TOLEDO: Accelerated Maestro GUI molecular dynamics simulations

01 June 2023, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


Classical Molecular Dynamics (MD) simulate the dynamical evolution of biological systems at the atomic level. Using MD in conjunction with high-performance computing (HPC) architectures we can evaluate the possible interactions between a ligand library against one protein target to find a drug that can influence a protein target to cure a disease. Simultaneously we can also obtain information about their dynamical evolution  One of the main software of MD is Desmond, which uses Maestro to set up, run and analyze MD with a graphical interface (GUI), allowing it to be used by non-expert users. However, using the GUI, users can typically run only one short (less than 1000 ns) MD simultaneously.  Our work aims to create a method/protocol to run several MD simultaneously on a remote HPC cluster within Maestro-Desmond. In this work, we provide a method called TOLEDO (Throughput Optimization of Ligand-Protein systems Exploration through Dynamics simulation in Optimized HPC systems) to overcome such limitations and run several MD simultaneously time. Also, TOLEDO is independent of the time limitation of many clusters, the only limitation is the storage space that users have in the cluster. To run TOLEDO, first, we prepare/set up the protein-ligand complex before running MD via Maestro GUI. Next, we run the main script of TOLEDO to run several MD in a supercomputer such as Turgalium of CIEMAT ( or SAGA (, when the MD are finished. TOLEDO run the analysis. Finally, the results obtained by users are the reports and the graphics, which are very simple to interpret. In summary, TOLEDO is a tool that allows researchers to run MD with higher throughput than the Maestro GUI.


Molecular Dynamics
High Perfomance Computing
Structural Bioinformatics

Supplementary materials

TOLEDO: Accelerated Maestro GUI molecular dynamics simulations Supplemental File
Supplemental File with the configuration of the server, examples of TOLEDO, and all the information about the Case Studies


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