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Molecular Dynamics Simulation Protein Jobs (NOW HIRING)

UAB

SCIENTIST III

Tampa, FL

The role requires deep technical expertise across AI for science protein and antibody design, AI-driven molecular dynamics, agentic AI and autonomous research systems, clinical trial simulations ...

UAB NOVA RENT

SCIENTIST III

Birmingham, AL · On-site

The role requires deep technical expertise across AI for science protein and antibody design, AI-driven molecular dynamics, agentic AI and autonomous research systems, clinical trial simulations ...

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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.

Manager, Molecular Simulation Engineering

NVIDIA

Santa Clara, CA • On-site

Full-time

Re-posted 16 days ago

Nvidia rating

9.6

Company rating: 9.6 out of 10

Based on 17 frontline employees who took The Breakroom Quiz

8th of 242 rated software companies

Job description

Job Summary:
NVIDIA is a leader in computer graphics and AI technology, seeking a hands-on technical manager for their MD Simulation Engineering team. The role involves leading engineers to develop GPU-native simulation software and collaborating with the scientific community to enhance biological simulations.
Responsibilities:
• Lead, hire, and develop software engineers within a collaborative unit; build a culture of ownership, engineering excellence, and direct collaboration with researchers and authorities in the field.
• Define vision, strategy, and roadmap for the division's GPU-accelerated simulation software.
• Own end-to-end delivery across multiple workstreams; align partners, lead cross-team dependencies, and drive predictable execution.
• Partner with Applied Science teams to translate research prototypes into production-quality, benchmarked software.
• Build and maintain relationships with the community dedicated to molecular dynamics' modeling to ensure the team is delivering what the community needs.
• Drive engineering completion: code quality, CI/CD, multi-SKU validation, and documentation standards.
• Communicate progress, risks, and decisions clearly.
Qualifications:
Required:
• 8+ overall years of software engineering experience, including 3+ years being responsible for an engineering team with direct reports.
• Strong technical foundation in GPU computing and high-performance scientific software; ability to review builds, influence architectural directions, and maintain a high engineering standard across the team's work.
• Experience shipping production GPU libraries, scientific computing software, or developer-facing APIs — you understand what it takes to go from prototype to a product that external developers depend on.
• Familiarity with molecular dynamics simulation concepts (force fields, electrostatics, neighbor lists, periodic boundary conditions) sufficient to engage credibly with both colleagues and the MD simulator community.
• Proven record to lead multi-functional dependencies, work across interpersonal boundaries without direct authority, and communicate technical progress clearly to senior leadership.
• BS/MS in Computer Science, Computational Science, Physics, Chemistry, or a related field, or equivalent experience.
Preferred:
• You have shipped a GPU-accelerated scientific computing library or supplied to a major open-source MD simulation engine.
• PhD-level education or comparable experience in computational chemistry, biophysics, applied mathematics, or computer science with a focus on HPC or scientific computing.
• Experience with GPU compiler toolchains or kernel delivery mechanisms.
• You have worked across the boundary between applied science and engineering — taking algorithmic research and turning it into a shipped, benchmarked product.
• Active engagement in the MD simulation or computational chemistry community through publications, conference talks, or open-source contributions.
Company:
NVIDIA is a computing platform company operating at the intersection of graphics, HPC, and AI. Founded in 1993, the company is headquartered in Santa Clara, USA, with a team of 10001+ employees. The company is currently Late Stage.

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Hours and flexibility

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About Nvidia

Sourced by ZipRecruiter

NVIDIA has been transforming computer graphics, PC gaming, and accelerated computing for more than 25 years. It's a unique legacy of innovation that's fueled by great technology--and amazing people. Today, we're tapping into the unlimited potential of AI to define the next era of computing. An era in which our GPU acts as the brains of computers, robots, and self-driving cars that can understand the world. Doing what's never been done before takes vision, innovation, and the world's best talent.

Industry

Computer and electronic product manufacturing

Company size

10,000+ Employees

Headquarters location

Santa Clara, CA, US

Year founded

1993

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