相关论文: Discretization errors in molecular dynamics simula…
We have investigated temperature trends of the microscopic structure of the SPC/E and TIP4P-Ew water models in terms of the pair distribution functions, coordination numbers, the average number of hydrogen bonds, the distribution of bonding…
In computational system biology, the mesoscopic model of reaction-diffusion kinetics is described by a continuous time, discrete space Markov process. To simulate diffusion stochastically, the jump coefficients are obtained by a…
We investigate how the transport properties of a united atoms fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the…
We have revisited the composition dependence of principal properties of liquid water-DMSO mixtures by using the isobaric-isothermal molecular dynamics computer simulations. A set of non-polarizable semi-flexible models for the DMSO molecule…
A thermostat of the Nose-Hoover type, based on relative velocities and a local definition of the temperature, is presented. The thermostat is momentum-conserving and Galilean-invariant, which should make it suitable for use in Dissipative…
In this paper we investigate the possibility to detect the hypothesized liquid-liquid critical point of water in supercooled aqueous solutions of salts. Molecular dynamics computer simulations are conducted on bulk TIP4P water and on an…
Discrete diffusion models have gained increasing attention for their ability to model complex distributions with tractable sampling and inference. However, the error analysis for discrete diffusion models remains less well-understood. In…
A series of 20 ps ab initio molecular dynamic simulations of water at ambient density and temperatures ranging from 300 to 450K are presented. Both Car-Parrinello (CP) and Born-Oppenheimer (BO) molecular dynamics techniques are compared for…
This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal…
A number of crystal structures of water have been `superheated' in Monte Carlo simulations. Two well known models for water were considered; namely the TIP4P model and the SPC/E model. By comparing the fluid-solid coexistence temperature to…
The numerical investigation of the statics and dynamics of systems in nonequilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium…
The minimization of operation costs for natural gas transport networks is studied. Based on a recently developed model hierarchy ranging from detailed models of instationary partial differential equations with temperature dependence to…
Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering…
Molecular dynamics is a powerful method for studying the behaviour of materials at high temperature. In practice, however, its effectiveness in representing real systems is limited by the accuracy of the forces, finite size effects,…
We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev.…
By using the direct coexistence method, we have calculated the melting points of ice Ih at normal pressure for three recently proposed water models, namely, TIP3P-FB, TIP4P-FB, and TIP4P-D. We obtained Tm = 216 K for TIP3P-FB, Tm = 242 K…
The use of excessively long timesteps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational…
The effect of the applied trajectory length on the convergence of the static dielectric constant and the self-diffusion coefficient were examined for the SPC/E water model in the NVT ensemble with different system size at 293 K. Very long…
Introduction of polarizability in classical molecular simulations holds the promise to increase accuracy as well as prediction power to computer modeling. To introduce polarizability in a straight-forward way one strategy is based on Drude…
We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare'…