AMOEBA force

As electric fields and potential of molecules can be generated upon distributed p, the second order energies schemes of the SIBFA approach can be directly fueled by the density fitted coefficients. To conclude, an important asset of the GEM approach is the possibility of generating a general framework to perform Periodic Boundary Conditions (PBC) simulations. Indeed, such process can be used for second generation APMM such as SIBFA since PBC methodology has been shown to be a key issue in polarizable molecular dynamics with the efficient PBC implementation [60] of the multipole based AMOEBA force field [61]. 

Piquemal J-P, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA (2006) Towards accurate solvation dynamics of divalent cations in water using the polarizable Amoeba force field from energetics to structure. J Chem Phys 125 054511... 

More recently, Ponder and co-workers [40-48] developed the AMOEBA force field based on a modification of the formulation of Applequist [49] and Thole [50], It is based on a modification of Eq. (9-3) with the static electric field due to permanent charges replaced by permanent multipoles ... 

In the AMOEBA force field the permanent atomic multipoles are determined from QM calculations [40], The prescription considers that the resulting multipoles on the atoms result from two components, the permanent and the induced moments ... 

Cisneros, G. A. [2012], Application of gaussian electrostatic model [GEM] distributed multipoles in the AMOEBA force field, J. Chem. Theory Comput. 8, pp. 5072-5080, doi 10.1021/ct300630u. 

Shi, Y., et al.. Polarizable atomic multipole-based AMOEBA force field for proteins./. Chem. Theory Comput, 2013. 9, 4046-4064. 

It is has been known that the atomic multipole moments for atoms in AMOEBA model can be calculated through quantum mechanics method and Stone s distributed multipole analysis [61]. Thus, it is straightforward to obtain the parameters of electric multipole potentials based on the distributed multipole analysis after the EMP sites of Gay-Berne particles are decided or directly from AMOEBA force field. However, the EMP parameters of Gay-Berne particles need to be optimized because they are derived based on the gas-phase ab initio quantum mechanics. One possible solution would be to match GBEMP and AMOEBA results for the electrostatic energies between CG particles and water molecules, or between CG particle dimers, at various separations and/or in different orientations. 

The electric multipole moments are derived from ab initio quantum mechanics calculation. First, the model chemical compound is used to represent a certain t3rpe of CG particle. The structure of this compound is taken from the Cambridge Structural Database (CSD) (Allen, 2002). From there, the derivation of EMP moments follows the procedure used to parameterize the AMOEBA force field (Ren etal., 2011). 

One of the common approaches used, e.g., in the AMOEBA force field [106], employs an exponentially decaying fractional charge density ... 

The vast majority of CSP has been limited to using intermolecular potentials that lack explicit inclusion of polarization,although its importance has become a topic of interest.Nonpolarizable force fields, based on fixed partial charges or fixed atomic multipoles, must implicitly account for the 20-40% of the lattice energy attributable induction. " On the contrary, polarizable models such as the AMOEBA force field for organic molecules... 

J.-P. Piquemal, L. Perera, G. A. Cisneros, P. Ren, L. G. Pedersen, and T. A. Darden,/. Chem. Phys., 125 (5), 054511 -7 (2006). Towards Accurate Solvation Dynamics of Divalent Cations in Water Using the Polarizable AMOEBA Force Field From Energetics to Structure. 

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