorthEastern

Postdoctoral Research Associate

Boston, MA

$60K - $85K/yr

Experience with at least one of the following areas: excited-state simulation methods, multiscale simulations (QM/MM a plus), catalysis (biological, homogeneous, or heterogeneous), molecular dynamics ...

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Entry Level Molecular Dynamics Simulation information

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$39K

$123.4K

$190.5K

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

As of Jul 16, 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 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.

What are the typical day-to-day tasks for someone in an entry-level molecular dynamics simulation role?

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 entry level molecular dynamics simulation jobs?

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 are the key skills and qualifications needed to thrive as an Entry Level Molecular Dynamics Simulation professional, and why are they important?

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.
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What cities are hiring for Entry Level Molecular Dynamics Simulation jobs? Cities with the most Entry Level Molecular Dynamics Simulation job openings:
What are the most commonly searched types of Molecular Dynamics Simulation jobs? The most popular types of Molecular Dynamics Simulation jobs are:
What job categories do people searching Entry Level Molecular Dynamics Simulation jobs look for? The top searched job categories for Entry Level Molecular Dynamics Simulation jobs are:
Entry Level Molecular Dynamics Simulation jobs near you
Infographic showing various Entry Level Molecular Dynamics Simulation job openings in the United States as of July 2026, with employment types broken down into 83% Full Time, 16% Part Time, and 1% Contract. Highlights an 80% Physical, 3% Hybrid, and 17% Remote job distribution, with an average salary of $123,399 per year, or $59.3 per hour.
Computational Protein Research Associate (Contract)

Computational Protein Research Associate (Contract)

Zymo Research Corporation

Tustin, CA • On-site

$75K - $85K/yr

Contractor

Medical, Dental, Vision, Life, Retirement, PTO

Posted 19 days ago

Job description

Job Summary:
Zymo Research is seeking a highly motivated and innovative Computational Protein Research Associate to join our multidisciplinary research team focused on protein engineering, enzyme discovery, antibody design, and AI-driven molecular modeling.
The successful candidate will work at the intersection of computational biology, machine learning, structural biology, and protein engineering. Key responsibilities will include developing scalable protein sequence-structure-function analysis platforms, building predictive AI/ML models, and identifying or designing proteins with desired biological properties. This role offers the opportunity to contribute to cutting-edge platform technologies in enzymes, antibodies, synthetic biology, and molecular diagnostics.
Join us in making a meaningful impact!
Essential Duties and Responsibilities
  • Apply protein language models and other machine-learning approaches, including model fine-tuning, to analyze protein sequences, predict molecular properties, and annotate protein functions.
  • Use structural modeling and simulation tools, including AlphaFold 3, Rosetta, and molecular dynamics simulations, to investigate protein structures, conformational stability, molecular interactions, and functional mechanisms.
  • Apply AI/ML methods to de novo protein design, protein optimization, enzyme engineering, antibody design, and functional prediction.
  • Perform computational screening and prioritization of candidate proteins for experimental validation.
  • Collaborate closely with wet-lab scientists to design experiments, interpret results, and iteratively improve engineered proteins.
  • Contribute to active-learning-driven Design-Build-Test-Learn cycles for protein engineering and optimization.
  • Present research findings internally and externally through reports, publications, and scientific conferences.
  • Contribute to intellectual property generation and platform development.

Education and Experience:
  • Bachelor's degree or higher in computational biology, bioinformatics, structural biology, computer science, biophysics, protein engineering, or related field.
  • Strong foundation in computational protein science, or structural biology.
  • Experience applying machine-learning or deep-learning methods to biological sequence, structure, or functional data.
  • Proficiency in Python and commonly used scientific computing and machine-learning libraries.
  • Experience with protein language models, structure-based modeling, or molecular simulation is highly desirable.
  • Strong analytical, problem-solving, and communication skills.
  • Ability to work independently while contributing effectively within a multidisciplinary research environment.

About Us:
Since its inception in 1994, Zymo Research has been proudly serving the scientific community by providing innovative, reliable, and high-quality research tools and products. Whether it's DNA, RNA, epigenetics, microbiomics, protein, or yeast-based research, our philosophy remains the same: To provide the highest quality products in the industry while ensuring they are both simple to use and reliable in their performance.
Recognized as a Top Workplace by the Orange County Register in 2021, 2022, and named a Top Workplace USA in 2023, Zymo Research continues to be a vibrant community where employees thrive, feel connected, and are inspired by their work. If you are passionate about contributing to scientific advancement and want to be part of an exceptional team in a dynamic, growing company, we'd love to hear from you!
Compensation, Benefits, and Perks:
The estimated base compensation range for this position is $75,000-85,000 at the time of posting. Actual compensation details will be provided in writing at the time of offer, if applicable, and is based on several factors we believe fairly and accurately impact compensation, including geographic location, experience, knowledge, skills, abilities, and other job permitted factors.
Zymo Research also offers competitive benefits and perks including:
  • Medical, Dental, Vision, and Life Insurance Coverages
  • EAP Sessions
  • Vacation Time plus Company Holidays
  • Paid Sick Leave
  • Generous 401(K) with matching
  • Employee Referral Bonus
  • Complimentary fruit, snacks, and beverages
  • Complimentary catered lunches on Thursdays
  • Complimentary EV Charging
  • Cell phone stipend

Equal Employment Opportunity Employer:
Zymo Research welcomes candidates of all backgrounds. These include sex, age, color, race, religion, marital status, national origin, ancestry, sexual orientation, gender, gender identity, gender expression, physical & mental disability, medical condition, genetic information, military and veteran status, or any other protected status as defined by federal, state, or local law.
Location:
Onsite - Zymo Research- 2961 Dow Ave, Tustin, CA, 92780
Disclaimer: At Zymo, we take the integrity of our hiring process seriously. Please be aware of fraudulent recruitment activities that may use our name to deceive job seekers. We will never ask for payment, sensitive personal information, or financial details during the recruitment process.
All legitimate communications will come from an official Zymo or TriNet Hiring email address. If you are contacted by anyone claiming to represent us using a free email service (e.g., Gmail, Yahoo, Hotmail) or asking for payment, please treat this as fraudulent and report it immediately to jobs@zymoresearch.com

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