Polarizable DNA based on the classical Drude oscillator

Objective and Overview

The next generation empirical force fields will include explicit treatment of electronic polarizability. One approach to do this is via a classical Drude oscillator as described in the corresponding lecture and in references 1-4. In this tutorial, the steps involved in generating DNA that includes Drude-based polarization will be presented. This tutorial assumes that a solvated DNA duplex generated and equilibrated with the additive force field is available for use as the starting structure (see the RNA_Tutorial). It should be noted that the Drude model is still under development and its current implementation is quite burdensome as well as computationally inefficient.Efforts are ongoing to overcome these limitations.

The example scripts are based on a GAGTACTC DNA duplex (B form) in a box of 1746 water molecules with 14 Na+ counterions. Generation of the solvated DNA is performed in the script, gen_drude_dna.inp. The process involves generating the DNA, water and sodiums as normally performed in CHARMM (this uses files md_gagtactc_bform_300mm_dna.crd, md_gagtactc_bform_300mm_water.crd and md_gagtactc_bform_300mm_sod.crd) followed by creation of the Drudes based on a number of stream files in the toppar subdirectory (see description in 00readme. The script also includes initial minimization and MD equilibration using the recently implemented Velocity Verlet integrator [4].

The second script, dyn_npt_drude_dna.inp, reads the structure output from the initial script (gagtactc_1c3_cf1c_eq_harm.crd) and performs a production NPT simulation. Due to limitations in the current implementation of the Drude in CHARMM, it is necessary to again generate the entire system prior to the MD simulation.


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Written by A.D. Mackerell, Jr.