IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot… (More)
Multiscale modeling of a polymeric system is a challenging task in polymer physics. Here we introduce a bottom-up and then top-down scheme for the simulation of polyethylene (PE). The coarse-grained numerical potential for PE is derived through an automatic updating program by mapping its radial distribution function (RDF) from the Lowe-Andersen temperature… (More)
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to… (More)
We present new algorithms to improve the performance of ENUF method (F. Hedman, A. Laaksonen, Chem. Phys. Lett. 425, 2006, 142) which is essentially Ewald summation using Non-Uniform FFT (NFFT) technique. A NearDistance algorithm is developed to extensively reduce the neighbor list size in real-space computation. In reciprocal-space computation, a new… (More)
At crystal or larger scales, natural cellulose was generally recognized to be a rigid material. Our single-chain mechanical measurements, however, reveal that the natural cellulose is as flexible as common synthetic polymers at the single-chain level, creating new opportunities in the designing of nano materials.
GALAMOST [graphics processing unit (GPU)-accelerated large-scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self-assembly, phase transition, and other properties of polymeric… (More)
We study the phase behavior of bolaamphiphilic solution performing the dissipative particle dynamics simulations of coarse-grained bolaamphiphilic molecules with explicit solvent molecules. Our simulations show that there are six kinds of phases: isotropic micellar, micellar, rod-shaped micellar, hexagonal, network-structure and lamellar. The… (More)