On the Investigation of Coarse-Grained Models for Water: Balancing Computational Efficiency and the Retention of Structural Properties (original) (raw)
Related papers
Clusters of Coarse-Grained Water Molecules
The Journal of Physical Chemistry A, 2014
Global optimization for molecular clusters can be significantly more difficult than for atomic clusters because of the coupling between orientational and translational degrees of freedom. A coarse-grained representation of the potential can reduce the complexity of this problem, whilst retaining the essential features of the intermolecular interactions. In this study, we use a basin-hopping algorithm to locate putative global minima for clusters of coarse-grained water molecules modeled using a monatomic water potential for cluster sizes 3 ≤ N ≤ 55. We characterize these structures and identify structural trends using ideas from graph theory. The agreement with atomistic results and experiment is rather patchy, which we attribute to the tetrahedral bias in the three-body potential that results in too few nearest neighbor contacts and premature emergence of bulk-like structure. In spite of this, the results offer further useful insight into the relationship between the structure of clusters and bulk phases, and the mathematical form of a widely used model potential.
Simulations of Phospholipids Using a Coarse Grain Model
The Journal of Physical Chemistry B, 2001
A computationally efficient coarse grain model designed to closely mimic specific phospholipids is used to study a number of phospholipid systems to demonstrate its strengths and weaknesses. A study of a membrane containing an anesthetic, halothane, illustrates the shortcomings of this model in treating systems without extensive parametrization. In contrast, the power of the model is demonstrated by its ability to successfully simulate the self-assembly of two phospholipid phases from random initial configurations: a lamellar phase and a reverse hexagonal phase in a ternary system containing water, a hydrocarbon, and a phospholipid. The aqueous columns in the reverse hexagonal phase tend to adopt polygonal cross sections and the local structure of phospholipids is still bilayer-like. Molecular dynamics was found to be much more efficient at simulating self-assembly in the current systems than Monte Carlo.
Coarse Grained Model for Semiquantitative Lipid Simulations
The Journal of Physical Chemistry B, 2004
This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of magnitude can be achieved. Micrometer length scales or millisecond time scales are therefore within reach. To encourage applications, the model is kept very simple. Only a small number of coarse grained atom types are defined, which interact using a few discrete levels of interaction. Despite the computational speed and the simplistic nature of the model, it proves to be both versatile in its applications and accurate in its predictions. We show that densities of liquid alkanes from decane up to eicosane can be reproduced to within 5%, and the mutual solubilities of alkanes in water and water in alkanes can be reproduced within 0.5 kT of the experimental values. The CG model for dipalmitoylphosphatidylcholine (DPPC) is shown to aggregate spontaneously into a bilayer. Structural properties such as the area per headgroup and the phosphate-phosphate distance match the experimentally measured quantities closely. The same is true for elastic properties such as the bending modulus and the area compressibility, and dynamic properties such as the lipid lateral diffusion coefficient and the water permeation rate. The distribution of the individual lipid components along the bilayer normal is very similar to distributions obtained from atomistic simulations. Phospholipids with different headgroup (ethanolamine) or different tail lengths (lauroyl, stearoyl) or unsaturated tails (oleoyl) can also be modeled with the CG force field. The experimental area per headgroup can be reproduced for most lipids within 0.02 nm 2 . Finally, the CG model is applied to nonbilayer phases. Dodecylphosphocholine (DPC) aggregates into small micelles that are structurally very similar to ones modeled atomistically, and DOPE forms an inverted hexagonal phase with structural parameters in agreement with experimental data.
The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one.
Development and application of coarse-grained models for lipids
I'll discuss a number of topics that represent our efforts in developing reliable molecular models for describing chemical and physical processes involving biomembranes. This is an exciting yet challenging research area because of the multiple length and time scales that are present in the relevant problems. Accordingly, we attempt to (1) understand the value and limitation of popular coarse-grained (CG) models for lipid membranes with either a particle or continuum representation; (2) develop new CG models that are appropriate for the particular problem of interest. As specific examples, I'll discuss (1) a comparison of atomistic, MARTINI (a particle based CG model) and continuum descriptions of a membrane fusion pore; (2) the development of a modified MARTINI model (BMW-MARTINI) that features a reliable description of membrane/water interfacial electrostatics and its application to cell-penetration peptides and membrane-bending proteins. Motivated specifically by the recen...
2010
We study the lipid and phase transferability of our recently developed systematically coarsegrained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.
Clustering of water molecules in aqueous solutions: Effect of water–solute interaction
Physical Chemistry Chemical Physics
Clustering of water molecules in partially miscible aqueous solutions (with immiscibility gap) was studied by Monte Carlo (MC) simulations. Liquid-liquid coexistence curves were determined by MC simulations in the Gibbs ensemble. Water cluster size distributions were studied in the organic-rich one-phase region. At the coexistence curve we observe the broadest distribution of cluster sizes in agreement with the Fisher droplet model. There are no percolating water clusters in aqueous mixtures of solutions of hydrophobic particles in the studied concentration range. In contrast, in an aqueous solution of hydrophilic solutes crossing the coexistence curve approximately coincides with the 3D percolation threshold of water. An infinite water cluster (percolating cluster or droplet of the second phase) appears in an aqueous solution, when the average number of water-water H-bonds per molecule exceeds ca. 1.6.
JCIS Open, 2021
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of computationally expensive interactions with a huge number of solvent particles, the smaller number of interaction sites in the model molecules, and the lack of fast sub-molecular degrees of freedom. Without an explicit solvent, the solvent mediated effects, e.g. the hydrophobic effect and the hydration force, are mimicked entirely through the interactions between the model molecules. In this paper, we describe a maximally coarse-grained model for lipids in implicit water. The model is called SiMPLISTIC, which is an acronym for 'Single-site Model with Pairwise interaction for Lipids in Implicit Solvent with Tuneable Intrinsic Curvature'. SiMPLISTIC lipids rapidly self-assemble into realistic nonlamellar and lamellar phases such as inverted micelles and bilayers, the spontaneous curvature of the phase being determined by a single free parameter of the model. Model membrane simulations with lamellar SiMPLISTIC lipids show satisfactory fluid and gel phases with no interdigitation or tilt. Despite being rigid molecules, SiMPLISTIC lipids can generate experimentally relevant values for the bending stiffness of model membrane bilayers with no significant interleaflet coupling. SiMPLISTIC can also simulate mixtures of lipids that differ in their packing parameter or length, the latter leading to the phenomenon of hydrophobic mismatch driven phase separation or domain formation. The model has a large scope due to its speed, conceptual and computational simplicity, and versatility. Applications may range from academic and industrial research in various lipid-based systems, such as lyotropic liquid crystals, biological and biomimetic membranes, vectors for drug and gene delivery, emulsions for cosmetic products, to education, such as teaching/learning concepts like self-assembly, polymorphism, biomembrane organization etc. through interactive molecular dynamics simulations.
The Journal of Chemical Physics, 2009
We present a two-dimensional coarse-grained (CG) model for a lipid membrane composed of phospholipids and cholesterol. The effective CG interactions are determined using radial distribution functions (RDFs) from atom-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique, based on our earlier work [T. Murtola et al., J. Chem. Phys. 121, 9156 (2004); J. Chem. Phys. 126, 075101 (2007)]. Here, the original model is improved by including an internal discrete degree of freedom for the phospholipid tails to describe chain ordering. We also discuss the problem of RDF inversion in the presence of internal states, in general, and present a modified IMC method for their inclusion. The new model agrees with the original models on large-scale structural features such as density fluctuations in pure dipalmitoylphosphocholine and cholesterol domain formation at intermediate concentrations and also indicates that ordered and disordered domains form at all cholesterol concentrations, even if the global density remains uniform. The inclusion of ordering also improves transferability of the interactions between different concentrations, but does not eliminate transferability problems completely. We also present a general discussion of problems related to RDF inversion.