The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former method, the peptide was studied in vacuo with a dielectric constant of 80, whereas using the latter study the p...

In this note we present results for the heat capacity at constant pressure for the TIP4PQ/2005 model, as obtained from path-integral simulations. The model does a rather good job of describing both the heat capacity of ice I(h) and of liquid water. Classical simulations using the TIP4P/2005, TIP3P, TIP4P, TIP4P-Ew, simple point charge/extended, and TIP5P models are unable to reproduce the heat ...

The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able to achieve supercomputing scale performance of 40 ns/day for all-atom protein syst...

Transphosphorylation thio effects in solution are studied using hybrid QM/MM calculations with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed for a 3' ribose-phosphate model in an explicit 20 A sphere of TIP3P water surrounded by a solvent boundary potential, and free energy analysis was performed using the weighted histogram analysis method. Single thio-su...

The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of...

Hydrophobic coatings, such as octadecyltrichlorosilane or n-alkyl monolayers, enhance the slippage of liquids on solid walls. For a given alkyl chain length, the main structural parameter for homogeneous coatings is the tilt angle between coating molecules and the surface normal. In this paper, ab initio calculations are used to calculate the equilibrium configuration of coating molecules, show...

The new symplectic molecular dynamics (MD) integrators presented in the first paper of this series were applied to perform MD simulations of water. The physical properties of a system of flexible TIP3P water molecules computed by the new integrators, such as diffusion coefficients, orientation correlation times, and infrared (IR) spectra, are in good agreement with results obtained by the stand...

سابقه و هدف: ورود گونه­­ های ماهی مهاجم دراکوسیستم ­های آبی، سبب بروز انواع اثرات منفی اکولوژیکی اقتصادی-اجتماعی می ­­شود. اولین گام در تجزیه تحلیل مخاطرات ناشی از گونه­ غیر­بومی، شناسایی خطر است بر این اساس ابزارهای متعددی برای ارزیابی خطرات تهاجمی غیربومی به منظور پشتیبانی تصمیم گیرندگان گونه ­­ها ایجاد شده است. هدف پژوهش قدرت تیلاپیای شکم قرمز (Coptodon zillii) حوضه آبریز تالاب شادگان (حوضه‌...