The Quasi-Gaussian Entropy theory (QGE) is a new statistical mechanics theory (Amadei et al., J. Chem. Phys. (1996), 104, 1560-1574), that can be used to predict the physical-chemistry properties of real and simulated systems in a very wide temperature range. A new expression of the Clausius-Clapeyron equation, based on the QGE, for the evaluation of the liquid-vapor equilibrium pressure of pure liquids, was developed [1]. The new equation is able to predict the liquid-vapor equilibrium pressure curve, with high accuracy, over a large temperature range and for different fluids like water, methanol, and mercury.
Continue readingAuthor: Danilo Roccatano
Molecular Dynamics Simulations Combined to X-Ray Spectroscopies XANES and EXAFS
In Laurea thesis (equivalent to M.Sc. Diploma Thesis, discussed in 1992), I have for the first time investigated and attempted the combination Molecular Dynamics (MD) simulations and theoretical spectra calculation for the interpretation of experimental XANES (X-ray Absorption Near-Edge Spectroscopy) [4]. The method was used to study the aquatrisimidazole copper (II) sulfate complex’s crystal structure, but the results not yet published. The thesis is in Italian, and it is available on request to the interested reader.
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Parallel computing and molecular dynamics simulations
The recent technical developments in parallel computing have made available large parallel computing facilities at relatively contained costs that have stimulated an intense developing activity to realize efficient parallel programs for the scientific and technical calculation. One of the scientific fields that most benefit from these developments is computational chemistry and in particular Molecular Dynamics (MD). The reason of that is related to the increasing interest in the study, with this technique, larger molecular systems for long simulation times. Continue reading
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A Practical Introduction to the C Language for Computational Chemistry. Part 1
Write in C (Let it Be)
When I find my code in tons of trouble,
Friends and colleagues come to me,
Speaking words of wisdom:
“Write in C.”
As the deadline fast approaches,
And bugs are all that I can see,
Somewhere, someone whispers:
“Write in C.”
Write in C, write in C,
Write in C, oh, write in C.
LISP is dead and buried,
Write in C.
I used to write a lot of FORTRAN,
For science, it worked flawlessly.
Try using it for graphics!
Write in C.
If you’ve just spent nearly 30 hours
Debugging some assembly,
Soon you will be glad to
Write in C.
Write in C, write in C,
Write in C, yeah, write in C.
Only wimps use BASIC.
Write in C.
Write in C, write in C,
Write in C, oh, write in C.
Pascal won’t quite cut it.
Write in C.
Write in C, write in C,
Write in C, yeah, write in C.
Don’t even mention COBOL.
Write in C.
Parody Song by
Brian Marshall
This series of tutorials will provide a short and practical introduction to the C language aiming students with interest in computational or physical chemistry. At the end of this tutorial, you will be able to write simple programs that can read data from files elaborate them and write the results of the calculations in output files. This tutorial is not a course in C programming language, therefore the motivated readers are encouraged to look for more comprehensive introductions to this language.
The tutorial is also based on OS based Unix systems such as Linux or MacOSX. Therefore, I recommed to give a look to my introductions to Unix OS:
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Notes on the Quasi-Gaussian Entropy Theory Applied to Complex Systems
INTRODUCTION
The Quasi-Gaussian Entropy theory (QGE) is a theoretical method based on a novel statistical mechanics reformulation of the free energy distributions. It was originally developed by Dr. Andrea Amadei (University of Rome “Tor Vergata”, Italy) in collaboration with Prof Herman Berendsen, Dr. Emil Apol (the University of Groningen, The Netherlands) and Prof Alfredo Di Nola (University of Rome “La Sapienza”, Italy). The foundations of the QGE theory are reported in a series of papers collected in the Ph.D. thesis of both Dr. Amadei and Dr. Apol cited in the bibliography. The theory was further developed and applied to different systems spanning from simple fluids to proteins.
In these brief note, the mathematical basis of QGE for the study of the thermodynamics of proteins in solution as in the Ref. [1] is detailed.
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Retro Programming Nostalgia: Commodore Amiga and Molecular Visualization
Italy 1989, it was the age of Commodore Amiga with its BOING demo, the bouncing ball that conquest the heart of the millions of young people living the microcomputer revolution.
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Le Forze Intermolecolari
Le forze interatomiche o intermolecolari che tengono uniti i cristalli molecolari sono di origine elettrostatica e possono essere classificate in forze a corto e lungo raggio a seconda di quanto si estende nello spazio la loro azione. Essendo funzione della distanza tra gli atomi (o molecule), queste forze sono dei campi vettoriali conservativi e sono pertanto derivabili dal gradiente di un potenziale di energia scalare, ovvero 
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L’Energia Reticolare
Con il termine energia reticolare si definisce l’energia necessaria per scomporre, alla temperatura T = 0 K, una mole di un cristallo ionico nei suoi costituenti fondamentali e portarli a distanza infinita.
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Il calcolo della costante di Madelung
In un precedente articolo è stato mostrato che il termine elettrostatico dell’energia reticolare di un cristallo contiene un fattore (A) che dipende dal tipo di reticolo cristallino. Ora esamineremo più in dettaglio come calcolare questo termine e il suo valore per un semplice sistema ionico.
L’energia potenziale totale di un cristallo ionico è uguale alla somma dei contributi di interazione elettrostatica del tipo
degli ioni (A,B) di carica 
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PERL Programming II: Applications to Bioinformatics
This article is the second part of my previous introduction to the PERL language. Here, I am going to show the use of the Perl language in simple bioinformatics applications. I will introduce by examples other aspects of this powerful language.
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