Paper Citing NAMD - Abstract
Morriss-Andrews, Alex; Rottler, Joerg; Plotkin, Steven S.
A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 035105, JAN 21 2010
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain for both single- and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse, which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.
