MD Simulation Pipeline

Protein Structure Input

Upload PDB File

Drag and drop your PDB file here or click to browse

Fetch from PDB

PDB ID:

Fill Missing Residues

Detect missing residues in the experimental structure using RCSB annotations and complete them with ESMFold. You can choose which chains to include in the completion.

If you use this workflow in your research, please cite: ESM Atlas

Detect Missing Residues

Structure Comparison Preview

Compare the completed structure (right) with the original crystal structure (left) to see the added missing residues.

Original Crystal Structure

Completed Structure

Structure Preparation for AMBER

Prepare the protein structure for AMBER force field generation by cleaning and modifying the PDB file.

Remove Components

Remove water molecules

Remove all water molecules (HOH, WAT, TIP3, etc.) from the structure

Remove ions

Remove all ions (Na+, Cl-, K+, Mg2+, etc.) from the structure

Remove hydrogen atoms

Remove all hydrogen atoms from the protein structure

Add Capping Groups and Select Protein Chains

Add NME group (C-terminal)

Add N-methyl amide (NME) group to C-terminal residues

Add ACE group (N-terminal)

Add acetyl (ACE) group to N-terminal residues

Preserve Chains for FF Generation:

Select one or more protein chains to include in preparation

Ligand Handling

Preserve ligands

Keep ligands in the structure and append them at the end

Create separate ligand file

Extract ligands to a separate PDB file for individual processing

Select Ligands to Preserve

Tick ligands to include. Unselected ligands will be ignored.

Ligand Docking

Configure docking for preserved ligands using AutoDock Vina and Meeko. Select which ligands to dock, define the Vina bounding box with live visualization, then run docking and choose poses.

Select Ligands to Dock

Choose which preserved ligands should be included in docking calculations.

Docking Search Space Setup

Search Space Visualization

The protein–ligand system is shown below. For each selected ligand, a bounding box (10×10×10 Å by default) represents the Vina search space. Adjust box dimensions below to update the visualization live.

Box Dimensions for Selected Ligands

Simulation Parameters

System Setup

Box Type:

Distance (Å):

Ligand Force Field

Ligand Force Field:

Force Field & Water Model

Protein Force Field:

Water Model:

Add Ions:

Temperature & Pressure

Temperature (K):

Pressure (atm):

Thermostat:

Integration Parameters

Time Step (ps):

Cutoff Distance (Ang):

Electrostatic:

Simulation Steps Configuration

Restrained Minimization

Steps:

Force Constant (kJ/mol/Å²):

Minimization

Steps:

Algorithm:

NPT Heating

Steps:

Target Temperature (K):

NPT Equilibration

Steps:

Temperature (K):

Pressure (atm):

Production Run(NPT)

Steps:

Temperature (K):

Pressure (atm):

Click on Generate All Files. If you want to run biased simulations using PLUMED, proceed to the next section (PLUMED) to configure collective variables. Otherwise, download all files here and you're all set!

Generate Simulation Files

Note: All CVs are taken from PLUMED v2.9 documentation.

If you use PLUMED in your research, please cite it. Citation information

PLUMED Collective Variables

Configure Collective Variables (CVs) for biased MD simulations. Select a CV from the sidebar to view documentation and examples.

Select a Collective Variable

Choose a CV from the left sidebar to view its documentation and configure it for your simulation.

Module

Description

Syntax

Glossary of keywords and components

Options

Components

Examples

Notes

Write Custom PLUMED File

Write your custom PLUMED configuration from scratch. This editor allows you to create a complete PLUMED input file.

Custom PLUMED Configuration

Generate Simulation Files

Generate and download simulation files for your PLUMED setup.

Protein Structure Input

Upload PDB File

Fetch from PDB

Protein Preview

Fill Missing Residues

Detect Missing Residues

Select Chains for Completion

Trim Residues from Edges (Optional)

Energy Minimization (Optional)

Missing Residues Summary

Protein Sequence Viewer

Structure Comparison Preview

Original Crystal Structure

Completed Structure

Superimposed Structure View

Structure Preparation for AMBER

Remove Components

Add Capping Groups and Select Protein Chains

Ligand Handling

Preparation Status

Prepared Structure Preview

Ligand Docking

Search Space Visualization

Box Dimensions for Selected Ligands

Visualize Binding Poses

Simulation Parameters

System Setup

Ligand Force Field

Force Field & Water Model

Temperature & Pressure

Integration Parameters

Simulation Steps Configuration

Restrained Minimization

Minimization

NPT Heating

NPT Equilibration

Production Run(NPT)

Generate Simulation Files

Generated Files

Download Files

Simulation Summary

PLUMED Collective Variables

Collective Variables

Select a Collective Variable

Module

Description

Syntax

Glossary of keywords and components

Options

Components

Examples

Notes

Related Collective Variables

Your Configuration

Saved Configurations

Write Custom PLUMED File

Custom PLUMED Configuration

Generate Simulation Files

Viewer PDB File