English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

The 3D reference interaction site model (3D-RISM) of molecular solvation is apowerful tool for computing the equilibrium thermodynamics and densitydistributions of solvents, such as water and co-ions, around solute molecules.However, 3D-RISM solutions can be expensive to calculate, especially forproteins and other large molecules where calculating the potential energybetween solute and solvent requires more than half the computation time. Toaddress this problem, we have developed and implemented treecode summation forlong-range interactions and analytically corrected cut-offs for short-rangeinteractions to accelerate the potential energy and long-range asymptoticscalculations in non-periodic 3D-RISM in the AmberTools molecular modelingsuite. For the largest single protein considered in this work, tubulin, thetotal computation time was reduced by a factor of 4. In addition, parallelcalculations with these new methods scale almost linearly and the iterativesolver remains the largest impediment to parallel scaling. To demonstrate theutility of our approach for large systems, we used 3D-RISM to calculate thesolvation thermodynamics and density distribution of 7-ring microtubule,consisting of 910 tubulin dimers, over 1.2 million atoms.

Accelerating the 3D-RISM theory of molecular solvation with treecode summation and cut-offs