FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2044017870> ?p ?o ?g. }

• W2044017870 abstract "In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call “Hamiltonian dielectric solvent” (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation." @default.
• W2044017870 created "2016-06-24" @default.
• W2044017870 creator A5032995111 @default.
• W2044017870 creator A5037695758 @default.
• W2044017870 creator A5042470831 @default.
• W2044017870 date "2014-03-10" @default.
• W2044017870 modified "2023-09-27" @default.
• W2044017870 title "Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics" @default.
• W2044017870 cites W1964009616 @default.
• W2044017870 cites W1964652029 @default.
• W2044017870 cites W1968096530 @default.
• W2044017870 cites W1968916468 @default.
• W2044017870 cites W1971139734 @default.
• W2044017870 cites W1975053245 @default.
• W2044017870 cites W1976499671 @default.
• W2044017870 cites W1977867181 @default.
• W2044017870 cites W1984015691 @default.
• W2044017870 cites W1984942356 @default.
• W2044017870 cites W1985113548 @default.
• W2044017870 cites W1990294803 @default.
• W2044017870 cites W1999670894 @default.
• W2044017870 cites W2002484456 @default.
• W2044017870 cites W2003348801 @default.
• W2044017870 cites W2003626295 @default.
• W2044017870 cites W2011842427 @default.
• W2044017870 cites W2012551774 @default.
• W2044017870 cites W2013183108 @default.
• W2044017870 cites W2017686863 @default.
• W2044017870 cites W2018312454 @default.
• W2044017870 cites W2022492426 @default.
• W2044017870 cites W2027408247 @default.
• W2044017870 cites W2028993370 @default.
• W2044017870 cites W2040809566 @default.
• W2044017870 cites W2046001409 @default.
• W2044017870 cites W2047730466 @default.
• W2044017870 cites W2049475242 @default.
• W2044017870 cites W2050333027 @default.
• W2044017870 cites W2054160223 @default.
• W2044017870 cites W2057664120 @default.
• W2044017870 cites W2059466103 @default.
• W2044017870 cites W2061411013 @default.
• W2044017870 cites W2064869494 @default.
• W2044017870 cites W2065101872 @default.
• W2044017870 cites W2067178485 @default.
• W2044017870 cites W2068306188 @default.
• W2044017870 cites W2080131977 @default.
• W2044017870 cites W2083206954 @default.
• W2044017870 cites W2088294132 @default.
• W2044017870 cites W2088957939 @default.
• W2044017870 cites W2089258285 @default.
• W2044017870 cites W2093221728 @default.
• W2044017870 cites W2093381148 @default.
• W2044017870 cites W2103734924 @default.
• W2044017870 cites W2107317356 @default.
• W2044017870 cites W2113149246 @default.
• W2044017870 cites W2127116852 @default.
• W2044017870 cites W2134544924 @default.
• W2044017870 cites W2149979295 @default.
• W2044017870 cites W2159010139 @default.
• W2044017870 cites W2161077193 @default.
• W2044017870 cites W2171891719 @default.
• W2044017870 cites W2317980690 @default.
• W2044017870 cites W2320771862 @default.
• W2044017870 cites W2323178299 @default.
• W2044017870 cites W2334736369 @default.
• W2044017870 cites W3101006260 @default.
• W2044017870 cites W3104017686 @default.
• W2044017870 cites W3104163644 @default.
• W2044017870 cites W404752071 @default.
• W2044017870 cites W4230466483 @default.
• W2044017870 cites W4247951394 @default.
• W2044017870 cites W4376999360 @default.
• W2044017870 doi "https://doi.org/10.1063/1.4867281" @default.
• W2044017870 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24628148" @default.
• W2044017870 hasPublicationYear "2014" @default.
• W2044017870 type Work @default.
• W2044017870 sameAs 2044017870 @default.
• W2044017870 citedByCount "10" @default.
• W2044017870 countsByYear W20440178702014 @default.
• W2044017870 countsByYear W20440178702015 @default.
• W2044017870 countsByYear W20440178702016 @default.
• W2044017870 crossrefType "journal-article" @default.
• W2044017870 hasAuthorship W2044017870A5032995111 @default.
• W2044017870 hasAuthorship W2044017870A5037695758 @default.
• W2044017870 hasAuthorship W2044017870A5042470831 @default.
• W2044017870 hasConcept C10803110 @default.
• W2044017870 hasConcept C117626034 @default.
• W2044017870 hasConcept C121332964 @default.
• W2044017870 hasConcept C121864883 @default.
• W2044017870 hasConcept C126255220 @default.
• W2044017870 hasConcept C130787639 @default.
• W2044017870 hasConcept C133386390 @default.
• W2044017870 hasConcept C139287275 @default.
• W2044017870 hasConcept C147597530 @default.
• W2044017870 hasConcept C16653646 @default.
• W2044017870 hasConcept C185592680 @default.
• W2044017870 hasConcept C30475298 @default.
• W2044017870 hasConcept C32909587 @default.
• W2044017870 hasConcept C33923547 @default.
• W2044017870 hasConcept C37798101 @default.

• next