2015
DOI: 10.1002/9781118889886.ch2
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Polarizable Force Fields for Biomolecular Modeling

Abstract: Classical electrostatics models that take into account polarization appeared as early as the 1950s. Barker in his 1953 paper "Statistical Mechanics of Interacting Dipoles" discussed the electrostatic energy of molecules in terms of "permanent and induced dipoles". 13 Currently, polarizable models generally fall into three categories: those based on induced point dipoles, 9, 14-23 the classical Drude oscillators, 24-26 and fluctuating charges. 27-30 More sophisticated force fields that are "electronic structure… Show more

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Cited by 70 publications
(114 citation statements)
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“…The metenkephalin solute is solvated in a 42 3 Å 3 box of TIP4P/Ew waters. The U5A3 system is solvated in a 46 3 Å 3 box of TIP4P/Ew waters and an ion environment of 7 Na + and 6 Cl − .…”
Section: Illustrative Examplesmentioning
confidence: 99%
See 1 more Smart Citation
“…The metenkephalin solute is solvated in a 42 3 Å 3 box of TIP4P/Ew waters. The U5A3 system is solvated in a 46 3 Å 3 box of TIP4P/Ew waters and an ion environment of 7 Na + and 6 Cl − .…”
Section: Illustrative Examplesmentioning
confidence: 99%
“…The U5A3 system is solvated in a 46 3 Å 3 box of TIP4P/Ew waters and an ion environment of 7 Na + and 6 Cl − . These systems were prepared by performing pure-MM simulations (1 fs/step) for 1 ns at 298 K and 1 atm to equilibrate the density.…”
Section: Illustrative Examplesmentioning
confidence: 99%
“…Recently, there has been an increasing amount of research developing polarizable force fields . Among the most popular ones is atomic multipole optimized energetics for biomolecular applications (AMOEBA), which is available in several packages, such as Tinker, Force Field X, OpenMM, and AMBER .…”
Section: Introductionmentioning
confidence: 99%
“…23 Thus, to apply the configurational sampling algorithms needed to quantify thermodynamics, multipolar force fields must address transferability of their multipole moments as a function of molecular conformation, while also consistently treating both intra- and intermolecular polarization. 23, 24 A few examples of multipolar energy functions include AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) 2426 , GMM (Gaussian Multipolar Model) 27, 28 , SIBFA (Sum of Interactions Between Fragments Ab Initio Computed) 29, 30 and NEMO (Non-empirical Molecular Orbital) 31 , which are described in recent reviews 3234 . The accuracy and transferability improvements of AMOEBA relative to FC force fields have been demonstrated in the context of water 25, 35 , ion solvation 36 , the properties of small organic molecules 24, 26, 3638 and for protein energetics.…”
Section: Introductionmentioning
confidence: 99%
“…The accuracy and transferability improvements of AMOEBA relative to FC force fields have been demonstrated in the context of water 25, 35 , ion solvation 36 , the properties of small organic molecules 24, 26, 3638 and for protein energetics. 34, 39 …”
Section: Introductionmentioning
confidence: 99%