AmberMD

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.

Software Information

Column 1	Column 2
Name	AmberMD
Description	Suite of biomolecular simulation programs
Creator	Originally by Peter Kollman's group, evolved by a large community
Website	https://ambermd.org/
GitHub	https://github.com/Amber-MD

Industries

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 Post-processing: Supports energy mapping, RMSD calculation, and hydrogen bond analysis.
Flexible Constraints: Can be based on various types of NMR data for diverse applications.

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 DiPhyx

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.
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.
Configure Run Script: In the Run Script field, enter run_script.sh as the input.
Create the Project: Click on Create to prepare your project environment.
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.

Tutorials

1- Nucleic Acids simulations A-DNA to B-DNA transition

This tutorial focuses on the analysis of nucleic acids simulations, specifically studying the transition from A-DNA to B-DNA. The workshop, conducted by Thomas E. Cheatham III, Christina Bergonzo, and Rodrigo Galindo-Murillo, provides a hands-on approach to simulating a 12-base pair DNA molecule starting in the A-DNA configuration and observing its conversion to B-DNA. Using the AmberTools collection, participants generate the initial structure and employ the CPPTRAJ tool to analyze the transition characteristics. The tutorial emphasizes the creation of topology and coordinate files, minimization, equilibration, and the use of CPPTRAJ for detailed trajectory analysis.