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• W3100256459 endingPage "26437" @default.
• W3100256459 startingPage "26419" @default.
• W3100256459 abstract "In molecular dynamics (MD) simulations of condensed-phase systems, straight-cutoff truncation of the non-bonded interactions is well known to cause cutoff noise and serious artifacts in many simulated properties. These effects can be drastically reduced by applying the truncation based on distances between neutral charge groups (CG) rather than between individual atoms (AT). In addition, the mean effect of the omitted electrostatic interactions beyond the cutoff distance can be reintroduced using the reaction-field (RF) method, where the medium outside the cutoff sphere is approximated as a dielectric continuum of permittivity equal to that of the solvent. The RF scheme is generally applied with CG truncation. This is justified for low solvent permittivities, where the RF correction is small and an AT truncation would lead to severe issues, just as in the straight-cutoff case. However, it is less appropriate for solvents with high permittivities, where the RF correction acts as a physically motivated shifting function, and a CG truncation may in turn lead to artifacts and poorer energy conservation. In this study, we assess the impact of truncation artifacts considering the 57 organic liquids which were used in the calibration of the GROMOS-compatible 2016H66 force field. Combinations of shifting or switching schemes with RF-based electrostatic interactions as well as van der Waals (Lennard-Jones) interactions are then introduced to resolve the issues with AT truncation. These shifting and switching schemes have the following properties: (i) they bring the force but not the potential energy to zero at the cutoff; (ii) as a result, they lead to a modification of the interaction that is comparatively small; (iii) they permit to conduct rigorously conservative simulations; (iv) the energies can easily be corrected back to the unmodified form, either on the fly or in a post-processing step. The mathematical formalism of these schemes is presented in detail, and their validation is performed using the 57 organic liquids." @default.
• W3100256459 created "2020-11-23" @default.
• W3100256459 creator A5005181934 @default.
• W3100256459 creator A5016007455 @default.
• W3100256459 creator A5019754904 @default.
• W3100256459 date "2020-01-01" @default.
• W3100256459 modified "2023-10-12" @default.
• W3100256459 title "Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff" @default.
• W3100256459 cites W1651084065 @default.
• W3100256459 cites W1778838665 @default.
• W3100256459 cites W1963957612 @default.
• W3100256459 cites W1966867657 @default.
• W3100256459 cites W1967316693 @default.
• W3100256459 cites W1967617304 @default.
• W3100256459 cites W1968583410 @default.
• W3100256459 cites W1971063953 @default.
• W3100256459 cites W1975945758 @default.
• W3100256459 cites W1977194203 @default.
• W3100256459 cites W1978393297 @default.
• W3100256459 cites W1979837325 @default.
• W3100256459 cites W1980609122 @default.
• W3100256459 cites W1982510256 @default.
• W3100256459 cites W1983793204 @default.
• W3100256459 cites W1985070997 @default.
• W3100256459 cites W1987981639 @default.
• W3100256459 cites W1990871033 @default.
• W3100256459 cites W1990948072 @default.
• W3100256459 cites W1992865572 @default.
• W3100256459 cites W1992882086 @default.
• W3100256459 cites W1993728228 @default.
• W3100256459 cites W1995535139 @default.
• W3100256459 cites W1997975224 @default.
• W3100256459 cites W2001676859 @default.
• W3100256459 cites W2002635476 @default.
• W3100256459 cites W2002897372 @default.
• W3100256459 cites W2005433348 @default.
• W3100256459 cites W2006936505 @default.
• W3100256459 cites W2009828755 @default.
• W3100256459 cites W2010414544 @default.
• W3100256459 cites W2010474566 @default.
• W3100256459 cites W2013228407 @default.
• W3100256459 cites W2013821125 @default.
• W3100256459 cites W2016860778 @default.
• W3100256459 cites W2016877494 @default.
• W3100256459 cites W2017316247 @default.
• W3100256459 cites W2017417570 @default.
• W3100256459 cites W2017502848 @default.
• W3100256459 cites W2017642323 @default.
• W3100256459 cites W2017984696 @default.
• W3100256459 cites W2023940150 @default.
• W3100256459 cites W2024726841 @default.
• W3100256459 cites W2025521218 @default.
• W3100256459 cites W2027154929 @default.
• W3100256459 cites W2027988831 @default.
• W3100256459 cites W2029940779 @default.
• W3100256459 cites W2030765885 @default.
• W3100256459 cites W2034031073 @default.
• W3100256459 cites W2034624515 @default.
• W3100256459 cites W2035266068 @default.
• W3100256459 cites W2035687084 @default.
• W3100256459 cites W2038337607 @default.
• W3100256459 cites W2039198815 @default.
• W3100256459 cites W2041666726 @default.
• W3100256459 cites W2046829278 @default.
• W3100256459 cites W2047607838 @default.
• W3100256459 cites W2056081735 @default.
• W3100256459 cites W2056940848 @default.
• W3100256459 cites W2059566793 @default.
• W3100256459 cites W2060757799 @default.
• W3100256459 cites W2060966157 @default.
• W3100256459 cites W2063852048 @default.
• W3100256459 cites W2064847013 @default.
• W3100256459 cites W2065419564 @default.
• W3100256459 cites W2067174909 @default.
• W3100256459 cites W2067597831 @default.
• W3100256459 cites W2068644111 @default.
• W3100256459 cites W2071827681 @default.
• W3100256459 cites W2077622157 @default.
• W3100256459 cites W2078146440 @default.
• W3100256459 cites W2079102984 @default.
• W3100256459 cites W2083474267 @default.
• W3100256459 cites W2084282274 @default.
• W3100256459 cites W2085478435 @default.
• W3100256459 cites W2091443139 @default.
• W3100256459 cites W2093221728 @default.
• W3100256459 cites W2100510559 @default.
• W3100256459 cites W2103734924 @default.
• W3100256459 cites W2104841748 @default.
• W3100256459 cites W2106140689 @default.
• W3100256459 cites W2112959255 @default.
• W3100256459 cites W2113149246 @default.
• W3100256459 cites W2127886102 @default.
• W3100256459 cites W2136278162 @default.
• W3100256459 cites W2136473673 @default.
• W3100256459 cites W2144062946 @default.
• W3100256459 cites W2152950087 @default.
• W3100256459 cites W2152977647 @default.
• W3100256459 cites W2153508513 @default.

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