MD Simulation
List of widely used MD Simulation Analysis Tools.
Molecular Dynamics (MD) simulation analysis involves interpreting the vast amounts of data generated during the simulation of molecular systems. These analyses are necessary to study the physical movements of atoms and molecules, the stability of molecular conformations, reaction mechanisms, and thermodynamic properties, among other aspects. In this article, we will give a brief overview of some widely used MD simulation analysis tools.
1. MDAnalysis
MDAnalysis is a Python library that offers a flexible framework for the analysis of molecular dynamics trajectories.
- It allows users to read, write, and analyze trajectory data and molecular structures.
- It supports multiple file formats,
- provides a variety of built-in analysis functions,
- integrates well with other Python scientific libraries like NumPy and SciPy, and
- enables custom analysis through an extensible API.
Availability: Freely available on GitHub- https://github.com/MDAnalysis/mdanalysis
2. MDTraj
MDTraj is a Python library designed for analyzing MD trajectories. MDTraj is known for its speed and efficiency in handling large datasets and performing common analysis tasks.
- Fast and efficient trajectory analysis.
- supports multiple file formats such as pdb, xtc, trr, dcd, binpos, netcdf, prmtop, and more.
- integrates seamlessly with other Python data analysis tools.
- fast RMSD calculations.
- extensive MD trajectory analysis including computing bonds, angles, dihedrals, hydrogen bonds, secondary structure, and NMR observables.
Availability: Freely available at https://www.mdtraj.org/1.9.8.dev0/installation.html
3. VMD (Visual Molecular Dynamics)
As we are aware, VMD is a tool for the visualization, animation, and analysis of large biomolecular systems. VMD supports the visualization of molecular structures and simulation trajectories and can be extended through scripting.
- interactive visualization
- supports a wide range of file formats, and
- includes powerful scripting capabilities with TCL and Python.
- It is widely used for displaying complex molecular animations and analyzing structural properties.
Availability: Freely available at https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
4. CPPTRAJ
It is a versatile program within the AmberTools suite designed for processing and analyzing molecular dynamics trajectory data. CPPTRAJ allows users to perform a wide range of analyses, from simple data extraction to complex manipulations.
- Supports multiple trajectory formats,
- offers extensive analysis and data manipulation functions,
- provides scripting capabilities for automated analyses.
Availability: Freely available on GitHub – https://github.com/Amber-MD/cpptraj
5. GROMACS Tools
The GROMACS suite itself has a collection of utilities tailored for analyzing MD trajectories generated by GROMACS simulations. These tools facilitate a broad spectrum of analyses, from simple measurements to detailed statistical evaluations.
- Highly optimized for performance,
- integrated seamlessly with GROMACS simulation workflows,
- provides a comprehensive set of analysis functions.
Availability: Comes with GROMACS suite available at https://manual.gromacs.org/
6. PyEMMA (Python Essential MD Analysis)
PyEMMA is a Python library specialized in the analysis of molecular dynamics simulations, with a strong focus on Markov state models (MSMs). PyEMMA helps in estimating kinetic models and performing statistical analysis of MD data.
- Includes tools for MSM estimation and validation and Bayesian estimation of MSMs, Time-lagged independent component analysis (TICA).
- supports all generally used MD formats
- Plotting functions for data visualization and production of publishable figures.
- Systematic coarse-graining of MSMs to transition models with few states.
Availability: Freely available at http://www.emma-project.org/latest/
7. PLUMED (The community-developed PLUgin for MolEcular Dynamics)
It is an open-source library that can be used in conjunction with many MD codes for enhanced sampling and free energy calculations. PLUMED is also useful for post-processing and analyzing MD data.
- Provides advanced algorithms for enhanced sampling,
- supports various free energy calculation methods,
- includes versatile tools for data analysis.
Availability: Freely available at https://www.plumed.org/download
8. Free_Energy_Landscape-MD
Free_Energy_Landscape-MD is a Python package designed for the analysis and visualization of free energy landscapes derived from molecular dynamics (MD) simulations. Free energy landscapes provide critical insights into the conformational states of molecular systems and the transitions between these states, which are essential for understanding various biological processes such as protein folding, ligand binding, and conformational changes.
- Designed to work seamlessly with output data from popular MD simulation package – GROMACS
- provides a 3D Free Energy Landscape (FEL) plot showing the minima points.
- utilizes Principal Component Analysis (PCA) of the Molecular Dynamics (MD) trajectory to generate the FEL.
- offers specific time frames corresponding to the minima regions in the FEL.
Availability: Freely available on GitHub – https://github.com/MunibaFaiza/Free_Energy_Landscape-MD
9. g_mmpbsa
It is a script that works with GROMACS to perform MM/PBSA and MM/GBSA calculations.
- Compatible with GROMACS,
- allows for the calculation of binding free energies,
- provides tools for generating input files and analyzing output data.
Availability: Freely available at https://rashmikumari.github.io/g_mmpbsa/
10. gmx_MMPBSA
A Python-based tool that integrates with GROMACS to perform MM/PBSA and MM/GBSA calculations.
- Provides an easy-to-use interface for setting up and performing free energy calculations,
- works with all GROMACS versions along with AmberTools >= 20.
Availability: Freely available on GitHub – https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
Bioinformatics Programming
Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.
In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It is difficult to understand and plot a meaningful FEL and then extract the time frames at which the plot shows minima. In this article, we introduce a new Python package (Free_Energy_Landscape-MD) to generate an FEL based on principal component analysis (PCA) from MD simulation done by GROMACS [1].
![[Tutorial] Installing VIAMD on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/12/01184130/viamd.jpg)
Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).
In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.
In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.
Visualizing plots of molecular dynamics simulation is easy once you have generated them. Previously, we provided a few articles on MD output analysis (check the Further Reading section). This article explains how you can easily visualize the plots generated from GROMACS output. (more…)
MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)
We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)
It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)
GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)
We have provided several articles on GROMACS [1] installation on Ubuntu including the easy installation method for GROMACS version 5.x.x. In this article, we will provide shell scripts to install the latest (2021 series) of GROMACS on Ubuntu 18.04 and 20.04. (more…)
MD simulation is a tricky technique if you don’t understand what you are doing through various parameters and algorithms in GROMACS [1]. That may lead to several errors. In this article, we are going to create an index file for the protein groups in GROMACS to solve such errors. (more…)
Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. (more…)
GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of small organic molecules. (more…)
In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD simulation of a simple protein and a protein-ligand complex. (more…)
We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein, and a complex. In this article, we will analyze the GROMACS [1] output of MD simulation of a complex. (more…)
Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers. It requires software to upload and download files to and from the server. In this article, we have explained how to submit MD simulation jobs on cluster computers using PBS scripts. (more…)
GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation using GROMACS including its installation on Ubuntu. In this article, we will install GROMACS with GPU acceleration. (more…)
GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex as well. In this article, we will install GROMOS96 on Ubuntu. (more…)
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)
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