02 July 2023 1 1K Report

I encountered an article that is about enhanced sampling method of protein - ligand system.

The paper is 'Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics'. (J. Chem. Theory Comput. 2020, 16, 9, 5526–5547)

The following sentences appear in the paper.

"Next, one can add multiple ligand molecules in the solvent to facilitate ligand binding to proteins in MD simulations. "

"Multiple ligand molecules are added to directly increase ligand concentration in the solvent and enhance ligand binding in LiGaMD simulations. "

How to add multiple ligand molecules to the simulation?

I would appreciate it if you could let me know which tool has such a function.

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