Expanded Functionality and Portability for the Colvars Library.

Colvars is an open-source C++ library that provides a modular toolkit for collective-variable-based molecular simulations. It allows practitioners to easily create and implement descriptors that best fit a process of interest and to apply a wide range of biasing algorithms in collective variable space. This paper reviews several features and improvements to Colvars that were added since its original introduction.

Type Label Framework for Bonded Force Fields in LAMMPS.

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input.

Surfactin at the Water/Air Interface and in Solution.

The lipopeptide surfactin produced by certain strains of Bacillus subtillis is a potent biosurfactant with high amphiphilicity and a strong tendency for self-aggregation. Surfactin possesses a number of valuable biological properties such as antiviral, antibacterial, antifungal, and hemolytic activities. Owing to these properties, in addition to the general advantages of biosurfactants over synthetic surfactants, surfactin has potential biotechnological and biomedical applications.

Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation.

Long-range dispersion interactions have a critical influence on physical quantities in simulations of inhomogeneous systems. However, the perceived computational overhead of long-range solvers has until recently discouraged their implementation in molecular dynamics packages. Here, we demonstrate that reducing the cutoff radius for local interactions in the recently introduced particle-particle particle-mesh (PPPM) method for dispersion [Isele-Holder et al.

Self-assembly of charged surfactants: full comparison of molecular simulations and scattering experiments.

We present a study of the self-assembly of charged surfactants by a combination of molecular simulations and anomalous small-angle X-ray scattering (ASAXS). Solvent-free grand canonical Monte Carlo simulations are used to obtain the equilibrium structure of tetradecyltrimethylammonium bromide (TTAB) micelles. Subsequent molecular dynamics simulations of multiple micelles were used to calculate the scattering intensity obtained at low surfactant concentrations (17 mM).

Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics.

The computational design of advanced materials based on surfactant self-assembly without ever stepping foot in the laboratory is an important goal, but there are significant barriers to this approach, because of the limited spatial and temporal scales accessible by computer simulations. In this paper, we report our work to bridge the gap between laboratory and computational time scales by implementing the coarse-grained (CG) force field previously reported by Shinoda et al. [Shinoda, W.

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming.

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs).

Ab initio molecular dynamics study of supercritical carbon dioxide including dispersion corrections.

Density functional theory based ab initio molecular dynamics simulations with explicit inclusion of empirical van der Waals (vdW) corrections of supercritical carbon dioxide have been performed. Significant changes in the intermolecular pair correlation functions of the fluid modeled with the added vdW interactions are observed, particularly at lower densities. The closest neighbor to a molecule is seen to be oriented in a distorted T-shaped geometry, consistent with earlier experiments and simulations.

Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics.

The DNA-carbon nanotube hybrid (DNA-CN) consists of a single-wall carbon nanotube (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments have demonstrated that this nanomaterial is ideal for numerous nanotechnological applications. Despite this importance, the structure of this material remains poorly understood.

Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics.

Self-assembly at a liquid-liquid interface is a powerful experimental route to novel nanomaterials. We report herein a computational study of peptide nanotube formation at an oil-water interface. We probe interfacial self-assembly and nanotube formation of the cyclic octapeptide, cyclo [(-L-Trp-D-Leu-)4] as an illustrative example.

Inverse temperature transition of a biomimetic elastin model: reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation.

The inverse temperature transition (ITT) of a biomimetic model for elastin, capped GVG(VPGVG) in liquid water, is investigated by a comprehensive classical molecular dynamics study. The temperature dependence of the solvation structure and dynamics of the octapeptide are compared using three common force fields, CHARMM, GROMOS, and OPLS. While these force fields differ in quantitative detail, they all predict this octapeptide to undergo a "folding transition" to closed conformations upon heating and a subsequent "unfolding transition" to open conformations at still higher temperatures, thus reproducing the ITT scenario.

Folding and unfolding of an elastinlike oligopeptide: "inverse temperature transition," reentrance, and hydrogen-bond dynamics.

The temperature-dependent behavior of a solvated oligopeptide, GVG(VPGVG), is investigated. Spectroscopic measurements, thermodynamic measurements, and molecular dynamics simulations find that this elastinlike octapeptide behaves as a two-state system that undergoes an "inverse temperature" folding transition and reentrant unfolding close to the boiling point of water. A molecular picture of these processes is presented, emphasizing changes in the dynamics of hydrogen bonding at the protein/water interface and peptide backbone librational entropy.

Temperature-dependent conformational transitions and hydrogen-bond dynamics of the elastin-like octapeptide GVG(VPGVG): a molecular-dynamics study.

A joint experimental/theoretical investigation of the elastin-like octapeptide GVG(VPGVG) was carried out. In this article a comprehensive molecular-dynamics study of the temperature-dependent folding and unfolding of the octapeptide is presented. The current study, as well as its experimental counterpart (see companion article in this issue) find that this peptide undergoes an inverse temperature transition (ITT), leading to a folding at approximately 40-60 degrees C.