The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods hasbecome alternative tool for many applications that pure QM and MM could not be suitable.The QM/MM method has been used for different type of problems, for example: structuralbiology, surface phenomena, and liquid phase. In this paper we have performed these methods forsome antibiotics and vitamins and then we comp...

Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid methods have become very popular schemes to incorporate environmental effects in the calculation of molecular properties, when it is mandatory both a quantum description electrons compute these properties and an atomistic environment. However, even Density Functional Theory/MM may timecosting large part system should be treated at QM level or...

The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chem...

Although quantum mechanical/molecular mechanics (QM/MM) methods are now routinely applied to the studies of chemical reactions in condensed phases and enzymatic reactions, they may experience technical difficulties when reactive region is varying over time. For instance, solvent molecules directly participating reaction, exchange water between QM MM regions occur on a time scale comparable reac...

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)-based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER c...

The (1)H and (13)C nuclear magnetic resonance (NMR) spectra of the retinyl chromophore in rhodopsin are investigated by using quantum mechanics/molecular mechanics (QM/MM) hybrid methods at the density functional theory (DFT) B3LYP/6-31G*:Amber level of theory, in conjunction with the gauge independent atomic orbital (GIAO) method for the ab initio self-consistent-field (SCF) calculation of NMR...

The role of inhomogeneous phases in the phase diagram of the Nambu–Jona-Lasinio (NJL) and the quark meson (QM) model is examined. By means of a generalized Ginzburg-Landau (GL) expansion it is concluded that the critical point in the mean-field phase diagram of the NJL model is in fact a Lifshitz point where homogeneous spontaneously broken, inhomogeneous and restored phases meet. This picture ...

We present a relatively straightforward way to integrate existing software packages into a full multi-scale simulation package in which each application runs in its own address space and there is no run-time intervention by the researcher. The PUPIL (Program for User Package Interfacing and Linking) architectural concept is to provide a simulation Supervisor, implemented as a Manager and variou...

Steiner 3-wise balanced designs are constructed for parameters 3-(3n − 1, {4, 8}, 1), 3(qnm− qm, {q− 1, q, q+ 1}, 1), 3-(qnm− 2qm− 1, {qm− 3, qm− 2, qm− 1, qm, qm+ 1}, 1), 3-(qnm − 2qm, {qm − 3, qm − 2, qm − 1, qm, qm + 1}, 1), 3-(qnm − 2qm + 1, {qm − 3, qm − 2, qm−1, qm, qm+1}, 1), where q is a prime power and n ≥ 2, m ≥ 1 are integers. Further designs are obtained from these. © 2008 Elsevier ...