Computer modelling in chemistry - master computational practice

Article reading and calculation report tasks for the lab of András Baranyai and Gergely Tóth

held on 3rd September, 2020 room Chemistry 534

Unfortunately, a part of the students was not able to take part on the practice. Maybe, it was due to the lack of information, e.g., lack of schedule in the Neptun system. Usually there are two tasks after the practice, one relates to the calculations performed and one to the understanding of an article and writing a summary. Now, the students skipped the practice have to write only an article summary, but in a longer format. The articles to be reported can be downloaded by clicking in the row of the student name. In some cases, there are additional articles to be used during the report on the numerical results. These articles are need not to be summarized. The deadline of the article and the calculation reports is 30th of September. Please send it in PDF to toth@chem.elte.hu. Hungarian students may write the reports in Hungarian.

 

Tasks for students taking part on the practice:

a) 2-3 pages long report on a journal article. The emphasis is on the understanding of the aims and goals of the article (e.g. new method and results) and its interpretation using your own words.

b) 1-2 pages long report. It starts with a short description of the simulation including data like number of particles, number of steps, potential function and the used method. Thereafter the asked figures are to be presented together with discussion of the figures. In some cases small theoretical calculations are asked, too.

Liquid argon:  Monte Carlo simulation, 200 Lennard-Jones particles (T in the first case = 88K), 500000 MC trials.

M. Baglyas – graph on the temperature dependence of pair-correlation function, article to summarize

Flexible BJH water, molecular dynamics (200 molecules, 298.3 K, 20000 timestep, Δt=0,2 fs, NVT canonical)

B. Széles - H and O autocorrelation functions and spectral densities, discussion of the peaks in the spectral densities, (material to help the understanding of the velocity projections in the report part), , article to be summarized

P. Varga - O and centre of mass autocorrelation functions and spectral densities, discussion of the peaks in the spectral densities, (material to help the understanding of the velocity projections in the report part) , article to be summarized

B. Keresztes – rotational autocorrelation functions and spectral densities, moment of inertia calculation on the principal axis of water, article to be summarized

Á. Szirmai – intramolecular vibrational autocorrelation functions and spectral densities, , discussion of the peaks in the spectral densities, , (material to help the understanding of the velocity projections in the report part), , article to be summarized

Crystal growth, Kinetic Monte Carlo simulation

L. Tulipán – figures on urea crystals grown in water and methanol, article to be summarized

B. Kozma – figures on urea crystals grown in water and methanol, article to be summarized

 

Tasks for students were not able to take part on the practice:

a) 3-5 pages long report on a journal article. The emphasis is on the understanding of the aims and goals of the article (e.g. new method and results) and its interpretation using your own words. The selected articles are more complex ones than those of the other students.

D. Forrayarticle to be reported

Reis Fernando Felipe – article to be reported

B. Bónis –article to be reported

 

G. Tóth, last modified 4th September, 2020