Boosting conformational sampling in lipid bilayer simulations using hamiltonian replica exchange

In this report we have tested a parallel implementation for the simulation of lipid bilayers at atomistic level, based on a generalized ensemble (GE) protocol where only the torsional degrees of freedom of the alkyl chains of the lipid are scaled. To this aim, we have used our in-house code ORAC where parallelism is implemented exclusively via the Hamiltonian Replica Exchange algorithm (H-REM) with the atomic forces being integrated serially for each simultaneously evolving GE trajectories. The results in terms of configurational sampling enhancement have been compared with a conventional simulation produced with a widespread molecular dynamics code with parallelism based on a domain decomposition approach for parallel computation of the forces. Results show that the proposed thermodynamic-based multiple trajectories parallel protocol for membrane simulations is competitive with the conventional single trajectory domain decomposition approach as far as area and volume fluctuations are concerned while the gain is only moderate for transport/mixing properties, decisively pointing to a mixed strategy as the optimal parallelization approach in lipid bilayer.