Paper Citing NAMD - Abstract
Voltz, Karine; Trylska, Joanna; Tozzini, Valentina; Kurkal-Siebert, Vandana; Langowski, Joerg; Smith, Jeremy
Coarse-grained force field for the nucleosome from self-consistent multiscaling
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1429-1439, JUL 15 2008
A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtained from a 5-ns all-atom molecular dynamics (MD) simulation, and were refined to produce agreement with the all-atom MD simulation. This self-consistent multiscale approach yields a coarse-grained model that is capable of reproducing equilibrium structural properties calculated from a 50-ns all-atom MD simulation. This coarse-grained model speeds up nucleosome simulations by a factor of 10(3) and is expected to be useful in examining biologically relevant dynamical nucleosome phenomena on the microsecond timescale and beyond. (C) 2008 Wiley Periodicals, Inc.
