ELF Details

ELF Details

ELF employs the continuum approximation wherein the solvent is modeled as a structureless medium of specified relative permittivity . The absence of explicit solvent molecules results in a substantial savings in CPU time and memory that is essential for modeling medium and large molecules in vivo.

ELF resembles the well-known product DelPhi developed at Columbia University by Barry Honig and coworkers. However ELF goes beyond DelPhi in that the analytic energy gradient is computed with respect to Cartesian atomic displacements. This allows ELF to be directly incorporated into a molecular dynamics simulation as a computationally "cheap" means of investigating solvent-based effects on molecular conformation. Solvent effects are known to greatly impact drug-substrate interactions. Hence the raison d’être for ELF: pharmaceutical companies can more efficiently use molecular modeling in their drug development process.

The following models are available within ELF:

Reaction field model (similar to DelPhi but with gradient information).
Boundary element method (BEM). This is a concept borrowed from the engineering community where it is known as the finite element method. I conceived of, wrote, debugged and tested a sparse matrix diagonalization function that is an order of magnitude faster for computing the required reaction field energy than Delphi.
An analog of the conducting sphere model (COSMO) as propounded by Dr. Andreas Klamt of Baeyer Pharmaceutical in Germany. Whereas his original COSMO is inherently quantum mechanical, my analog is entirely classical as befits the far larger molecules it is intended to model. In this approximation, the medium is considered to be a perfect conductor. For solvent water with a dielectric constant epsilon of 78 this results in perhaps a 1-2% error in computed energies (the fractional error scales as 1/epsilon).
A generalized Born model that is computationally faster but less accurate.
Various approximate "envelope" models that differ in their model parameters for atom types.

ELF is completely documented both in hard text and electronically as HTML script.

ELF is available from within the InsightII graphical user interface. The DISCOVER molecular mechanics/dynamics program interfaces with ELF with an IPC (Inter-Process Connection).

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