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Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
BMC Bioinformatics volume 24, Article number: 107 (2023)
The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists.
Here, we have developed the VisualDynamics—a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation.
VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at https://visualdynamics.fiocruz.br/login, is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. The code is freely available for download at GitHub https://github.com/LABIOQUIM/visualdynamics.
The Molecular Dynamics (MD) is one of the techniques incorporated into bioinformatics, specifically by structural bioinformatics. With that, it is possible to obtain kinetic and thermodynamic characteristics of biomolecular structures. For example, macromolecular stability, identification of allosteric sites, elucidation of mechanisms of enzymatic activity, molecular recognition and properties of complexes with small molecules, association between proteins, protein folding and its hydration. Furthermore, MD enables a wide range of studies, including molecular design (widely used in drug design), in determining structure and its refinement (X-ray, NMR and protein modeling) . The results obtained at the end of a MD are the richest and most complete in terms of non-quantum simulation . However, implementing a MD experiment is not trivial .
Since its first applied approach to biology in 1977 much has evolved due to increased computational processing as well as improved coding. More than three decades ago, the first MD softwares that were intended for biological problems were launched: Gromacs , AMBER  and NAMD . Since its first versions, these softwares still remain as the most used and cited. However, they continue with the same common implementation difficulties that plague researchers who are not computer specialists .
While structural analysis, modeling and docking methodologies evolved from CLI paradigms to GUI and finally to WEB, MD continues mostly supported by command line execution (CLI type). Some good initiatives have emerged to improve this panorama. Examples of these initiatives are the implementation of plugins in existing software such as QwikMD  plugin to VMD, GROMACS Plugin to PyMOL  and the Molecular Dynamics Simulation option in UCSF Chimera . Although the use of these plugins is an advance, their implementation is still a challenge for most unskilled researchers. It is common for difficulties to install and configure the adaptation that often compromise the full execution of the simulation.
Despite this, two excellent initiatives have emerged that facilitate the use of MD by beginning users of this technique: MDWEB , WebGRO . MDWeb is a portal with several services for molecular dynamics. However, there is no possibility of performing molecular dynamics of protein–ligand complexes and the preparation of the dynamics has been a separate step of the execution. As mentinoed in their tutorial , it is necessary to download and modify the output script files from the preparation step. Just after these modificantions the MD can be performed. WebGRO, in turn, allows performing MD of protein–ligand complexes. However, using only the parameters assigned to the ligand by the PRODRG2 server , limiting the use of the GROMOS force field .
The objective of this work is to present a WEB tool developed to automate biological simulations performed in Gromacs. The application has two options of execution depending on the type of simulation you want to perform. The first is when the simulation is of an isolated biomolecule (Apoprotein) and the second when it is intended to simulate the dynamics of a macromolecule interacting with one small ligand (protein + ligand). Additionally, the user will be able to download the list of commands to run on their own server without any modification necessary. For researchers who want to implement it in their institutions, the application can be installed and served to other users via the WEB.
The application has characteristics of a classic WEB application in which a client terminal consumes the.html content in its station (front-end) provided by a server (back-end) through the internet (or a local network). The application was named VisualDynamics (VD) and uses the Queue-Request or Web-Queue-Worker architecture. The application is accessible through the electronic address http://visualdynamics.fiocruz.br/login and login access must be requested on the same website. Each user can only run one dynamic at a time. Just browse and enjoy the ease. VD offers you the possibility to leave your processes, disconnect from the server, and reconnect again later on, to check the progress of your projects. After completion of Molecular Dynamics, an email is sent to the user.If the goal is to implement a server, the components and libraries are all available for download from the project requirements list available on GitHub (https://github.com/LABIOQUIM/visualdynamics). In this case, the developer will need to install three main groups: (a) Gromacs 2018 (or higher) as shown in the developers’ portal (http://manual.gromacs.org/documentation/current/install-guide/index.html); (b) Python version 3.5 (https://www.python.org/), or higher and (c) The Flask micro framework and all libraries and dependencies (https://flask.palletsprojects.com/en/1.1.x/tutorial/layout/). Optionally, a virtual environment (virtualenv) was used to separate environments. All instructions and components for installing a new server are available on Github already mentioned. On the client side there are no special instructions.
Results and discussion
The simulations follow all the classic steps of a preparation, solvation, neutralization, two-step minimization, two-step equilibration and finally production simulation . The MD has been fixed at 2 ns, but can be changed in the software itself upon request by e-mail to the administrator before running. The application provides simulation in two options: isolated macromolecule (apoprotein) (Fig. 1) and conjugated macmacromolecule with a ligand (protein + ligand) (Fig. 2). Using an apoprotein option, we show the case study of a structure of twenty residues remaining belonging to the n-terminal region of protein-2 of the surface of the merozoite of plasmodium falciparum (PDB code 2mu8). The simulation on VD took about 32 min using the Amber99 force field with a cubic simulation box 2 Angstroms away from the protein boundary.
Isolated macromolecule (apoprotein)
Without any difficulty, the user uploads the.PDB file containing the biomolecule to be simulated, selects the force field, the water model, the type of simulation box, the distance of the biomolecule to the edge of the box, indicates if you want Gromacs to automatically neutralize the system and ignore the hydrogens from the original structure. Finally, alternatively, you have the option of downloading a text file containing all the commands in order of execution and analysis. This situation was considered when the user already has Gromacs installed in his laboratory and only wants to facilitate the execution of the simulation commands sequence. But if the researcher chooses to execute the complete dynamic on the web server, just click on 'Execute' and the server will execute it step by step (Fig. 3).
Conjugated macromolecule with a ligand (protein + ligand)
There are two ways to generate the topology files (.itp file) and the structure's Cartesian coordinates file (.gro file) for simulation the biomolecule conjugated to a ligand: (a) with the ligand prepared in PRODRG2 server  or (b) ACPYPE server . If the user has operational difficulty there are available some tutorial videos on the page. After obtaining the files, just upload them in the indicated fields, configure the desired parameters and run the simulation, or download the command list to run locally.
Analysis and availability of results
After completing a dynamic, the trajectories are converted in order to centralize the biomolecule (gmx trjconv command). From these trajectories, many analyses are performed and compressed into a file that can be downloaded. This file contains the files in.png format generated by the Grace application  which reads the.xvg files produced according to each analysis application in the Gromacs package. This way, the user can quickly observe the results in the graphics in.png (Fig. 4). But in this case, the images come with low resolution.
Alternatively, the user can use the original files (.xvg) and submit them to another preferred software to generate images with better resolution (Table 1).
The researches can also download the Run Log files online. Furthermore, can download all.mdps files used in the simulation online. As previously mentioned, the VD allows the user to choose to generate a command script file for download instead of running it on our servers locally. To do this just click on “Download command list”. This option is useful when the user already has Gromacs installed in his computer park and only wants to speed up, in a standardized way, the simulation process of a biomolecule and/or a biomolecule conjugated with a ligand. This file contains the list of ordered commands and all parameters filled out. Simply batch run it on Linux or copy and paste each line and run at the prompt.
The learning curve for implementing a MD is long. There is a lot of knowledge added in the technique. Even for computationally experienced users, the challenge persists and advances into other areas that are often limiting the success of the simulation. Aspects brought by molecular biophysics, chemistry or physical chemistry make up many obstacles to be overcome. VisualDynamics brings agility in the execution of in silico MD experiment using Gromacs. Inexperienced users with no computer skills will be able to produce dynamics and manage of the data produced at the end of the dynamics. Whether in online or scripted form, the application advances towards allowing the community of researchers interested in applying the MD in their analysis without worrying about intermediate details.
In addition, we are continuously working so that future versions bring more options for parameterization of no-protein ligands using other force field options and other topologies with more improved loading methods. The group's objective is also to implement its own methodology to calculate partial charges and topologies directly on the software, thus allowing to reduce steps.
Availability and requirements
Project name: VisualDynamics. Project home page: http://visualdynamics.fiocruz.br/. Operating system: Linux. Programming language: Python 3.5 or higher, Flask, HTML5. Other requirements: GROMACS 2018 or higher; Grace or Xmgrace. License: FreeBSD. Any restrictions to use by non-academics: None.
Availability of data and materials
All sources codes are freely available at https://github.com/LABIOQUIM/visualdynamics.
Command line interfaces
Graphical user interfaces
World Wide Web
Visual molecular dynamics
Antechamber python parser interface
Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev. 2006;106(5):1589–615.
Stillinger FH, Rahman A. Improved simulation of liquid water by molecular dynamics. J Chem Phys. 1974;60(4):1545–57.
Zinovjev K, van der Kamp MW. Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible. Bioinform. 2020;36(20):5104–6.
Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun. 1995;91(1–3):43–56.
Pearlman DA, Caseb DA, Caldwell JW, Ross WS, Cheatham TE III, DeBolt S, et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun. 1995;91(1–3):1–41.
Nelson MT, Humphrey W, Gursoy A, Dalke A, Kalé LV, Skeel RD, Schulten K. NAMD: a parallel, object-oriented molecular dynamics program. Int J Supercomput Appl High Perform Comput. 1996;10(4):251–68.
Wigdor D, Wixon D. Brave NUI world: designing natural user interfaces for touch and gesture. Elsevier; 2011.
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, et al. Comparative protein structure modeling using Modeller. Curr Protoc Bioinform. 2006;15(1):5–6.
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–91.
Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997;18(15):2714–23.
DeLano WL, Bromberg S. PyMOL user’s guide. DeLano Scientific LLC, 629; 2004.
Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33–8.
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF chimera – a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–12.
HTML5: A vocabulary and associated APIs for HTML and XHTML. W3C Working Draft 24 June 2010. https://www.w3.org/TR/2010/WD-html5-20100624/ (2010). Accessed 20 Sept 2022.
W3C: Cascading Style Sheets. https://www.w3.org/Style/CSS/ (2021). Accessed 20 Sept 2022.
ECMA-262: ECMAScript® 2022 language specification 13th edition. https://www.ecma-international.org/publications-and-standards/standards/ecma-262/. (2022). Accessed 20 Sept 2022.
Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2006;34(suppl_1):D291–5.
Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 2009;37(suppl_1):D387–92.
De Vries SJ, Van Dijk M, Bonvin AM. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc. 2010;5(5):883–97.
Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011;39(suppl_2):W270–7.
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, et al. The ClusPro web server for protein–protein docking. Nat Protoc. 2017;12(2):255–78.
Ribeiro JV, Bernardi RC, Rudack T, Stone JE, Phillips JC, Freddolino PL, Schulten K. QwikMD – integrative molecular dynamics toolkit for novices and experts. Sci Rep. 2016;6(1):1–14.
Makarewicz T, Kazmierkiewicz R. Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL. J Chem Inf Model. 2013;53:1229–34.
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012;28(9):1278–9.
WebGRO for Macromolecular Simulations. University of Arkansas for Medical Sciences. https://simlab.uams.edu/ (2022). Accessed 20 Sept 2022.
Schuettelkopf AW, van Aalten DMF. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Sect D Acta Crystallogr. 2004;60:1355–63.
Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004;25(13):1656–76.
Lemkul JA. GROMACS tutorials, Lysozyme Water. http://www.mdtutorials.com/gmx/lysozyme/index.html (2013). Accessed 15 Jan 2022.
Sousa da Silva AW, Vranken WF. ACPYPE - Antechamber PYthon parser interfacE. BMC Res Notes. 2012;5:367.
Turner P. XMGRACE, Version 5.1. 19. Cent. Coast. Land-Margin Res. Or. Grad. Inst. Sci. Technol. Beaverton OR. https://plasma-gate.weizmann.ac.il/Grace/. (2005). Accessed 15 Jan 2022.
Special thanks to the developers and organization that maintain Gromacs in free format. Without this aspect, the automation proposed in this article would have absolutely nothing to add to the scientific world.
This work has been supported by the The Fundação Oswaldo Cruz (Fiocruz), the Fundação para o Desenvolvimento Científico e Tecnológico em Saúde (Fiotec), the Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental – INCT-EpiAmO, the Fundação Rondônia de Amparo ao Desenvolvimento das Ações Científicas e Tecnológicas e à Pesquisa do Estado de Rondônia (FAPERO), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superiorao (CAPES) and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
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Vieira, I.H.P., Botelho, E.B., de Souza Gomes, T.J. et al. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS. BMC Bioinformatics 24, 107 (2023). https://doi.org/10.1186/s12859-023-05234-y
- Molecular dynamics