Written by A.D. Mackerell, Jr.
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_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 .
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
Anisimov, V. M.; Lamoureux, G.; Vorobyov, I. V.; Huang, N.; Roux, B.; MacKerell, A. D., Jr. J Chem Theory and Comp. 2005, 1, 153.
Lamoureux, G.; .; MacKerell, A. D.; Roux, B. J Chem Phys. 2003, 119, 5185.
Lamoureux, G.; Harder E.; Vorobyov I. V.; Roux, B.; MacKerell, A. D., Jr. Chem Phys Lett. 2006, 418, 245.
Lamoureux, G.; Roux, B. J Chem Phys. 2003, 119, 3025.