{"id":436,"date":"2018-10-27T06:31:42","date_gmt":"2018-10-27T06:31:42","guid":{"rendered":"https:\/\/doublelayer.eu\/vilab\/?p=436"},"modified":"2018-10-27T14:03:38","modified_gmt":"2018-10-27T14:03:38","slug":"md-simulation-of-bulk-bmpyrdca-ionic-liquid","status":"publish","type":"post","link":"https:\/\/doublelayer.eu\/vilab\/2018\/10\/27\/md-simulation-of-bulk-bmpyrdca-ionic-liquid\/","title":{"rendered":"MD simulation of bulk BMPyrDCA ionic liquid"},"content":{"rendered":"

Simple demonstration of a molecular dynamics simulation of 25 BMPyrDCA ionic pairs in a box.<\/p>\n

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<\/a>.\u00a0The force fields are taken from github: github.com\/vladislavivanistsev\/RTIL-FF<\/a>. References are given within the files.<\/p>\n

<\/p>\n

Let’s execute some commands to tell the computer how to run the simulation. First, we pack 25 BMImDCA into a predefined box. For packmol we should thank J. M. Mart\u00ednez and L. Mart\u00ednez. Visit m3g.iqm.unicamp.br\/packmol\/<\/a> to see details.\u00a0In case packmol does not work, I have put packmol.gro file.
\n.\/packmol < packmol.inp<\/code>
\ngmx editconf -f packmol.pdb -o packmol.gro<\/code><\/p>\n

Now let’s create an index of the ionic pairs. Enter q.
\ngmx make_ndx -f packmol.gro -o index.ndx<\/code><\/p>\n

Prepare an executable file for the simulation.
\ngmx grompp -f STEEP.mdp -c packmol.gro -p topol.top -n index.ndx -o STEEP<\/code><\/p>\n

Execute the first simulation step.
\ngmx mdrun -deffnm STEEP<\/code><\/p>\n

Prepare another executable file for the simulation.
\ngmx grompp -f RUN.mdp -c STEEP.gro -p topol.top -n index.ndx -o NVT<\/code><\/p>\n

Run the simulation, so-called production run. Note, it should use all available CPUs.
\ngmx mdrun -deffnm NVT<\/code><\/p>\n

Convert the trajectory for the whole system. Enter 0.
\ngmx trjconv -f NVT.xtc -s NVT.tpr -o NVT.trr -ur compact -pbc mol<\/code><\/p>\n

To see the equilibrated system, open a terminal and type “vmd NVT.gro”. In the “VMD main” window select the single line “0 T A D F NVT.gro …”, then from File menu choose “load data into molecule”, select “NVT.trr” file.
\nvmd NVT.gro<\/code><\/p>\n

Examine the spatial distribution. For example select group 2 and then 3 to see the destribution of 3 (DCA anion) around 2 (Pyr cation).
\ngmx spatial -f NVT.xtc -s NVT.tpr -n index.ndx<\/code><\/p>\n

Visualize the grid.cude in VMD. Chech the representations and drawing method: isosurface.
\nvmd grid.cube<\/code><\/p>\n

You can do much more when you have a longer trajectory. For example, you may calculate density or diffusion coefficient.<\/p>\n","protected":false},"excerpt":{"rendered":"

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.\u00a0The force fields are taken from github: github.com\/vladislavivanistsev\/RTIL-FF. References are given within the files.<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[30,12,41],"tags":[44],"class_list":["post-436","post","type-post","status-publish","format-standard","hentry","category-conferences","category-know-how","category-teaching","tag-gromacs"],"_links":{"self":[{"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/posts\/436","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/comments?post=436"}],"version-history":[{"count":7,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/posts\/436\/revisions"}],"predecessor-version":[{"id":450,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/posts\/436\/revisions\/450"}],"wp:attachment":[{"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/media?parent=436"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/categories?post=436"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/tags?post=436"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}