Aassoc. prof. at the University of Latvia
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”
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”
A long time ago a student told me that I am a mascot of the chemistry olympiad. Since then I have graduated, made a post-doc, and after that returned to the olympiad business. It is very touching that the Estonian team named its mascot “Vlad”. Apparently, I am a mascot again.
Jasper Adamson visited Tartu. As always, it was a pleasure to meet him. Here he is holding an actuator.
A group of students and tutors from Paris 13 visited Chemicum. Aurélie and Chris on the left and David with sunglasses in the middle. Georgi (on the right) made a nice excursion. Next year two Erastus students from Paris 13 will be studying in Tartu!
At the evening of the best lecturers recongnition. My supervisor Karmen Lust receinved the award.
Vladislav, Meeri and Karl at the FMTDK2018 near the Karl’s poster.
Assume that all the requirements are fulfilled:
Optional, but highly recommended:
LibXC compilation:
svn co http://www.tddft.org/svn/libxc/trunk/ libxc
cd libxc
autoreconf -i
./configure --enable-shared --prefix=/home/USER/xc
make -j N
make install
The LibXC compilation might not work, and GPAW would complain, so configure as follows:
./configure CFLAGS="-O2 -fPIC" --prefix=/home/USER/xc
After compiling LibXC add these lines to your .bashrc:
export C_INCLUDE_PATH=/home/USER/xc/include
export LIBRARY_PATH=/home/USER/xc/lib
export LD_LIBRARY_PATH=/home/USER/xc/lib
Let’s install ASE using pip, because it is easy.
pip install --upgrade --user ase
Get the GPAW source code and remove in libxc.c in c/xc/ line xc_mgga_x_tb09_set_params(self->functional[0], c);. Them compile GPAW with python setup.py install --user. You might want to add the .local/bin to the path.
Use either Python or Python3, and be consistent with that.
The official guideline also recommends adding these lines to your .bashrc:
export PYTHONPATH=/home/USER/gpaw:$PYTHONPATH
export PATH=/home/USER/tools:$PATH
Don’t forget to get setups. E.g. execute gpaw install-data DIR. After that run the tests.
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.
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.
