Associate Scientist, Post Doc Fellow - Computational Chemistry

Merck & Co.; Boston (MA); On-site; USD 82,000 - 92,000; Full time

Benefits offered by this job

Medical, dental, vision

401(k) retirement benefits

Paid holidays

Vacation

Compassionate and sick days

Job summary

Merck & Co. in Boston, MA invites applications for Associate Scientist, Postdoctoral Fellow – Computational Chemistry in the Modeling & Informatics (M&I) department.

The incumbent will design and run free energy calculations to probe protein–ligand binding and contribute to method development and publications. Required PhD with computational emphasis and experience in MD simulations (NAMD/AMBER/GROMACS), Python scripting, and solid statistical mechanics knowledge.

Qualifications

• PhD in chemistry/biophysics or related field with computational emphasis.
• PhD expected by spring 2027 is acceptable.

Responsibilities

• Design, execute, and analyze free energy calculations for protein-ligand systems.
• Investigate methods to maximize information from free energy calculations.
• Interpret results in context of experimental data and SAR.
• Contribute to method development and internal workflows.
• Present findings at meetings, conferences, and publications.

Skills

Molecular dynamics

Programming Python

Statistical mechanics

Independent work

Communication skills

Education

PhD in chemistry/biophysics

Tools

NAMD

AMBER

GROMACS

Job description

Associate Scientist, Postdoctoral Fellow - Computational Chemistry

We are seeking a highly motivated postdoctoral researcher with expertise in physics-based simulation and free energy perturbation (FEP) calculations to join our Modeling & Informatics (M&I) department in Boston, MA, USA. Our M&I team is an inclusive group of approximately 50 computational chemists, cheminformaticians, data scientists, and machine learning specialists who employ state-of-the-art capabilities to drive drug design. Join us to research innovative free energy methods to aid the discovery of better molecules.

Responsibilities

• Design, execute, and analyze free energy calculations of protein-ligand binding and biomolecular systems
• Investigate analysis methods for maximal information extraction from free energy calculations, including the atomic drivers of affinity
• Interpret simulation results in the context of experimental data and structure-activity relationships
• Participate in methods development, investigate and implement novel computational methods, and contribute to internal workflows for M&I
• Present scientific findings via internal meetings, external conferences, and scientific publications

Qualifications

• Must currently hold a PhD OR
• Receive a Ph.D. no later than spring 2027
• Ph.D. in chemistry, biochemistry, biophysics, or equivalent with a computational emphasis

Required Experience and Skills

• Strong expertise in molecular dynamics or related atomistic simulation methods, including experience with one or more simulation packages such as NAMD, AMBER, GROMACS
• Proficiency in programming/scripting, preferably Python, and familiarity with data analysis workflows
• Solid understanding of statistical mechanics, thermodynamics, and molecular interactions
• Demonstrated ability to work independently and collaboratively in a research environment
• Strong oral and written communication skills, with a proven publication record in computational chemistry or related journals

Preferred Experience and Skills

• Experience with enhanced sampling methods, free energy calculations, or alchemical approaches
• Familiarity with protein-ligand binding, protein dynamics, membrane systems, or nucleic acid simulations
• Exposure to high-performance computing environments and parallel computing
• Experience with automated simulation pipelines or workflow orchestration

As a postdoctoral fellow at our research laboratories, you will be exposed to a fast-paced, interdisciplinary drug discovery environment with opportunities to learn about the pharmaceutical industry and the impact of computational chemistry. You will have access to High Performance Computing and modern computational chemistry software packages. We are looking for a self-driven individual with a desire to research cutting-edge simulation methods to impact drug discovery.

The salary range for this role is: $82,000-$92,000

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days.

Required Skills

Chemistry, Computational Chemistry, Computational Methods, Data Science, Drug Design, Drug Discovery Research, Molecular Biophysics, Molecular Dynamics (MD), Molecular Modeling, Statistical Mechanics

US and Puerto Rico Residents Only

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. If you need an accommodation during the application or hiring process.

San Francisco Residents Only

We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only

We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring Ordinance

Search Firm Representatives Please Read Carefully-

Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company 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.

Employee Status

Regular

Relocation

Domestic

VISA Sponsorship

Yes

Travel Requirements

10%

Flexible Work Arrangements

Not Applicable

Shift

Not Indicated

Valid Driving License

No

Hazardous Material(s)

N/A

Job Posting End Date

10/26/2026

*A job posting is effective until 11:59:59PM on the day BEFORE -the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.

Requisition ID

R420834