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Molecular Dynamics Simulation Protein Jobs (NOW HIRING)

UNC-Chapel Hill

Open Rank

Chapel Hill, NC · On-site

... protein structure prediction, and high-performance computing for large-scale molecular dynamics simulations. 3. Experience with Bioluminescence Resonance Energy Transfer (BRET) or comparable cell ...

Battelle

Computational Biologist

Columbus, OH · On-site

Molecular dynamics simulations and structure based optimization * Integration of AI/ML tools for protein design and optimization * Development and maintenance of reproducible computational protein ...

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Molecular Dynamics Simulation Protein information

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$11K

$80.7K

$103.5K

How much do molecular dynamics simulation protein jobs pay per year?

As of Aug 6, 2026, the average yearly pay for molecular dynamics simulation protein 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 are the key skills and qualifications needed to thrive as a molecular dynamics simulation protein specialist?

To thrive as a Molecular Dynamics Simulation Protein Specialist, you need a solid background in biophysics, computational chemistry, and molecular biology, often supported by an advanced degree such as a Ph.D. in a related field. Expertise in simulation software like GROMACS, AMBER, or CHARMM, along with proficiency in programming languages such as Python or C++, is typically required. Strong analytical thinking, problem-solving ability, and effective collaboration are essential soft skills for interpreting results and working within interdisciplinary research teams. These competencies are crucial for accurately modeling protein behaviors, generating actionable insights, and advancing scientific understanding in pharmaceutical and academic research environments.

What is a molecular dynamics simulation protein?

Molecular dynamics simulation proteins refer to the use of computer simulations to study the physical movements and interactions of protein molecules over time. These simulations help scientists understand protein structure, folding, stability, and interactions with other molecules at an atomic level. By modeling the behavior of proteins in various environments, researchers can gain insights into biological processes and design new drugs or therapies. Molecular dynamics is a powerful tool in structural biology and bioinformatics, enabling the exploration of phenomena that are difficult to observe experimentally.

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

AspectMolecular Dynamics Simulation ProteinComputational Chemist
Required CredentialsDegree in Biochemistry, Chemistry, or related field; knowledge of molecular modeling softwareDegree in Chemistry, Chemical Engineering, or related; strong background in computational methods
Work EnvironmentResearch labs, pharmaceutical companies, academic institutionsResearch labs, industry R&D, academia
Industry UsageBiotechnology, pharmaceuticals, academic researchPharmaceuticals, chemical industry, academia

While both roles involve computational modeling, Molecular Dynamics Simulation Protein focuses specifically on simulating protein behavior at the atomic level, whereas Computational Chemist covers a broader range of chemical systems and methods. The roles often overlap but differ in their specific applications and focus areas.

What are some common challenges faced when running molecular dynamics simulations of proteins, and how can they be addressed?

One common challenge in this role is ensuring the accuracy and stability of protein simulations, as factors like force field selection, system size, and simulation timescale can significantly impact results. Balancing computational resources with scientific goals is crucial, as longer or more complex simulations require more processing power. Effective troubleshooting of simulation errors and optimizing workflows with automation tools are key skills. Collaboration with experimental biochemists and other computational scientists often helps validate findings and guide simulation design.
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Molecular Dynamics Simulation Protein jobs near you
Infographic showing various Molecular Dynamics Simulation Protein job openings in the United States as of August 2026, with employment types broken down into 91% Full Time, 5% Part Time, and 4% Contract. Highlights an 93% In-person, 2% Hybrid, and 5% Remote job distribution, with an average salary of $80,687 per year, or $38.8 per hour.

Computational Chemist - Generative Molecule & Protein Design

F. Hoffmann-La Roche Ltd

Santa Clara, CA • On-site

$145K - $269K/yr

Full-time

This job post has expired 1 day ago. Applications are no longer accepted.

Job description

At Roche you can show up as yourself, embraced for the unique qualities you bring. Our culture encourages personal expression, open dialogue, and genuine connections, where you are valued, accepted and respected for who you are, allowing you to thrive both personally and professionally. This is how we aim to prevent, stop and cure diseases and ensure everyone has access to healthcare today and for generations to come. Join Roche, where every voice matters.
The Position
A healthier future. It's what drives us to innovate. To continuously advance science and ensure everyone has access to the healthcare they need today and for generations to come. Creating a world where we all have more time with the people we love. That's what makes us Roche.
At Roche Sequencing Solutions, we are building the next generation of sequencing and diagnostic platforms powered by advanced computation and AI. As part of our Computational Science & Informatics Chapter, you will sit at the intersection of computational chemistry, structural biology, and applied AI to directly impact real-world commercial instruments and R&D workflows.
The Opportunity
You will join an innovative, collaborative environment where you will:
  • Drive Molecular & Protein Design: Build and run structure-based and ligand-based virtual screening workflows to find new substrates, cofactors, and small molecules for our sequencing and biocatalysis platforms.
  • Enzyme Modeling & De Novo Design: Perform advanced structural modeling and molecular docking simulations on natural and engineered enzyme variants, with a heavy focus on optimizing multi-ligand binding pathways. Lead in silico de novo enzyme design, creating novel protein scaffolds and active sites tailored for multi-ligand binding, optimal catalysis, and enhanced structural stability.
  • Simulate Molecular Dynamics: Explore conformational changes, reaction mechanisms, transition states, and electronic structures using advanced physics-based modeling and quantum chemistry tools.
  • Use Computational Tools: Analyze and optimize biopolymers and biomimetic polymers, leveraging rich internal datasets to design new derivatives and tune properties relevant to sequencing and diagnostic performance.
  • Advance Generative AI Pipelines: Develop and scale generative workflows (including Transformers, GNNs, and diffusion models) for property-guided molecule generation and Computer-Aided Synthesis Planning (CASP).
  • Collaborate for Impact: Partner closely with experimental wet-lab biochemists, protein engineers, and synthetic chemists to turn computational insights into real-world experiments.
  • Pilot Emerging Technologies: Scout and implement cutting-edge tools from the literature and the vibrant local AI ecosystem into production-grade workflows.

Who You Are
You are a curious, collaborative, and driven scientist who loves combining physics-based modeling with modern machine learning to solve complex biological puzzles. You explain complex models clearly to diverse teams, value reproducible research, and are excited to co-design experiments that bridge the digital and physical worlds.
  • You have a a Ph.D. Computational Chemistry, Biochemistry, Biophysics, Structural Biology, or a highly quantitative related field or a Master's degree in Computational Chemistry, Biochemistry with 2 years of related experience or Bachelors with 3 years of related experience.
  • You have a 1+ years of intensive research experience (academic or industry) focused on protein modeling, molecular design, virtual screening, or AI/ML for molecules.
  • You have hands-on experience with docking tools, molecular dynamics packages (such as GROMACS, AMBER, or OpenMM), and quantum chemistry tools.
  • You are proficient in Python (NumPy, SciPy, Pandas, PyTorch) combined with practical experience using RDKit for cheminformatics and developing generative molecular models.
  • You have a strong grasp of enzyme kinetics, binding thermodynamics, transition-state theory, and how synthetic modifications alter macromolecular structures.

The expected salary range for this position is based on the primary location of Santa Clara, CA is $145,300 - $269,800 Annual. Actual pay will be determined based on experience, qualifications, geographic location, and other job-related factors permitted by law. A discretionary annual bonus may be available based on individual and Company performance.
This position also qualifies for the benefits detailed here: Benefits
Relocation benefits are not available for this position
Where pay transparency applies, details are provided based on the primary posting location. For this role, the primary location is Santa Clara. If you are interested in additional locations where the role may be available, we will provide the relevant compensation details later in the hiring process.
Who we are
A healthier future drives us to innovate. Together, more than 100'000 employees across the globe are dedicated to advance science, ensuring everyone has access to healthcare today and for generations to come. Our efforts result in more than 26 million people treated with our medicines and over 30 billion tests conducted using our Diagnostics products. We empower each other to explore new possibilities, foster creativity, and keep our ambitions high, so we can deliver life-changing healthcare solutions that make a global impact.
Let's build a healthier future, together.
Roche is an equal opportunity employer. It is our policy and practice to employ, promote, and otherwise treat any and all employees and applicants on the basis of merit, qualifications, and competence. The company's policy prohibits unlawful discrimination, including but not limited to, discrimination on the basis of Protected Veteran status, individuals with disabilities status, and consistent with all federal, state, or local laws.
If you have a disability and need an accommodation in relation to the online application process, please contact us by completing this form Accommodations for Applicants.

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