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Molecular Dynamics Simulations

End-to-end GROMACS 2024.4 GPU-accelerated MD pipeline — from complex preparation and equilibration to production runs, binding energy calculations, and publication-quality analysis.

What We Offer

Our MD simulation platform provides a complete workflow built on GROMACS 2024.4 with GPU acceleration. The pipeline covers every step from receptor-ligand complex preparation with the CHARMM36 force field, through energy minimization and NVT/NPT equilibration, to production MD simulations.

Advanced post-simulation analysis includes MM-PBSA/GBSA binding free energy calculations, PCA analysis for conformational dynamics, and a comprehensive suite of publication-ready visualization tools for RMSD, RMSF, SASA, Rg, hydrogen bonds, FEL, DCCM, and more.

MD Simulation Platform — 6-Tool Pipeline Overview

MD Simulation Workflow

A complete 6-step pipeline from preparation to analysis

1
LigPrep

Ligand topology with SwissParam / CGenFF

2
Complex Setup

REC-LIG complex with CHARMM36 force field

3
Equilibration

EM → NVT → NPT with MDP editor

4
Production MD

GPU-accelerated simulation runs

5
MMPB/GBSA

Binding free energy calculations

6
Analysis

Plots, PCA, FEL, DCCM

Available Tools

Six integrated steps in the web-based GROMACS 2024.4 MD platform

Step 1 — Prepare Input
  • Upload receptor-ligand complex (PDB) or select from docking results workspace
  • Automated ligand topology generation via SwissParam / CGenFF web API
  • CHARMM36 force field assignment with PROPKA3 protonation at physiological pH
  • Interactive chain/atom inspector and 3D structure preview before submission
Step 2 — MDP Parameter Editor
  • Web-based tabbed editor for EM, NVT, NPT, and Production MD parameter files
  • Embedded baseline templates; live preview of MDP file content
  • Configurable: time step, temperature (ref_t), pressure (ref_p), cut-offs, integrator
  • Batch save to all ligand folders simultaneously with one click
Steps 3–4 — Equilibration & Production MD
  • Automated 8-step pipeline: solvation → ion addition → EM → NVT → NPT → production
  • GPU-accelerated GROMACS 2024.4 on 3× NVIDIA A30 (multi-GPU via CUDA)
  • Duration selection: 5 ns, 10 ns, 50 ns, 100 ns, or 200 ns production runs
  • Real-time GPU usage monitoring, progress tracking, and completed job history
Steps 5–6 — Analysis & Binding Free Energy
  • One-click auto-analysis: RMSD, RMSF, SASA, Rg, H-bonds, FEL, DCCM, PCA all generated in batch
  • MM-PBSA and MM-GBSA binding free energy with per-residue energy decomposition heatmap
  • 3D FEL surface, DCCM heatmap, 2D PCA, and binding site PCA with energy coloring
  • All plots exported as high-resolution PNG; energy tables in CSV/Excel

Screenshots & Output Gallery

Real outputs from the MD simulation platform

Prepare Input — Structure Inspector & 3D Preview
Prepare Input — Step 1

Upload receptor-ligand complexes, inspect chains/atoms, configure CHARMM36 force field, protonation (PROPKA3), and run preparation pipeline

MDP Parameter Editor — EM/NVT/NPT/Production MD Tabs
MDP Parameter Editor

Web-based editor for EM, NVT, NPT, and Production MD parameters with live preview and batch save to ligand folders

MD Production Run — GPU Monitor & Job History
MD Production Run

GPU usage monitoring, real-time simulation progress, duration selection (5 ns – 200 ns), and completed job history

MM-PBSA/GBSA Energy Decomposition Heatmap
MM-PBSA/GBSA Energy Decomposition

Per-residue energy contribution heatmap showing electrostatic, van der Waals, and solvation terms

RMSD Trajectory Analysis Plot
RMSD Analysis

Root Mean Square Deviation over simulation time for structural stability assessment

3D Free Energy Landscape
3D Free Energy Landscape

FEL surface with contour projection and conformational energy minima identification

Dynamic Cross-Correlation Matrix
DCCM Heatmap

Residue-residue dynamic cross-correlation analysis with customizable color scale

Video Demo

Watch a complete MD simulation workflow

MD Simulation Pipeline Demo

From complex preparation to publication-ready analysis — Coming soon

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