Coarse-Grained Models: MARTINI & Elastic Networks — Hands-on

Learn how to use coarse-grained (CG) models to explore slow, large-scale motions of biomolecules using MARTINI and elastic network models. This module covers mapping strategies, CG force fields, elastic networks and normal mode analysis so that you can design multi-scale simulations, interpret low-frequency motions and connect CG insights back to atomistic detail.

Coarse-Grained Models: MARTINI & Elastic Networks

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Session Index

Session 1 — Coarse-Graining Concepts & Mapping Session 2 — MARTINI Force Field Workflows Session 3 — Elastic Network Models & Normal Modes Session 4 — Multi-Scale Modeling & Case Study

Session 1

Fee: Rs 8800

Coarse-Graining Concepts & Mapping

Why coarse graining for biomolecules

time and length scale extension loss of detail vs gain in sampling use cases in structural biology

Mapping atomistic models to coarse-grained sites

bead definitions and mapping rules proteins, lipids and solvent ideas topology generation workflows

Strengths and limitations of CG models

what observables are meaningful when atomistic detail is required designing realistic expectations

Session 2

Fee: Rs 11800

MARTINI Force Field Workflows

MARTINI force field overview

bead types and interaction logic MARTINI for membranes and proteins recent developments and variants

Building MARTINI systems from structures

mapping atomistic proteins and lipids membrane and solvent setup topology and parameter files

Running and analysing MARTINI simulations

time step and integration settings common observables for CG simulations backmapping to atomistic overview

Session 3

Fee: Rs 14800

Elastic Network Models & Normal Modes

Elastic network models (ENMs) for proteins

nodes, springs and contact cutoffs Gaussian network and anisotropic models link to crystallographic B factors

Normal mode analysis and low-frequency motions

eigenvalues, eigenvectors, modes visualising collective motions link to conformational transitions

Practical ENM workflows and interpretation

generating ENMs from PDB structures mode selection and relevance connecting ENM insights to experiments

Session 4

Fee: Rs 18800

Multi-Scale Modeling & Case Study

End-to-end CG and ENM case study

Theory + Practical

Combining CG MD, ENMs and atomistic views

using ENM modes to guide simulations backmapping key CG conformations integrating with docking or FEP plans

Best practices, limitations and reporting

communicating CG assumptions clearly figures and movies for CG results methods text and reproducible scripts

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Coarse-Grained Models MARTINI & Elastic Networks Training | CG-MD & ENM Workflows

Coarse-Grained Models: MARTINI & Elastic Networks — Hands-on