Structure Formation of Toluene around C60: Implementation of the Adaptive Resolution Scheme (AdResS) into GROMACS

Abstract

For the example of C60 solutes in toluene, we present the implementation of the adaptive resolutions scheme (AdResS) for molecular simulations into GROMACS. In AdResS a local, typically all-atom cavity is coupled to a surrounding of coarse-grained, simplified molecules. This methodology can not only be used to reduce the CPU time demand of atomistic simulations but also to systematically investigate the relative influence of different interactions on structure formation. For this, we vary the thickness of the all atom layer of toluene around the C60 and analyze the first toluene layers in comparison to a full bulk simulation.

Hamiltonian Adaptive Resolution Simulation for Molecular Liquids

“…With this idea of mixed resolution in mind the AdResS (Adaptive Resolution Scheme) method was developed, in which one can dynamically couple specific regions of a simulation box at different levels of resolution, while maintaining the correct thermodynamic equilibrium between them [14,[20][21][22][23][24][25][26]. The particles move from one region to the other through a hybrid resolution zone ( Fig.…”

Computer Simulations of Soft Matter: Linking the Scales

“…This excess energy can be removed with a local thermostat, such as Langevin thermostat: in this way, the temperature of the system is kept constant everywhere. The equilibrium state of the system is then dynamical: the thermostat takes care of absorbing the extra heat produced in the transition region by non-conservative forces, and the system samples equilibrium configurations according to Boltzmann's distribution [24][25][26][27][28][29][30][31][32].…”

“…The possibility of treating a system with a reduced number of degrees of freedom except where it is strictly necessary was explored, making use of the AdResS method, in several applications [24][25][26][27][28][29][30]172]. From the numerical/computational point of view it clearly represents an advantage, since a much smaller number of force calculations are required in the coarse-grained region: this is particularly true for parallel MD codes such as GROMACS [173], where a dynamical decomposition of the simulation box allows one to subdivide the box with a finer grid in the AA and hybrid region, while a smaller number of processors is assigned to the CG region.…”

“…Adaptive resolution simulations methods [24][25][26][27][28][29][30][31][32][33][34] were developed to solve the contradiction between the necessity of simulating all parts of the system and the fact that, eventually, the detailed information from a large subgroup of them will be neglected. The underlying idea is to replace these "non-interesting" degrees of freedom of the system with a simpler, coarse-grained representation, such that a sensibly smaller number of computations (e.g., force calculations) is required, while the "interesting" region is treated at a higher resolution.…”

“…These two problems are obviously interconnected, since the way the high-and low-resolution regions interact at the interface naturally depends on the specific properties of the models used in each of them; a thorough discussion of these aspects will be carried out in the context of the Adaptive Resolution Simulation (AdResS) [24][25][26][27][28][29][30][31][32] and Hamiltonian AdResS [33,34] (H-AdResS) methods.…”