Kneth's Korner

Free Chemistry Software - Molecular Modeling

Molecular modeling is a very large and important field of chemistry. As computers have increased in raw computing power, the usage of computers to calculate molecular properties is not a specialized fields for the few. Today, every chemist can perform calculation for even large molecules.

Roughly speaking, you can divide the calculations in two separate groups: molecular mechanics and quantum chemistry. The first is based on classical mechanics, while the second group uses quantum mechanics as a underlying model and equations. The software list at http://en.wikipedia.org/wiki/Molecular_modeling shows a wide range of offerings. Many of them are commercial and closed-source solutions.

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Free Chemistry Software - Utilities

One of the major annoyances as chemists in front of computer is faced with is the vast number of file formats. The good news is that most file formats are text files so it is possible to reverse engineer them by looking at a number of examples. One open source project called OpenBabel tries to help chemists in converting between the formats (currently OpenBabel supports 113 file formats related to chemistry). Most Linux distributions have packages for OpenBabel, including Debian GNU/Linux (it’s a version from 2009 you find in Debian stable). Converting a molecular structure of caffeine from one file format (SDF) to another (PDB) is simply done by the following command: babel -isdf caffeine.sdf -opdb caffeine.pdb

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The year of 2011 has been declared the International Year of Chemistry by UNESCO (United Nations Educational, Scientific and Cultural Organization) and IUPAC (International Union of Pure and Applied Chemistry). The purpose of devoting a full year to chemistry is to spread the notion that chemistry is important for our daily life.

In this series of blog posts I have examined the state of free software in chemistry. This first post is an outline of the usage of computers in chemistry.

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Tjen penge på Open Source

Notes in English

• Co-authors: Peter Toft and Hanne Munkholm
• Published at sslug.dk
• Original license: http://www.opencontent.org/opl.shtml

Formål

Vi vil i denne artikel argumentere for at Open Source Software er bedre end det mere traditionelle lukkede software. Det vil blive beskrevet hvorfor Linux-verdenens måde at udvikle software på har store fordele - dels med hensyn til stabilitet og sikkerhed, men også med hensyn til den strategiske risiko, som en moderne erhvervsleder altid må tage, når der købes software.

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Open Source (TM)

Notes in English

• Co-author: Peter Toft
• Published at sslug.dk

Introduktion

En af de mest spændende udviklinger på software fronten det sidste stykke tid er konceptet Open Source (TM), der dækker over frigivelse af kildeteksten til et program. Dette sker under en licens, der giver lov til at alle - uanset kulturelle og geografiske skel - må anvende og ændre kildekode efter behov, og derefter frit videregive den modificerede kode under samme licens.

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