New Features in Visual Dynamics 3.0

Summary

Visual Dynamics is an open-source tool that accelerates implementations and learning in molecular dynamics simulation using Gromacs. The presented protocol will guide you through the steps to perform a protein-ligand simulation prepared in ACPYPE with ease and general steps to other simulation models.

Abstract

Visual Dynamics (VD) is a web tool that aims to facilitate the use and application of Molecular Dynamics (MD) executed in Gromacs, allowing users without computational familiarity to run short-time simulations for validation, demonstration, and teaching purposes. It is true that quantum methods are the most accurate. However, there is currently no computational feasibility to carry out the experiments that MD performs. The tool described here has continuously received improvements over the course of the last couple of years. This protocol will describe what is needed to run a simulation in VD with a protein-ligand complex previously prepared in ACPYPE and some general directions on the other simulation models available. For the detailed simulation, the FK506-binding protein from Plasmodium vivax complexed with the inhibitor D5 (PDB ID: 4mgv) will be used, and all files used will be provided. Note that this protocol will tell every option to be used to achieve the same results presented, but these options are not necessarily the only ones available.

Introduction

According to the IUPAC definition, MD is the simulation procedure that consists of computing the motion of atoms in a molecule or of individual atoms or molecules in solids, liquids, and gases, according to Newton's laws of motion. The forces acting on atoms, necessary to simulate their motion, are commonly calculated using force fields from molecular mechanics¹. It can be applied to any phenomenon that seeks to extract information at a molecular and often atomic level².

MD is one of the techniques incorporated into bioinformatics, specifically structural bioinformatics. With it, it is pos....

Protocol

1. Accessing the software and new user registration

1. Visit the Visual Dynamics (VD) web page. Click on the +Register icon at the top right to create an account. Register to use the software.
   NOTE: Only institutional email addresses are allowed. The user will receive an email notification once their registration is approved.
2. Click on Login at the top right to access the system login screen. Fill in the username/email and password fields and cli.......

Discussion

Automating processes is not easy, but it is also less difficult than reprogramming a system from scratch. Gromacs is currently the most popular molecular simulation software, and it is constantly updated. The Department of Biophysical Chemistry at Groningen University initially developed it, and it is now maintained by the Life Sciences Laboratory at the University of Stockholm⁴³.

For any new user, learning simulation techniques is a lengthy journey. VD emerges as an al.......

Materials

Name	Company	Catalog Number	Comments
ACPYPE Server	Bio2Byte		Available at https://www.bio2byte.be/acpype/
GRACE software	Plasma Laboratory at the Weizmann Institute of Science		Available at https://plasma-gate.weizmann.ac.il/Grace/
GROMACS software	GROMACS Team		Installation instructions at https://manual.gromacs.org/current/install-guide/index.html
The structure of the FK506-binding protein From Plasmodium vivax complexed with the inhibitor D5	RCSB Protein Data Bank		Available at https://www.rcsb.org/structure/4mgv Already contains the ligand complexed to the macromolecule.