Molecular Dynamics & Simulation Studies — Hands-on

Hands-on molecular dynamics from PDB to publication: parameterize systems, choose force fields wisely, equilibrate/produce safely, and turn trajectories into defensible insights.

Molecular Dynamics & Simulation Studies (GROMACS, AMBER, CHARMM)

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Session Index

Session 1 — System Prep & Force Fields Session 2 — Setup, Constraints & Equilibration Session 3 — Production & Trajectory Analysis Session 4 — Mini Capstone: PDB → Insights

Session 1

Fee: Rs 6300

System Preparation & Force Fields

PDB cleanup, missing atoms, protonation, termini capping

pdbfixer PDB2PQR propka

Force fields, water models & ions; parameterization of ligands

AMBER ff14SB/ff19SB CHARMM36m OPLS-AA/M TIP3P/TIP4P-Ew antechamber/CGenFF

Topology/coordinate generation and solvation boxes

gmx pdb2gmx tleap CHARMM GUI basics

Session 2

Fee: Rs 8400

Setup, Constraints & Equilibration

Energy minimization, NVT/NPT schedules, thermostats & barostats

grompp/mdrun sander/pmemd CHARMM V-rescale/Langevin Parrinello–Rahman/Berendsen

Constraints, cutoffs & long-range electrostatics

LINCS/SHAKE PME PBC & neighbor lists

Input file hygiene & GPU/CPU performance tips

mdp/in files domain decomposition precision/constraints tradeoffs

Session 3

Fee: Rs 11200

Production Runs & Trajectory Analysis

Running stable production and monitoring simulation health

checkpointing restraints log/EDR checks

Core analyses: RMSD/RMSF, R_g, H-bonds, SASA, diffusion

gmx rms/gyrate/hbond/sasa cpptraj VMD

Advanced: PCA, clustering, free-energy projections

MDAnalysis MDTraj PyEMMA/bioPCA

Session 4

Fee: Rs 14000

Mini Capstone: PDB → Insights

From prepared structure to short production and report bundle

Theory + Practical

Reproducibility: config templates, provenance & QC checklist

YAML/MDP versioning Conda/Mamba Quarto

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

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Molecular Dynamics & Simulation Studies Training | GROMACS, AMBER, CHARMM (Prep → Equilibration → Production → Analysis)

Molecular Dynamics & Simulation Studies — Hands-on