Density based visualization for molecular simulation

Molecular visualization of structural information obtained from computer simulations is an important part of research work flow. A good visualization technique should be capable of eliminating redundant information and highlight important effects clarifying the key phenomena in the system. Current methods of presenting structural data are mostly limited to variants of the traditional ball-and-stick representation. This approach becomes less attractive when very large biological systems are simulated at microsecond timescales, and is less effective when coarse-grained models are used. Real time rendering of such large systems becomes a difficult task; the amount of information in one single frame of a simulation trajectory is enormous given the large number of particles; at the same time, each structure contains information about one configurational point of the system and no information about statistical weight of this specific configuration. In this paper we report a novel visualization technique based on spatial particle densities. The atomic densities are sampled on a high resolution 3-dimensional grid along a relatively short molecular dynamics trajectory using hundreds of configurations. The density information is then analyzed and visualized using the open-source ParaView software. The performance and capability of the method are demonstrated on two large systems simulated with the MARTINI coarse-grained force field: a lipid nanoparticle for delivering siRNA molecules and monolayers with a complex composition under conditions that induce monolayer collapse.