Training Drug discovery

Molecular Dynamics Simulations of protein–ligand complexes

A two-week live program covering MD simulations of protein–ligand complexes, from system preparation and force-field parameterization to production runs, trajectory analysis and publication-quality results.

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  • 2 weeksMon–Sat, live online
  • 1 houra day, evening IST
  • 6 modulesHands-on in GROMACS

Next cohort

Dates to be announced

  • Duration2 weeks
  • ScheduleMon–Sat · 1 hour a day
  • ModeLive online (Google Meet)
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Curriculum

From setup to insight

Six modules that take you through a complete MD project.

GROMACSPyMOLChimeraChimeraXVMDAvogadroCGenFFMDAnalysisProLIFBio3DPythonRCommand line

01

Introduction to MD and force fields

Principles of molecular dynamics, force fields and parameterization.

02

System preparation

System setup, ligand parameterization and topology generation, solvation and ion placement. Tools: GROMACS, Avogadro, CGenFF.

03

Energy minimization and equilibration

Prepare a stable system for simulation. Tool: GROMACS.

04

Production MD simulations

Run production simulations. Tool: GROMACS.

05

Trajectory and interaction analysis

Basic and advanced trajectory analysis and protein–ligand interactions. Tools: MDAnalysis, ProLIF, Bio3D, VMD.

06

Visualization, reporting and interpretation

Visualize results and report them. Tools: PyMOL, ChimeraX, Matplotlib.

Who should apply

Eligibility

  • Students in B.Sc., B.Tech., M.Sc., M.Tech. or PhD programs in life sciences or computer science
  • Postdocs and research scholars
  • Teaching and industry professionals

What’s included

Program benefits

  • Live, instructor-led sessions
  • Recordings of every session
  • Workshop materials
  • Certificate
  • Online technical support after the workshop

Fees

Course fees

One fee covers all live sessions, recordings, materials and the certificate. Payment and registration open when the next cohort is announced.

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CategoryIndia (INR)International (USD)
Students (up to Master’s)₹2,250USD 40
PhD scholars₹2,500USD 45
Postdocs / research scholars₹2,750USD 50
Staff / faculty₹3,000USD 55
Industry professionals₹3,500USD 60
Fees for the next cohort. USD fees apply to anyone living, working or studying outside India.

Teaching team

Course instructors

PJDr. Petrina JebamaniBioinformatics Trainer, CBIRT

TADr. Tamanna AnwarFounder, CBIRT

Format

How the course runs

  • DatesTo be announced
  • SessionsMon–Sat, 1 hour a day (last cohort: 7:15–8:15 PM IST)
  • PlatformGoogle Meet (live)
  • Missed a session?Recordings provided

FAQ

Course questions

When does the next cohort start?

Dates are not announced yet. Click Notify me or message us on WhatsApp, and we’ll tell you when enrollment opens.

Do I need prior experience?

A basic understanding of bioinformatics is expected.

What will I need on my computer?

A computer running Windows 10/11, macOS or Linux, with a reliable internet connection. Google Meet runs in your web browser.

What if I miss a live session?

Every session is recorded, and you get access to the recordings.

Will I get a certificate?

Yes. The certificate is awarded on completing the course assignment.

Interested in Molecular Dynamics Simulations?

Get notified when the next cohort opens, or ask us about prerequisites and fees.

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