AmberMD

Advanced Molecular Dynamics Simulation

Developed by Peter Kollman's group at the University of California, San Francisco, AmberMD is a molecular dynamics software suite for biomolecular simulations, using force fields originally created for the AMBER force field. Written in Fortran 90 and C, AmberMD supports Unix-like operating systems and compilers, specializing in biomolecular systems simulations. Discover AmberMD and its AmberMD GitHub.

Features

• Force Fields for Biomolecules: Implements a set of force fields for molecular dynamics of biomolecules.

• GPU Acceleration: Supports explicit solvent PME and implicit solvent GB simulations, with enhanced speed on NVIDIA GPUs.

• Periodic Boundary Conditions: Efficient simulations with PME method for electrostatic interactions and continuum models for van der Waals interactions.

• Support for Various Biomolecules: Extensive support for proteins, nucleic acids, small organic molecules, and carbohydrate mimics.

• Advanced Simulation Types: Offers QM/MM calculations, constant pH calculations, and various molecular dynamics simulations.

Capabilities and Services

• Building Systems: Includes cleaning up protein PDB files and residue naming for AmberMD simulations.

• QM/MM Calculations: Features adaptive solvent QM/MM simulations and Born-Oppenheimer molecular dynamics.

• Constant pH Simulations: Conducts simulations at constant pH, including pH MD replica exchange.

• Molecular Dynamics: Supports protein, enzyme, RNA, DNA, lipid, and membrane protein molecular dynamics.

• Trajectory Analysis: Provides extensive tools for trajectory file observation and analysis.

Scientific Applications

• Quantum Dynamics: Engages in path-integral molecular dynamics, CMD, RPMD, and reactive dynamics.

• Trajectory Analysis and Postprocessing: Supports energy mapping, RMSD calculation, and hydrogen bond analysis.

• Flexible Constraints: Can be based on various types of NMR data for diverse applications.

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Explore "AmberMD" Tutorials.

How to Run Amber MD:

This guide outlines the procedure for conducting a Free Energy Calculation using Amber MD. The necessary files for this case study are conveniently packaged in tutorial3.zip. Additionally, you should obtain (or create) the run_script.sh, a script designed to setup and initiate the simulation inputs.

Steps to Execute on Our Platform

1. Upload Files: Click on the folder icon next to the Volume line and upload both tutorial3.zip and run_script.sh to the working directory (/data) of your project.
2. Set Project Directory: Make sure the Project Directory is set to /data (or the mounted volume to entered!).
   1. if you want to change the Project Directory, make sure to apply the changes in the run_script.sh accordingly.
3. Configure Run Script: In the Run Script field, enter run_script.sh as the input.
4. Create the Project: Click on Create to prepare your project environment.
5. Run the Container: Navigate to the project tab and start the container to run the script.

For further post-processing, our provided notebooks are available, and for visualization of results, tools such as Paraview, VMD, or others can be utilized.