Associate Scientist, Post Doc Fellow – Computational Chemistry

MSD; Boston (MA); On-site; USD 82,000 - 92,000; Full time

Benefits offered by this job

Medical, dental, vision benefits

401(k) retirement plan

Paid holidays

Job summary

Merck & Co., Inc. in Boston, MA, seeks an Associate Scientist, Postdoctoral Fellow in Computational Chemistry to advance physics-based simulations and free energy perturbation methods for drug design.

You will design and execute FEP studies, analyze results, and contribute to internal workflows in M&I. The role emphasizes independent research, collaboration with computational chemists, and presenting findings at meetings and conferences.

Qualifications

• Must currently hold a PhD OR receive by spring 2027 in a computational field.
• PhD with computational emphasis in chemistry/biophysics/biochemistry.

Responsibilities

• Design, execute, and analyze free energy calculations for protein-ligand systems.
• Develop methods and analyze data to extract insights from simulations.
• Interpret results in the context of experimental data and SAR.

Skills

Molecular Dynamics

Python

Statistical Mechanics

Independent Research

Communication Skills

Education

PhD in chemistry/biophysics/biochemistry or equivalent

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

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

Required Skills:

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

Salary and Benefits

• Salary range: $82,000-$92,000
• 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
• compassionate and sick days

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.

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.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics. As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit: EEOC Know Your Rights EEOC GINA Supplement. We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts.

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.

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.

Our company is a global health care leader with a diversified portfolio of prescription medicines, vaccines and animal health products. The difference between potential and achievement lies in the spark that fuels innovation and inventiveness; this is the space where we have codified our legacy for over a century. Our success is backed by ethical integrity, forward momentum, and an inspiring mission to achieve new milestones in global healthcare.