Coarse-graining is a systematic way of reducing the number of degrees of freedom representing a system of interest. Several coarse-graining techniques have so far been developed, such as iterative Boltzmann inversion, force-matching, and inverse Monte Carlo. However, there is no unified framework that implements these methods and that allows their direct comparison. We present a versatile object-oriented toolkit for coarse-graining applications (VOTCA) that implements these techniques and that provides a flexible modular platform for the further development of coarse-graining techniques. All methods are illustrated and compared by coarse-graining the SPC/E water model, liquid methanol, liquid propane, and a single molecule of hexane.

Abstract. We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geometric constraints of the water clusters. It is shown that for simple two-body potentials either the radial distribution function or the geometrical packing can be optimized. In a similar way, as needed for multiscale methods, either the pressure or the compressibility can be fitted to the all atom liquid. In total, a speed-up by a factor of about 50 in computational time can be reached by this coarse-graining procedure.

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.

We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite length, we find that the microcanonical entropy behaves convex in the transition region, leading to a negative microcanonical specific heat. As this effect is also seen in first-order-like transitions of other finite systems, our results provide clear evidence for recent hints that the characterisation of phase separation in first-order-like transitions of finite systems profits from this microcanonical view.PACS numbers: 87.15.Aa, 87.15.Cc Thermodynamic phase transitions in macroscopic, infinitely large systems are typically analysed in the thermodynamic limit of a canonical ensemble, i.e., the temperature T is treated as an intensive external control parameter adjusted by the heat bath, and the total system energy E is distributed according to the BoltzmannGibbs statistics. The probability for a macrostate with energy E is given by p(E) = g(E) exp(−E/k B T )/Z, where g(E) is the density of states, Z the partition sum, and k B the Boltzmann constant. As long as the microcanonical entropy S(E) = k B ln g(E) is a concave function of E, the microcanonical (caloric) temperature T (E) = (∂S(E)/∂E) −1 for fixed volume V and particle number N is a monotonically increasing function of E. Consequently, the microcanonical specific heat2 ) is positive. The specific heat can only become negative in an energetic regime, where S(E) is convex. In this region, the caloric T (E) curve exhibits a typical backbending, which means that the system becomes colder with increasing total energy. For this reason, the temperature T is not the most appropriate control parameter and the analysis of such, in particular finite, systems is more adequately performed in the microcanonical ensemble, where the system energy E is considered as the adjustable external parameter [1,2].It is a surprising fact that the backbending effect is indeed observed in transitions with phase separation. Although this phenomenon has already been known for a long time from astrophysical systems [3], it has been widely ignored since then as somehow "exotic" effect. Recently, however, experimental evidence was found from melting studies of sodium clusters by photofragmentation [4]. Bimodality and negative specific heats are also known from nuclei fragmentation experiments and models [5,6], as well as from spin models on finite lattices which experience first-order transitions in the thermodynamic limit [7,8]. This phenomenon is also observed in a large number of other isolated finite model systems for evaporation and melting effects [9,10].In this Letter, we demonstrate the usefulness of the microcanonical ensemble for studies of the aggregation process of small proteins (peptides), which, due to the fixed inhomogeneous sequence of amino acids, are necessarily systems of finite size. Understanding protein aggregation is esse...

We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, yet keeping the advantages of conserving Galilei invariance and within our error bar also hydrodynamics. This leads to a second friction parameter for tuning the transport properties of the system. Numerical simulations of a simple Lennard-Jones fluid and liquid water demonstrate a very sensitive behaviour of the transport properties, e.g., viscosity, on the strength of the new friction parameter. We envisage that the new thermostat will be very useful for the coarse-grained and adaptive resolution simulations of soft matter, where the diffusion constants and viscosity of the coarse-grained models are typically too high/low, respectively, compared to all-atom simulations.