ArticleThe Journal of chemical physics2020
A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.
Article in The Journal of chemical physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Before beginning the production phase of molecular dynamics simulations, i.e., the phase that produces the data to be analyzed, it is often necessary to first perform a series of one or more preparatory minimizations and/or molecular dynamics simulations in order to ensure that subsequent production simulations are stable. This is particularly important for simulations with explicit solvent molecules. Despite the preparatory minimizations and simulations being ubiquitous and essential for stable production simulations, there are currently no general recommended procedures to perform them and very few criteria to decide whether the system is capable of producing a stable simulation trajectory. Here, we propose a simple and well-defined ten step simulation preparation protocol for explicitly solvated biomolecules, which can be applied to a wide variety of system types, as well as a simple test based on the system density for determining whether the simulation is stabilized.
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Registered trials
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