Polarizable simulations

Lemkul, J. A., Roux, B., van der Spoel, D and MacKerell, A. D., Jr., Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model, In Press./ Comput. Chem., 2015. 36,1480-1486. 

To reduce the computational cost, a POSSIM (polarizable simulations with second-order interaction model) force field was later proposed, in which the calculation of induced dipoles stops after one iteration. The... 

G. A. Kaminski, S. Y. Ponomarev, and A. B. Liu, /. Chem. Theory Comput., 5(11), 2935-2943 (2009). Polarizable Simulations with Second Order Interaction Model - Force Field and Software for Fast Polarizable Calculations Parameters for Small Model Systems and Free Energy Calculations. 

Ah initio calculations of polymer properties are either simulations of oligomers or band-structure calculations. Properties often computed with ah initio methods are conformational energies, polarizability, hyperpolarizability, optical properties, dielectric properties, and charge distributions. Ah initio calculations are also used as a spot check to verify the accuracy of molecular mechanics methods for the polymer of interest. Such calculations are used to parameterize molecular mechanics force fields when existing methods are insulficient, which does not happen too often. 

DE Smith, LX Dang. Computer simulations of NaCl association m polarizable water. J Chem Phys 100 3757-3766, 1994. 

Raman intensities of the molecular vibrations as well as of their crystal components have been calculated by means of a bond polarizibility model based on two different intramolecular force fields ([87], the UBFF after Scott et al. [78] and the GVFF after Eysel [83]). Vibrational spectra have also been calculated using velocity autocorrelation functions in MD simulations with respect to the symmetry of intramolecular vibrations [82]. 

In order to demonstrate the efficiency of the g f) function in the calculation of the polarizability. Rerat et al. (13) have carried out the calculation of the polarizability for the ground state of the hydrogen atom. This computation has been made with aff N)) and without ai, N)) the dipolar factor, versus the number of the spectral l n) states involved in the calculation. The convergence of such series aif N) and ai (N) leads to discrete values of 4.4018 and 3.6632 (i.e. the result of Tarmer and Thakkar) corresponding respectively to 97.8% and 81.4% of the exact value. This result illustrates the fact that a large part of the continuum contribution is simulated through the use of the dipolar factor. Moreover the convergence of the series aif N) is faster as we can see on table 1. 

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]. 

The total electric field, E, is composed of the external electric field from the permanent charges E° and the contribution from other induced dipoles. This is the basis of most polarizable force fields currently being developed for biomolecular simulations. In the present chapter an overview of the formalisms most commonly used for MM force fields will be presented. It should be emphasized that this chapter is not meant to provide a broad overview of the field but rather focuses on the formalisms of the induced dipole, classical Drude oscillator and fluctuating charge models and their development in the context of providing a practical polarization model for molecular simulations of biological macromolecules [12-21], While references to works in which the different methods have been developed and applied are included throughout the text, the major discussion of the implementation of these models focuses... 

One method for treating polarizability is the assignment of both partial atomic charges and induced dipoles on the atoms in a molecule. In its most common implementation in biomolecular simulations, inducible point dipoles are added to some or all atomic sites in the molecule [22-25]. An alternative methodology proposed by Allinger and co-workers is the use of bond dipoles [26],... 

---