Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Abstract

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the Particle Mesh Ewald method (PME) for solution of Poisson’s Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17004, 68484 and 273936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (SCD), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.

RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles

“…A general purpose MD code should include electrostatic (Coulomb) interactions and these should be sufficiently accurate and computationally efficient. The smooth particle mesh Ewald method [22,[58][59][60] which can efficiently handle the long range part of the electrostatic interactions is planned, but for our needs so far we have found it sufficient to use Coulomb forces with a large shifted-force cut-off as documented in Ref. [61].…”

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

“…With the continuing advances in computational hardware [134,135] and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has slowly demonstrated the utility of polarizable force fields, particularly those based on the charge equilibration formalism, for a broad range of physical and biophysical systems.…”

Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems

“…With the continuing advances in computational hardware 122,123 and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has slowly demonstrated the utility of polarizable force fields, particularly those based on the charge equilibration formalism, for a broad range of physical and biophysical systems.…”