Performing MD in non-aqueous medium?

27 November 2023 0 3K Report

Hello everyone, is it possible to prepare a protein for molecular docking using MD simulation in NVT and NPT ensembles and then use the output file in one’s desired solvent and temperature as an input file for a molecular docking software such as Auto Dock? as you know, .pdb files available on the Protein Data Bank are all produced in aqueous medium and near 25C. I appreciate any help in advance.

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