in the current study, five different atomistic water models (awms) are implemented, in order to investigate the impact of awms treatment on the water velocity profile and density number. for this purpose, molecular dynamics simulation (mds) of poiseuille flow in a nano-channel is conducted. considered awms are spc/e, tip3p, tip4p, tip4pfq and tip5p. to assessment of the ability of each model in...

We present a new dual-resolution approach for coupling atomistic and coarse-grained models in molecular dynamics simulations of hydrated systems. In particular, a coarse-grained point dipolar water model is used to solvate molecules represented with standard all-atom force fields. A unique characteristic of our methodology is that the mixing of resolutions is direct, meaning that no additional ...

We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions. The use of a mass conserving specular wall results in turn to spurious oscillations in the density p...

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the ele...

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biologica...

In the current study, five different atomistic water models (AWMs) are implemented, In order to investigate the impact of AWMs treatment on the water velocity profile and density number. For this purpose, Molecular dynamics simulation (MDS) of Poiseuille flow in a nano-channel is conducted. Considered AWMs are SPC/E, TIP3P, TIP4P, TIP4PFQ and TIP5P. To assessment of the ability of each model in...

A coarse-grained model for polyethylene glycol (PEG) in water has been developed using a combination of the iterative Boltzmann inversion (IBI) methodology and a suitable coarse-grained water potential. The combined coarse-grained model is shown to be effective in reproducing the properties of single chains in bulk water and multiple chains across a series of chain lengths and concentrations, a...

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. In...