Create Binary Mixture in GROMACS

BINARY MIXTURE

Let say someone is interested to study some protein molecules in Water-Ethanol binary mixture. Now the question is how to create binary solvent like this?

In Gromacs genbox is very powerful in this context. If ratio does not matter, then one can use the following command

genbox_d -cp ethanol.gro -cs spc216.gro -p topol.top -o water_ethanol.gro -box a b c

The above commands will fill the simulation box with ethanol and water molecules with random numbers of water molecules and number of ethanol molecules presents in the ethanol.gro file. However, if one is intend to create some exact number percentage of ethanol-water mixture, the following method will be very useful

Water-Ethanol binary mixture of defined %

Create a .pdb file of single ethanol molecule. (It is very easy, just google it out or create .pdb from software like pymol, prodrg etc., if .gro file is there, no need to create the .pdb file).
Convert that .pdb file to .gro file by executing any one of the following commands

editconf -f ethanol.pdb -o ethanol.gro 

you can in principle also use pdb2gmx command, however it will ask for a forcefield and solvent type, by choosing appropriate forcecfield and solvent as none you will end up with the required .gro file.
You can similarly generate a single water .gro file or just copy and paste from existing spc216.gro file. The single water .gro file will be similar to this single water gro 

3
1SOL OW 1 .230 .628 .113
1SOL HW1 2 .137 .626 .150
1SOL HW2 3 .231 .589 .021

Now, you are ready to go. Let say you want to prepare 10% Water-Ethanol mixture and the numbers are 90Water + 10Ethanol molecules. You can use the following method

Create 10Ethanol.gro file:

genbox -ci ethanol.gro -nmol 10 -o ethanol10.gro -box a b c

Add 90 water molecules to it.

genbox -cp ethanol10.gro -ci water.gro -nmol 90 -o ethanol10_water90.gro

Now your binary solvent is ready for use. Enjoy the simulation!

N.B.: There exist some other alternate way also e.g. instead of specifying 90 water molecules and using -ci option for genbox, one can indeed use -cs spc216.gro option also. In this case one needs to delete the extra water molecules in the resultant .gro file manually :).