Accurate modeling of the solvent environment for biological molecules is crucial computational biology and drug design. A popular approach to achieve long simulation time scales large system sizes incorporate effect in a mean-field fashion with implicit models. However, challenge existing models that they often lack accuracy or certain physical properties compared explicit models, as many-body ...

molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. by this method we can calculate many chemical and biochemical properties of large scale biological systems. in this work all-atom molecular dynamics simulation of polyalanine (pa) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 m of guanidinium chlorid...

Raman and Raman optical activity (ROA) spectra of molecules reflect not only molecular structure and conformation but also the dynamics and interactions with the solvent. For polar, biologically relevant molecules in aqueous environment, this often complicates the band assignment and interpretation of the spectra. In the present study, implicit dielectric and explicit solvent models are compare...

We discuss the classes of machines for which implicit style design is appropriate, and give guidelines for safe simulation and synthesis of implicit style Verilog that ensure the results of cycle based simulation agree with the results of synthesis. We also propose a minor revision to IEEE 1364 for bottom testing loops that improves the clarity of safe implicit style Verilog.