[gmx-users] .top file for a mixed solvent

[Ehsan Sadeghi]

Hi gmx users,

I want to simulate ionomer is mixed solution of water and ethanol using gromos force field.
I tired to follow the steps suggested on gromacs website, which are:
   1- Determine the number of co-solvent molecules necessary, given the box dimensions of your system.
   2-  Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro).
   3-  Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box.
   4-  Fill the remainder of the box with water (or whatever your other solvent is) using genbox.
   5-  Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system.

Here are the commands that I used:

pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top -i ionomer4.itp (ionomer-4.pdb is the pdb file for 4 ionomer molecule)

pdb2gmx -f eth.pdb -o eth.gro -p eth.top -i eth.itp (eth.pdb is the pdb file for single ethanol molecule)

editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5

genbox -cp box.gro -ci eth.gro -nmol 1000 -o phase1.gro

genbox -cp phase1.gro -cs spc216.gro  -o solvated.gro


At the end, I have the solvated.gro file with 4 ionomer, 396 ethanol, and 423 water molecules. I don't know how to proceed step 5 and generated a combine .top file. What should I do with [ molecules ] directive?
I appreciate any suggestions.

Kind regards,
Ehsan