scripts

Beta PVDF

How to generate the topology

• Prepare (CH2CF2)n polymer with n=22(for example), using polygen 22 > pvdf_beta_22.gro
• Open pvdf_beta_22.gro using Avogadro
• Add terminal H and F - (CH3 and CF3 groups)
• Adjust the bondlengths (put values of other C-H and C-F bonds) in the CH3 and CF3 groups: View > Properties > Bond properties
• Save and quit Avogadro
• Open pvdf_beta_22.gro and edit : put the last F in the 22VDF residue and the last 3 Hs into 1VDF instead of 1UNL
• Generate top: gmx x2top -ff pvdf-cnt -nopbc -noparam -name pvdf_beta_22 -o topol.top -f pvdf_beta_22.gro
• In the [dihedrals] section change function 1 to 9. Use may be made of sed -i~ '/\[ dihedrals \]/,/\[ system \]/s/ 1 / 9 /g' topol.top for this. But be careful as the sed command can change atom number 1 to 9 as well.
• Generate .itp from topol.top if needed

How to generate periodic molecules

• https://gromacs.bioexcel.eu/t/periodic-molecules-infinite-graphene-layer/2021

• https://gromacs.bioexcel.eu/t/infinite-dna-across-boundary-conditions/1628

• https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/H75XEpG8/gmx-users-polymer-in-periodic-boundary-conditions

• Remove all references to atoms belonging to the terminal CH3 and CF3 groups (residue 1 and 22) from both .gro and .top.

• In .top file, when atoms in residue 1 (terminal group) interact with atoms in non-terminal groups, replace atoms in residue 1 with corresponding atoms in residue 21. Similarly replace atoms in residue 22 with corresponding atoms in residue 2. The 3rd H or F in the terminal groups that we added should be ignored completely as it has no correspondence in residue 21 or 2.

• The topology file now needs renumbering of the atoms as atom numbers start from 5. Download gmx_top_tools.tgz by Anton Feenstra from Gromacs's User contributions page.

• Extract the renumtop awk script and do renumtop topol.top > renumbered_topol.top

• Next we need to prepare the corresponding .gro file. It still has 22 residues and 134 atoms. Also needs renumbering. Delete residue 1 and 22, edit the total number of atoms to be 6x20=120, then run gmx editconf -f old.gro -o new.gro to renumber the atoms. Note that we don't renumber the residues (no -resnr option used). This is because the topology file still doesn't have the residues renumbered.

• DONOT forget to add periodic-molecules = yes in the .mdp file. Otherwise there would be errors while domain decomposition.

How to generate crystal structure

• crysgen <path/to/.gro> <nx> <ny> <nz> [<b>]. b is the unit cell dimension along y (dipole direction) default 0.491nm
• The gro file passed to crysgen must be that of a periodic n-mer properly aligned (long axis along z and dipole along y)
• crysgen renumbers the residues. Accordingly the topology file needs to be renumbered manually. To renumber the residues in the topology file (say, topol.top) : awk '/\[ atoms \]/,/\[ bonds \]/{$3-=1}1' topol.top. Note that this command also edits the lines containing [atoms] and [bonds] which you will have to correct for.

Single point energy calculation GROMACS

• http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Single-Point_Energy
• mdrun -s input.tpr -rerun configuration.pdb; Note that the configuration supplied must match the topology you used when generating the .tpr file with grompp. The configuration you supplied to grompp is irrelevant, except perhaps for atom names.