Leiden Classical

Finished Projects of Leiden Classical

Finished Projects of Leiden Classical

PGO 2006

This project was the first project on Leiden Classical. First year graduate students were given a simple question to adress and they had only a week time to answer it, making use of Leiden Classical. The question was whether or not HCl, in solution, for a given force field model, was able to dissociate or not. If so, how well, and if not, why? The original introductory document (Dutch), the presentation (Dutch) and the poster (English) made by the students can all be downloaded.

PF 2006

In this project several 2nd-year graduate students, in groups of two, were set out to verify the ideal gas law. They were given a document with basic theory on molecular bond vibrations, the ideal gas law and exercises they had to do individualy. The document (Dutch) and the inputfiles can be downloaded.

MM 2006

In this project Leiden Classical was used as a computer lab exercise. The Molecular Modeling course was made more interactive for the students by actually doing Molecular Dynamics simulations on Leiden Classical. The students were given a well-known paper from the literature on the simulation of liquid argon. Given an input file, they had to perform several simulations themselves and derive the diffusion coefficient the same way as Rahman did in 1964. The exercise document (English) can be downloaded, together with the input files.

MQC 2007

In this project Leiden Classical was again used as a computer lab, but now for the Modern Quantum Chemistry course. Students were given an input file of a flexible water simulation. They were asked to analyse the model and see what force field elements were present, and they were asked to run some simulations to determine the diffusion coefficient of this water model. The exercise document can be downloaded (English) together with the input files.

LO1 2007

In this project two 2nd-year gruaduate students in Chemistry were trained in doing research. Leiden Classical was used to see if the dissociative chemisorption of hydrogen on Cu(100) showed a rotational hindering effect. The two students were given an indroductory course in Surface Science. This course was based on the chapter Leiden Classical contributed to the RechenKraft book on Distributed Computing. Once the students were ready they had to perform a vast amount of calculations on Leiden Classical to answer the scientific question. They gave a presentation (English) which can be downloaded. Currently two new students are preparing themselves to continue on this work!


With the Pre-University project of 2007, two talented high-scool students did a project on Leiden Classical, concerning the flexible water model. They started off also by reading the theory of the RechenKraft chapter and then started out on the quest of determining the freezing / melting point for this flexible water model. In doing so they uncovered a anomality in one of the formulas used to calculate the pressure. It was found that the periodicity of the minimum system image convention was not obeyed in calculating the virial. The code was afterwards adapted for this. Their report (English) can be downloaded.

LO1 2008

In this project two first-year students continued on the work of a previous project (PGO 2006). Anniek and Frank tried to find reasonable Morse-parameters for the H-Cl interaction that was used in the HCl in water model. By performing MP2 level calculations with Spartan, and using a Newton-Raphson root solver in Excel, they were able to find improved parameters by performing a Least-Square fit to ab-initio data. Although not enough MP2 calculations were used in the fit yet, the students setup the basis for continuing along this line for future students! You can look at their presentation and the Excel sheet they used here.

LO2 2009

Sebastiaan Oldenbroek and Anne Hoekstra were students doing a Leren Onderzoeken project in their second year of their Bachelor in Chemistry. In this project they learned about classical dynamics, force fields and using this BOINC project with the Classical Builder. As part of their chosen research subject, they started with the development of a benzene system. They wanted to see if the benzene in their model would phase-separate in water. During the project they build a shell script that generates input files for Classical with their benzene model. The script, some input files and their report can be found here.

LO1 2011

Selwyn Hanselman and Tomek Diederen started their LO1 project in 2011 investigating a model for an fcc copper crystal. They are first year Bachelor Chemistry students who learned the basics of molecular dynamics and forcefields. During their project they setup a model for a copper slab using force field parameters from literature and investigated if this model yields the correct melting behaviour. To this end they wrote a python script to calculate radial distribution functions from Classical snapshots. The script, the model input files and their presentation can be found here.

LO1 2012

Jerwin Mierop and Mark Wielstra started their LO1 project in 2012. They adapted the argon simulation that was already available to krypton and tried to determine the diffusion coefficient. See their presentation here.

LO3 2012

In the LO3 project of 2012 two students participated, each with their own project. Dennis van der Meij tried to melt gold in a simulation and Maarten van der Geest investigated the theormodynamics of organic polymers. They both presented a poster.

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