Related papers: Water hexamer: Self-consistent phonons versus reve…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Many model potential energy surfaces (PESs) have been reported for water; however, none are strictly from "first principles". Here we report such a potential, based on a many-body representation at the CCSD(T) level of theory up to the…
The Diffusion Monte Carlo (DMC) method is applied to the water monomer, dimer, and hexamer, using q-TIP4P/F, one of the most simple, empirical water models with flexible monomers. The bias in the time step ($\Delta\tau$) and population size…
We report an improved implementation for evaluating the analytical gradients of the random phase approximation (RPA) electron-correlation energy based on atomic orbitals and the localized resolution of identity scheme. The more efficient…
Rearrangement mechanisms of the water dimer and the cage form of the water hexamer are examined theoretically with particular reference to tunneling splittings and spectroscopy. The three lowest barrier rearrangements of the water dimer are…
Second order Moeller-Plesset perturbation theory (MP2) at the complete basis set (CBS) limit and diffusion quantum Monte Carlo (DMC) are used to examine several low energy isomers of the water hexamer. Both approaches predict the so-called…
We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to $\sim 4\cdot 10^6$ molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to $\sim…
Reverse Monte Carlo modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, SPC/E, has been performed. The strictly rigid geometry of SPC/E water…
RMs (reverse micelles) provide a controlled system for studying the unique structural and dynamic behaviors of confined water, thus gaining a general insight into the behavior or water under confinement and at interfaces. This study employs…
Smoothed particle hydrodynamics (SPH) offers distinct advantages for modeling many engineering problems, yet achieving high-order consistency in its conservative formulation remains to be addressed. While zero- and higher-order…
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
We perform molecular dynamics simulations using the extended simple point charge SPC/E water model in order to investigate the dynamical behavior of supercooled-stretched water. We focus on the behavior of the translational diffusion…
We extend the range-separated double-hybrid RSH+MP2 method [J. G. Angyan et al., Phys. Rev. A 72, 012510 (2005)], combining long-range HF exchange and MP2 correlation with a short-range density functional, to a fully self-consistent version…
We compare the results for a set of hydrodynamical tests performed with the AMR finite volume code, MG and the SPH code, SEREN. The test suite includes shock tube tests, with and without cooling, the non-linear thin-shell instability and…
As a mesh-free method, smoothed particle hydrodynamics (SPH) has been widely used for modeling and simulating fluid-structure interaction (FSI) problems. While the kernel gradient correction (KGC) method is commonly applied in structural…
The smoothed-particle hydrodynamics (SPH) technique is a numerical method for solving gas-dynamical problems. It has been applied to simulate the evolution of a wide variety of astrophysical systems. The method has a second-order accuracy,…