Simple demonstration of a molecular dynamics simulation of 408 BMPyrDCA ionic pairs between two graphene walls.<\/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_Gr-BMPyrDCA_pbc<\/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. However, don’t forget to allow the computer to read and execute all files. To do so, in the terminal enter “chmod 755 *”.<\/p>\n First, we pack 408 BMImDCA ionic pairs into a predefined box. In case packmol does not work, I have put packmol.gro file. In the packmol.gro set the box length to 7.0 nm.<\/p>\n Now let’s create an index of the ionic pairs. Enter q.<\/p>\n Prepare an executable file for the simulation. Execute the first simulation step. Prepare an other executable file for the simulation. Run the simulation, so called production run. Note, it should use all available CPUs. Caution! The simulation requires a lot of time. Check the potential, field, and charge profiles. Plot the .xvg-resulting files using xmgrace (like xmgrace potential.xvg). Let’s apply field to induce the ionic layering at the modelled interface. Run the simulation with the field. Caution! The simulation requires a lot of time. Check the potential, field, and charge profiles. Plot the .xvg-resulting files using xmgrace (like xmgrace potential.xvg). Compare them with the ones obtained for the simulation without any applied field. 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.\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-442","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\/442","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=442"}],"version-history":[{"count":3,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/posts\/442\/revisions"}],"predecessor-version":[{"id":451,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/posts\/442\/revisions\/451"}],"wp:attachment":[{"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/media?parent=442"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/categories?post=442"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/doublelayer.eu\/vilab\/wp-json\/wp\/v2\/tags?post=442"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\n.\/packmol < packmol.inp<\/code>
\ngmx editconf -f packmol.pdb -o packmol.gro<\/code><\/p>\n
\ngmx grompp -f STEEP.mdp -c packmol.gro -p topol.top -n index.ndx -o STEEP<\/code><\/p>\n
\ngmx mdrun -deffnm STEEP<\/code><\/p>\n
\ngmx grompp -f RUN.mdp -c STEEP.gro -p topol.top -n index.ndx -o NVT<\/code><\/p>\n
\ngmx mdrun -deffnm NVT<\/code><\/p>\n
\ngmx potential -f NVT.trr -n index.ndx -s RUN.tpr -sl 1000 -o potential_0.xvg -oc charge_0.xvg -of field_0.xvg<\/code><\/p>\n
\ngmx grompp -f FIELD.mdp -c NVT.gro -p topol.top -n index.ndx -o FIELD<\/code><\/p>\n
\ngmx mdrun -deffnm FIELD<\/code><\/p>\n
\ngmx potential -f FIELD.trr -n index.ndx -s FIELD.tpr -sl 1000 -o potential_10.xvg -oc charge_10.xvg -of field_10.xvg<\/code><\/p>\n","protected":false},"excerpt":{"rendered":"