Gromacs topology files for common RTIL ions

Gromacs topology files for common RTIL ions are available at Most of them were written in 2012–2013 by Isabel Lage-Estebanez and Vladislav Ivaništšev, and tested in MD simulations of ionic liquid bulk. Some, like FEP-anion and B(CN)4-anion, were added recently and are not well tested. You are welcome to try and give the feedback at GitHub.

Transpose paste

Despite python etc we still heavily rely on the tables. Sometimes it is need to transpose a vertical data-set to a horizontal representation. That is easy. In LibreOffice Calc use special paste (Shift+Ctrl+v) and tick transpose and numbers. One can do similar trick in Excel. That is it.

Performance of SCAN density functional for a set of ionic liquids

We have evaluated the performance of a recently developed non-empirical Strongly Constrained and Appropriately Normed (SCAN) density functional on electronic structurecalculations of ionic liquids. We show that SCAN reproduces coupled-cluster results for describing the employed dataset of 48 ionic pairs, and we recommend it for the high-throughput screening of ionic liquids.

This paper was accepted to be published in the International Journal of Quantum Chemistry. For a limited time, it is available free of charge at:



Visiting Tartu in November

A list of things to bring with you:

  • Gloves, hat and scarf (the average temperature is −1.5°C)
  • Waterproof boots or trekking boots (with a good grip in case there is ice)
  • Layered clothing (like pullovers and cardigans, so that you can remove or add layers according to the weather and how fast you are moving)
  • Swimming equipment (for SPA and sauna or why not doing some winter swimming?)
  • Napkins for a runny nose
  • A postcard to pin in the office 5072 where Vladislav works

The dark side of submitting in LaTeX

Point 1. On the publishers portals, LaTeX looks old-fashioned. The compilation seemed romantic in the early students years, but currently it looks awful to me: LaTeX -> BibTeX -> LaTeX -> DVI -> PS -> PDF. ShareLaTeX is great, yet to submit a paper one has to return to the old-school compilation.

Point 2. Grammarly does not work with bare TeX even in ShareLaTeX. There is so much space for improvement, where publishers could significantly contribute. Do they?

Point 3. Vector figures are great. Why do publishers ask for eps? The encapsulated postscript is outdated. For instance, it does not support transparency and also gradients, to a certain extent.

Bird’s-eye View

Most of us work on the “dark” side of Chemicum. Meeri is from the “rusted” Physicus (on the back plan), where they have a nice sauna.

From left to right: A, B, C and D wings of Chemicum ( A is for lobby and cateen, B is for lecture halls, C and D are for offices and laboratory. On the back plan there is Physicum (
We are in the upper left corner of the middle-part of Chemicum.

A valuable message

My friend Olga Jasnovidova has recently finished her PhD studies in Brno in Czech republic. In her acknowledgement speech she concluded the 7 years-long work and gave a message for young ones. Here it is.

“Science is one of the most creative fields to work in”

Through my PhD studies I have learned that science has two dimensions: one scientific, and one human… and that, of the two, the human dimension is the more difficult to grasp.

I understood that, in order to achieve your goals, you must not only care about your work or yourself. You have got to care about the people around you: senior and junior students, technicians, facility managers, senior colleagues, your supervisors. As you step into PhD studies, you should not expect them to support and motivate you, but rather you yourself should start by supporting and motivating them.

I have also learned that one of the most effective ways to grow and develop is to ask for feedback, then learn to accept it and moreover learn to give constructive feedback yourself. This process can be painful for our egos, but it is the only way to grow.

Most importantly, I have learned that there are always several ways to achieve the same goal. There is no one correct way to reach one’s target. Therefore, you should always stay open to new ways to achieve your goals.

Based on my experience, I would like to say to younger students that they should not fear anything new or unfamiliar. Please don’t create any mental barriers for yourselves. Academic research seems like a very conventional and strict field after Bachelor’s or Master’s studies or peer review, but it is not so. Science is one of the most creative fields to work in, providing endless opportunities to grow and discover. Just learn the rules and then use them to create. You can do something truly unique for the first time in human history, something that will lay a path for many to follow. Believe in your own abilities. Every single day you have an opportunity to do something amazing — don’t waste it.

P.S. Olga, congratulations!

P.P.S. Meanwhile Samual Coles defended his PhD thesis in Oxford. Grande Sam! Sam, congratulations!