Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

Abstract

We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.

Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir

“…The same set up can be used for large molecules, for example, long polymers, in which case only the non‐bonded interactions are subject to the adaptive resolution process according to the position of each polymer segment in the box, while intramolecular interactions remain atomistic in nature regardless of the segment's position, see, for example, refs. []. Further, the thermodynamic force and the thermostat act only in the Δ and CG regions, that is, the dynamics in the AT region follows the untweaked atomistic Hamiltonian.…”

ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation

“…Both adaptive resolution schemes have been successfully applied for simulations of various different systems, including complex liquids, solutes in dilute solutions, large biomolecules, polymers and quantum systems [56,57,75,58,59,60,61,76,77,35,32,33,19,62,63,64,65,36,37]. The increase in computational efficiency compared to fully high-resolution simulations varies and depends strongly on the size and properties of the system, the employed AT and CG models, as well as the parallelization and domain-decomposition scheme (also see Sec.…”

“…In this methodology, solvent particles can freely diffuse between AT and CG regions, smoothly changing their resolution as they cross a hybrid or transition region. The AdResS approach can be useful for modeling a wide variety of different systems, such as simple solutes in dilute solution and complex biomolecular systems [56,57,58,59,60,61,35,32,33,19,62,63,64,65].…”

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

“…We consider a system of 918 water molecules in a slab-shaped box with dimensions The resolution function is given by a squared cosine, commonly used in adaptive resolution simulations 72,78,88,90,[101][102][103] . We perform the simulations at a temperature of 300 K and use a Trotter number P = 32, as this has been shown to provide well-converged results for most dynamical and structural water properties 22,23,25 .…”