Molecular dynamics/order parameter extrapolation for bionanosystem simulations.
A multiscale approach, molecular dynamics/order parameter extrapolation (MD/OPX), to the all-atom simulation of large bionanosystems is presented. The approach starts with the introduction of a set of order parameters (OPs) automatically generated with orthogonal polynomials to characterize the nanoscale features of bionanosystems. The OPs are shown to evolve slowly via Newton's equations, and the all-atom multiscale analysis (AMA) developed earlier (Miao and Ortoleva, J Chem Phys 2006, 125, 44901) demonstrates the existence of their stochastic dynamics, which serve as the justification for our MD/OPX approach. In MD/OPX, a short MD run estimates the rate of change of the OPs, which is then used to extrapolate the state of the system over time that is much longer than the 10(-14) second timescale of fast atomic vibrations and collisions. The approach is implemented in NAMD and demonstrated on cowpea chlorotic mottle virus (CCMV) capsid structural transitions (STs). It greatly accelerates the MD code and its underlying all-atom description of the nanosystems enables the use of a universal interatomic force field, avoiding recalibration with each new application as needed for coarse-grained models. The source code of MD/OPX is distributed free of charge at https://simtk.org/home/mdopx and a web portal will be available via http://sysbio.indiana.edu/virusx.
Miao
Yinglong
Y
Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
Ortoleva
Peter J
PJ
D017795:Bromovirus / Q000737:chemistry*; D036022:Capsid Proteins / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D017434:Protein Structure, Tertiary; D013997:Time Factors; D014732:Vibration
D036022:Capsid Proteins