Inhibition efficiencies of three amine derivatives (Diethylenetriamine (I), Triethylenetetramine (II), and Pentaethylenehexamine (III)) have been studied on corrosion of carbon steel using density functional theory (DFT) method in gas phase. Quantum chemical parameters such as EHOMO (highest occupied molecular orbital energy), ELUMO (lowest unoccupied molecular orbital energy), hardness (η), po...

We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport informat...

Molecular dynamics (MD) simulation, in which the classical equations of motion for all particles of a system are integrated over finite period of time, is one of the theoretical methods to investigate dynamical properties of molecular systems [1]. The problem which arises in performing MD simulations of such systems is that only short simulations can be performed due to the high-frequency motio...

The molecular mechanisms in both vibrational relaxation and proton transfer (PT) associated with infrared (IR)-induced PT in a dilute hydrofluoric acid solution at ambient temperature are studied by molecular dynamics (MD) simulations with the multistate empirical valence bond model. To investigate the solvation dynamics, a collective solvent coordinate and its perpendicular bath modes are defi...

Ž . The canonical molecular dynamics MD simulation was accelerated by the integrated method of the multiple time-step Ž . integrator algorithm combined with the particle mesh Ewald method PMEM applied not only to the calculation of the Coulomb interaction but also of the Van der Waals interaction. Although the previous integrated method, in which the PMEM was used in the calculation only for th...

Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We ...

In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvemen...

In the hybrid Molecular Dynamics (MD)/Brownian Dynamics (BD) algorithm for simulating the long-time, nonequilibrium dynamics of receptor-ligand interactions, the evaluation of the force autocorrelation function can be computationally costly but fortunately is highly amenable to multimode processing methods. In this paper, taking advantage of the computational grid’s large-scale computational re...

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to characterize the structure of aqueous guanidinium carbonate (Gdm2CO3) solutions. The MD simulations found very strong hetero-ion pairing in Gdm2CO3 solution and were used to determine the best structural experiment to demonstrate this ion pairing. The NDIS experiments conf...

The understanding of aqueous solution properties is recognized as being important in many areas of physical chemistry and molecular biophysics. Computer simulation has become an important tool in understanding the structure and dynamics of aqueous electrolyte solutions at the atomic or molecular level. Many works of molecular dynamics (MD) simulations have been carried out to investigate hydrat...