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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
