Matches in SemOpenAlex for { <https://semopenalex.org/work/W4280492646> ?p ?o ?g. }
- W4280492646 endingPage "1270" @default.
- W4280492646 startingPage "1251" @default.
- W4280492646 abstract "The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite. For the largest single protein considered in this work, tubulin, the total computation time was reduced by a factor of 4. In addition, parallel calculations with these new methods scale almost linearly and the iterative solver remains the largest impediment to parallel scaling. To demonstrate the utility of our approach for large systems, we used 3D-RISM to calculate the solvation thermodynamics and density distribution of 7-ring microtubule, consisting of 910 tubulin dimers, over 1.2 million atoms." @default.
- W4280492646 created "2022-05-22" @default.
- W4280492646 creator A5014335702 @default.
- W4280492646 creator A5030223056 @default.
- W4280492646 creator A5083684380 @default.
- W4280492646 date "2022-05-14" @default.
- W4280492646 modified "2023-10-16" @default.
- W4280492646 title "Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut‐offs" @default.
- W4280492646 cites W1825216778 @default.
- W4280492646 cites W1969434640 @default.
- W4280492646 cites W1976161355 @default.
- W4280492646 cites W1977255290 @default.
- W4280492646 cites W1979401635 @default.
- W4280492646 cites W1981225934 @default.
- W4280492646 cites W1993903061 @default.
- W4280492646 cites W1995933122 @default.
- W4280492646 cites W1996088267 @default.
- W4280492646 cites W2000702472 @default.
- W4280492646 cites W2000883098 @default.
- W4280492646 cites W2002431986 @default.
- W4280492646 cites W2005274401 @default.
- W4280492646 cites W2013810306 @default.
- W4280492646 cites W2014118668 @default.
- W4280492646 cites W2015580322 @default.
- W4280492646 cites W2023551164 @default.
- W4280492646 cites W2026926005 @default.
- W4280492646 cites W2027369153 @default.
- W4280492646 cites W2027713141 @default.
- W4280492646 cites W2027723257 @default.
- W4280492646 cites W2034746349 @default.
- W4280492646 cites W2037176511 @default.
- W4280492646 cites W2037242832 @default.
- W4280492646 cites W2041137266 @default.
- W4280492646 cites W2043701535 @default.
- W4280492646 cites W2049475242 @default.
- W4280492646 cites W2050270973 @default.
- W4280492646 cites W2061018719 @default.
- W4280492646 cites W2064414576 @default.
- W4280492646 cites W2064571598 @default.
- W4280492646 cites W2065283382 @default.
- W4280492646 cites W2068306188 @default.
- W4280492646 cites W2068376486 @default.
- W4280492646 cites W2070116427 @default.
- W4280492646 cites W2070645384 @default.
- W4280492646 cites W2071242009 @default.
- W4280492646 cites W2072683434 @default.
- W4280492646 cites W2073662804 @default.
- W4280492646 cites W2079280953 @default.
- W4280492646 cites W2083206954 @default.
- W4280492646 cites W2087271871 @default.
- W4280492646 cites W2088179443 @default.
- W4280492646 cites W2090560534 @default.
- W4280492646 cites W2091213355 @default.
- W4280492646 cites W2093806300 @default.
- W4280492646 cites W2102182691 @default.
- W4280492646 cites W2107115179 @default.
- W4280492646 cites W2110983237 @default.
- W4280492646 cites W2123712613 @default.
- W4280492646 cites W2131935603 @default.
- W4280492646 cites W2141002805 @default.
- W4280492646 cites W2143598945 @default.
- W4280492646 cites W2147970410 @default.
- W4280492646 cites W2147993766 @default.
- W4280492646 cites W2159582516 @default.
- W4280492646 cites W2167029191 @default.
- W4280492646 cites W2330806673 @default.
- W4280492646 cites W2336637512 @default.
- W4280492646 cites W2404280981 @default.
- W4280492646 cites W2472018069 @default.
- W4280492646 cites W2589948472 @default.
- W4280492646 cites W2772606519 @default.
- W4280492646 cites W2797907849 @default.
- W4280492646 cites W2799809717 @default.
- W4280492646 cites W2892377120 @default.
- W4280492646 cites W2968250638 @default.
- W4280492646 cites W3081855866 @default.
- W4280492646 cites W8777443 @default.
- W4280492646 doi "https://doi.org/10.1002/jcc.26889" @default.
- W4280492646 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/35567580" @default.
- W4280492646 hasPublicationYear "2022" @default.
- W4280492646 type Work @default.
- W4280492646 citedByCount "2" @default.
- W4280492646 countsByYear W42804926462023 @default.
- W4280492646 crossrefType "journal-article" @default.
- W4280492646 hasAuthorship W4280492646A5014335702 @default.
- W4280492646 hasAuthorship W4280492646A5030223056 @default.
- W4280492646 hasAuthorship W4280492646A5083684380 @default.
- W4280492646 hasBestOaLocation W42804926462 @default.
- W4280492646 hasConcept C11413529 @default.
- W4280492646 hasConcept C121332964 @default.
- W4280492646 hasConcept C121864883 @default.
- W4280492646 hasConcept C126255220 @default.
- W4280492646 hasConcept C147597530 @default.
- W4280492646 hasConcept C148093993 @default.
- W4280492646 hasConcept C159985019 @default.
- W4280492646 hasConcept C185592680 @default.
- W4280492646 hasConcept C18762648 @default.
- W4280492646 hasConcept C192562407 @default.