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Molecular Dynamics Simulation Phd Jobs (NOW HIRING)

1910

Computational Theoretical Chemist I

Boston, MA

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulations are changing the way we develop new drugs. At 1910 , we put computation at the ...

1910

Computational Theoretical Chemist I

Boston, MA · On-site

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulations are changing the way we develop new drugs. At 1910 , we put computation at the ...

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Molecular Dynamics Simulation Phd information

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

As of Aug 9, 2026, the average yearly pay for molecular dynamics simulation phd 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 Molecular Dynamics Simulation Phd vs Computational Chemist?

AspectMolecular Dynamics Simulation PhdComputational Chemist
Required CredentialsPhD in Chemistry, Physics, or related fieldMaster's or PhD in Chemistry, Chemical Engineering, or related field
Work EnvironmentResearch labs, academia, industry R&DLaboratories, industry, academia
Industry UsageFocuses on simulating molecular interactions and dynamicsDesigns and applies computational models to chemical problems

While both roles involve computational modeling and require advanced degrees, Molecular Dynamics Simulation Phd specializes in simulating molecular interactions using physics-based methods, often in research settings. Computational Chemists apply a broader range of computational techniques to solve chemical problems across academia and industry. The choice depends on whether the focus is on detailed molecular dynamics or broader chemical modeling.

What is a molecular dynamics simulation PhD?

A Molecular Dynamics Simulation PhD is a doctoral program focused on the use of computational methods to study the physical movements of atoms and molecules. Students learn to develop and apply simulation techniques to investigate molecular systems, understand material properties, and predict behaviors at the atomic scale. Research in this field is commonly applied in physics, chemistry, biology, and materials science, offering insights into phenomena such as protein folding, chemical reactions, and nanomaterial design. Graduates often pursue careers in academia, research, pharmaceuticals, or computational modeling industries.

What are the key skills and qualifications needed to thrive as a molecular dynamics simulation PhD?

To thrive as a Molecular Dynamics Simulation PhD, you need a solid background in physics, chemistry, or related fields, with advanced knowledge of computational modeling and statistical mechanics, typically supported by a doctoral degree. Proficiency in programming languages (such as Python, C++, or Fortran), experience with molecular dynamics software (like GROMACS, LAMMPS, or AMBER), and familiarity with high-performance computing environments are essential. Strong problem-solving ability, attention to detail, and effective collaboration and communication skills set top candidates apart. These competencies are crucial for designing robust simulations, interpreting complex results, and contributing to interdisciplinary research teams.

What are some common challenges faced by molecular dynamics simulation PhD researchers in collaborative projects?

Molecular Dynamics Simulation PhD researchers often collaborate with experimentalists, theorists, and computational scientists, which can present challenges such as aligning different research methodologies and timelines. Communication is key, as interpreting simulation data in the context of experimental results requires mutual understanding of each team's constraints and objectives. Additionally, managing computational resources and integrating diverse software tools can be complex, especially in large, interdisciplinary projects. Developing strong project management and communication skills is essential for effectively contributing to and benefiting from collaborative research environments.
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Infographic showing various Molecular Dynamics Simulation Phd job openings in the United States as of August 2026, with employment types broken down into 82% Full Time, 15% Part Time, 1% Temporary, and 2% Contract. Highlights an 79% Physical, 4% Hybrid, and 17% Remote job distribution, with an average salary of $123,399 per year, or $59.3 per hour.

Associate Director, Computational Chemistry

Jnana Therapeutics

Boston, MA

$154K - $222K/yr

Full-time

Medical, Dental, Vision, Life, Retirement, PTO

Re-posted 15 days ago

Job description

About Us

Jnana Therapeutics, a wholly owned subsidiary of Otsuka Pharmaceutical,is a clinical-stage biotechnology company leveraging its next-generationRAPIDchemoproteomics platform to discover medicines for highly validated, challenging-to-drug targets to treat diseases with high unmet needs. Jnana is focused on developing first- and best-in-class therapies to treat a wide range of diseases, including rare diseases and immune-mediated diseases. Jnana's lead program, JNT-517, which targets an allosteric site on the phenylalanine transporter SLC6A19, is a potential first-in-class oral approach for the treatment of PKU, a rare genetic metabolic disease. Located in Boston, Jnana brings together scientific leaders in small molecule drug discovery and development, and a highly experienced management team. For more information, please visitwww.jnanatx.comand follow us onTwitter/XandLinkedIn.

At Jnana, you'll join a diverse, passionate team dedicated to advancing therapies for challenging diseases. Our collaborative, purpose-driven culture fosters innovation, urgency, and belonging-making Jnana a great place to work!

About the Opportunity
As an Associate Director of Computational Chemistry, you will be integral to our drug discovery efforts, applying structure-based drug design methods to optimize molecules and guide medicinal chemistry strategy through all parts of the discovery process. This position will be working collaboratively in cross-functional teams to deliver models, predictions and actionable insights that accelerate progress toward clinical development.

You will join a team of highly skilled computational scientists eager to drive projects while developing and applying new tools and methods with exceptional scientific rigor. This is an exciting opportunity to join a growing computational chemistry team with the passion, resources and mandate to build a world-class group.

Responsibilities

  • Act as the computational lead on therapeutic projects, conducting structure-based drug design efforts including molecular dynamics simulations, free energy perturbations, docking and structure analysis to guide medicinal chemistry synthesis priorities.
  • Partner closely with medicinal chemists and project leads to interpret structural data, rationalize structure-activity relationships, and propose optimized compound designs that address potency, selectivity, and developability objectives.
  • Contribute to lead optimization strategy by integrating structural insights with ADME, safety, and physicochemical property considerations to drive molecules toward clinical candidates.
  • Communicate findings clearly to project teams and leadership, presenting design recommendations and structural insights that inform decision-making and advance programs.
  • Stay current with advances in computational chemistry methods and the drug discovery environment, evaluating and implementing new approaches that enhance capabilities and improve results.

Required Qualifications & Skills

  • PhD in Computational Chemistry, Medicinal Chemistry, or a related field with 7-10+ years experience and demonstrated ownership of cross-functional research projects.
  • Demonstrated track record of applying structure-based drug design to successfully advance multiple drug discovery projects through lead optimization stages.
  • Experience supporting IND-enabling activities and contributing to regulatory filings.
  • Deep expertise in molecular modeling techniques and industry-standard tools for molecular dynamics simulations, free energy calculations, protein-ligand docking, structure analysis, binding mode prediction, and design hypothesis generation from structural data.
  • Strong understanding of medicinal chemistry principles, structure-activity relationships, and the interplay between potency, selectivity, ADME properties, and developability.
  • Experience working with diverse structural biology data including X-ray crystallography and cryo-EM and translating these data into actionable medicinal chemistry recommendations.
  • Proven ability to work effectively in fast-paced, collaborative drug discovery teams and communicate complex computational results to non-computational scientists to advance molecules from lead optimization toward clinical development.

Preferred Qualifications

  • Experience and expertise evaluating chemical patent literature.
  • Programming or scripting skills (Python, Bash) for workflow automation and data analysis in a Linux-based environment.
  • Familiarity with covalent drug design and modeling of covalent fragments.
Minimum $154,800.00 - Maximum $222,525.00, plus incentive opportunity: The range shown represents a typical pay range or starting pay for individuals who are hired in the role to perform in the United States. Other elements may be used to determine actual pay such as the candidate's job experience, specific skills, and comparison to internal incumbents currently in role. Typically, actual pay will be positioned within the established range, rather than at its minimum or maximum. This information is provided to applicants in accordance with states and local laws.

Application Deadline: This will be posted for a minimum of 5 business days.

Company benefits: Comprehensive medical, dental, vision, prescription drug coverage, company provided basic life, accidental death & dismemberment, short-term and long-term disability insurance, tuition reimbursement, student loan assistance, a generous 401(k) match, flexible time off, paid holidays, and paid leave programs as well as other company provided benefits.

Come discover more about Jnana and our benefit offerings; https://www.jnanatx.com/join-us/

Disclaimer:

This job description is intended to describe the general nature and level of the work being performed by the people assigned to this position. It is not intended to include every job duty and responsibility specific to the position. Jnana Therapeutics reserves the right to amend and change responsibilities to meet business and organizational needs as necessary.

Jnana Therapeutics is an equal opportunity employer. All qualified applicants are encouraged to apply and will be given consideration for employment without regard to race, color, sex, gender identity or gender expression, sexual orientation, age, disability, religion, national origin, veteran status, marital status, or any other legally protected characteristic.

If you are a qualified individual with a disability or a disabled veteran, you may request a reasonable accommodation, if you are unable or limited in your ability to apply to this job opening as a result of your disability. You can request reasonable accommodations by contacting Accommodation Request.

Statement Regarding Job Recruiting Fraud Scams

At Jnana Therapeutics we take security and protection of your personal information very seriously. Please be aware individuals may approach you and falsely present themselves as our employees or representatives. They may use this false pretense to try to gain access to your personal information or acquire money from you by offering fictitious employment opportunities purportedly on our behalf.

Please understand, Jnana Therapeutics will never ask for financial information of any kind or for payment of money during the job application process. We do not require any financial, credit card or bank account information and/or any payment of any kind to be considered for employment. We will also not offer you money to buy equipment, software, or for any other purpose during the job application process. If you are being asked to pay or offered money for equipment fees or some other application processing fee, even if claimed you will be reimbursed, this is not Jnana Therapeutics. These claims are fraudulent, and you are strongly advised to exercise caution when you receive such an offer of employment.

Jnana Therapeutics will also never ask you to download a third-party application in order to communicate about a legitimate job opportunity. Scammers may also send offers or claims from a fake email address or from Yahoo, Gmail, Hotmail, etc, and not from an official Jnana Therapeutics email address. Please take extra caution while examining such an email address, as the scammers may misspell an official Jnana Therapeutics email address and use a slightly modified version duplicating letters.

To ensure that you are communicating about a legitimate job opportunity at Jnana Therapeutics, please only deal directly with Jnana Therapeutics through its official Jnana Therapeutics Career website https://www.jnanatx.com/join-us/.

Jnana Therapeutics will not be held liable or responsible for any claims, losses, damages or expenses resulting from job recruiting scams. If you suspect a position is fraudulent, please contact Jnana Therapeutics call center at: 800-363-5670. If you believe you are the victim of fraud resulting from a job recruiting scam, please contact the FBI through the Internet Crime Complaint Center at: https://www.ic3.gov, or your local authorities.

Jnana Therapeutics, Inc. does not accept unsolicited assistance from search firms for employment opportunities. All CVs/resumes submitted by search firms to any Jnana employee directly or through Jnana's application portal without a valid written search agreement in place for the position will be considered Jnana's sole property. No fee will be paid if a candidate is hired by Jnana as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.

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