MD/OPX

Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX)

MD/OPX is designed to simulate large bionanosystems over long time periods by using short replica MD run(s) to extrapolate the structural order parameters (OPs) of the system over large time intervals and thus advance the system over long time. The present implementation of MD/OPX is based on NAMD using its Tcl scripting interface and requires NAMD for running. A Fortran code is used to read the output structure of a short dt NAMD run, calculate the resultant OPs, extrapolate the OPs for dT, generate an atomic configuration at t+dT with the extrapolated OPs and put the result all-atom structure back into NAMD to start the next (dt, dT) cycle. Please refer to the following papers for the theoretical details and implementation algorithms of MD/OPX:

Miao, Y. and P. J. Ortoleva, Molecular dynamics/order parameter extrapolation for bionanosystem simulations. J. Comp. Chem., 2008, 30(3): 423-437. (Abstract | PDF)

Miao, Y. and P. J. Ortoleva (2009), Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation, Biopoplymers, 93, 61. (Abstract | PDF)

For simulating solvated systems, i.e., nanostructures solvated in a host medium, modules “solvation”, “extraction of nanostructure snapshots” and “resolvation” are added to account for water molecules and ions. Refer to the following paper for the MD/OPX implementation and its application ot CCMV capsid swelling:

Miao, Y., J. E. Johnson and P. J. Ortoleva (2010), All-atom Multiscale Simulation of CCMV Capsid Swelling, J. Phys. Chem. B, 114(34), 11181–11195. (Abstract | PDF)

A copy of the latest version of MD/OPX source code can be downloaded at MDOPX1.4.zip (~18MB).