GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Importance of verifying queue model assumptions before planning with simulation software

This case study uses empirical data gathered at an Australian refinery to verify the assumptions for queue distributions before using special-purpose software to plan the off-road-truck hauling of titanium dioxide to a refinery (n = 773). Easy-to-use spreadsheet software is utilized to verify assumptions for queue models. Managers are able to make decisions based on economic implications of queue models to avoid making costly planning mistakes. Analysts can use nonparametric hypothesis-testing techniques to verify distribution assumptions for optimization without having to write hard-to-maintain and complex algebraic linear equations or nonlinear search routines.     

‘New mathematics’ and teaching

Inside the scientific world it is not always understood that the mood of mathematics, which is a product and a part of culture, can change with time. This is partly why many have been surprised by the coming of the so‐called new mathematics.

In the truly creative mathematical mind two opposite tendencies coexist: the logical and the imaginative. Apparently it seems that new mathematics can be reduced to a purely logical machinery. In fact it contains as much imaginative contributions as classical mathematics. But it is difficult to show simultaneously the logical sequence of propositions and the clumsy progression of research itself. Mathematical exposition does not always follow the ‘ most natural slopes’ of the mind. Unfamiliar presentations often give an impression of ‘ abstraction ‘, more familiar ones an impression of concreteness ‘.

So it appears that difficulties with new mathematics are mostly of psychological origin. Misuses of it can easily raise up intolerance reactions and emotional blocks. Perhaps insisting upon the fact that, here as elsewhere, it is important to be able to guess, to realize that intuition and imagination are essential, could help to make new mathematics better understood, more useful and more able to be considered as a unifing element among sciences.     

Classroom note: The area under x α by geometry

By stretching the area under the curve x ^α it is shown to be of the form x ^{α + 1} p(α). Geometry is then used to prove p(α) = 1/(α + 1).     

An improved exponential transformation for nearly singular boundary element integrals in elasticity problems

This paper presents an improved exponential transformation for nearly singular boundary element integrals in elasticity problems. The new transformation is less sensitive to the position of the projection point compared with the original transformation. In our work, the conventional distance function is modified into a new form in the polar coordinate system. Based on the refined distance function, an improved exponential transformation is proposed in the polar coordinate system. Moreover, to perform integrations on irregular elements, an adaptive integration scheme considering both the element shape and the projection point associated with the improved transformation is proposed. Furthermore, when the projection point is located outside the integration element, another nearest point is introduced to subdivide the integration elements into triangular or quadrilateral patches of fine shapes. Numerical examples are presented to verify the proposed method. Results demonstrate the accuracy and efficiency of our method.     

SpecPad: device‐independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology

SpecPad is a new device‐independent software program for the visualization and processing of one‐dimensional and two‐dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device‐independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off‐line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR‐related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd.