A local resampling trick for focused molecular dynamics

We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can lead to incorrect sampling if the selection depends on the configuration in a way that is not accounted for. We avoid this pitfall by introducing appropriate auxiliary variables. This results in an implementation that is closely related to configurational freezing and elastic barrier dynamical freezing. We implement the method and validate that it can be used to supplement conventional molecular dynamics in free energy calculations (absolute hydration and relative binding).

• Publication year

  2023

• Venue

  Unknown venue

• Publication date

  2023-05-09

• Fields of study

  Mathematics, Physics, Chemistry

• Identifiers
  arXiv 2305.05475
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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