Installing the metalwalls

Here is a quick and dirty instruction for installation of the metalwalls code.

Download the source code using https protocol:

git clone https://gitlab.maisondelasimulation.fr/amarinla/mw2.git

You will be prompted for your username and password.

Preinstall gfortran and openmpi. Then copy compile.something.mk from the computer directory to the mw2 folder as compile.mk. Add a line “FPPFLAGS := -DMW_USE_MPI”. Comment the path to the pFUnit package.

Execute make.

Go to tests directory and execute tests:

python regression_tests.py -s nist

python regression_tests.py -s nacl

python regression_tests.py -s lammps

MD simulation of BMPyrDCA between graphene walls

Simple demonstration of a molecular dynamics simulation of 408 BMPyrDCA ionic pairs between two graphene walls.

Inputs (packmol.inp, STEEP.mdp, RUN.mdp, topol.top) and force field parameters: github.com/vilab-tartu/LOKT.02.048/tree/master/MD_Gr-BMPyrDCA_pbc. The force fields are taken from github: github.com/vladislavivanistsev/RTIL-FF. References are given within the files.

Continue reading “MD simulation of BMPyrDCA between graphene walls”

MD simulation of bulk BMPyrDCA ionic liquid

Simple demonstration of a molecular dynamics simulation of 25 BMPyrDCA ionic pairs in a box.

Inputs (packmol.inp, STEEP.mdp, RUN.mdp, topol.top) and force field parameters: github.com/vilab-tartu/LOKT.02.048/tree/master/MD_BMPyrDCA_box. The force fields are taken from github: github.com/vladislavivanistsev/RTIL-FF. References are given within the files.

Continue reading “MD simulation of bulk BMPyrDCA ionic liquid”

Gromacs topology files for common RTIL ions

Gromacs topology files for common RTIL ions are available at https://github.com/olunet/RTIL-FF. 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.

Some useful notes about LaTeX

First, when advanced spell checking is needed, the LaTeX could be converted to plain-text using: detex filename > filename.txt (note the omission of .tex extension).
Most LaTeX distributions come with detex program which simply strips LaTeX commands.

Second, when working with vector figures it might be a good idea to convert all texts to paths. Remember that eps-format does not support transparency.

Third, in order to count words in the final pdf-file use pdftotext filename.pdf - | tr -d '.' | wc -w. This will return the number of words in our file.

Finally, to generate a pdf-file that is acceptable by manuscriptcentral add \pdfminorversion 4 to your LaTeX-source.
Otherwise, if you use pdflatex to produce your pdf-file, manuscriptcentral will give a notice “failed to convert to the appropriate pdf”. Read this blog-post for details.

Hello world!

We are a group of chemists connected by the University of Tartu. Tartu is located in Estonia. Estonia is a small country in Baltic region of Northern Europe.

The University of Tartu was founded in 1632 by the Swedish king Gustavus Adolphus. It was initially called Academia Dorpatensis.
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