Hybrid particle‐field molecular dynamics simulations: Parallelization and benchmarks

Abstract

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where selfconsistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle-field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD-SCF program profiles, serial MD-SCF and parallel MD-SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs.

Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

“…Simulations reported here have been performed using the parallelized version of the OCCAM code [41]. The compositions of each simulated system are reported in Table 1.…”

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics

“…Previous MD-SCF simulations were carried out using the parallel molecular dynamics suite OCCAM, 27 which can be easily adapted to incorporate MPCD and the improved discrete gradient operator. Since the kinetics is considerably accelerated by MPCD, and CGMD Martini representations are readily available for a wide range of biologically-relevant systems, one can efficiently simulate intricate phenomena in much larger systems than the current standard.…”

“…27 Nevertheless, the key advantage is the alternative physical description: since we replace the 'hard' Lennard-Jones interactions in (CG)MD by 'soft' mean-field interactions in MD-SCF/MPCD, we may replace the usual time step Dt B fs that is required for stable integration in (CG)MD by the Dt B ps time step of methods that consider soft-core interactions, like DPD. As a consequence, the sampling in the time domain is enhanced by several orders of magnitudes, unless bonded interactions dictate otherwise or the reference methods is already based on soft-core potentials.…”

“…A recent coarse-grained molecular dynamics study for DMPC lipids corroborates that vesicle formation from such an initial structure should be spontaneous. 56 Although the code can efficiently be parallelised, 27 the current implementation is serial and all calculations were carried out on a single 2.8 GHz Intel Core 5 processor (8 GB memory), with the largest simulation taking roughly 1.5 days. For this reason, a thorough investigation of even larger systems, including an analysis of structure formation pathways, is left for the future.…”

“…Apart from that fact that softening enables a significantly larger time step for stable numerical integration of Newton's equations of motion, the simulation algorithm can also be parallelised efficiently, since it only considers fields and individual particle chains. 27 The transferability between CGMD and MD-SCF was validated for a number of cases, including for phospholipid membranes. 29 By selecting a global Andersen thermostat for the particle evolution, 26 however, the advantage of retaining solvent degrees of freedom has not been fully exploited.…”