We will use the TIP4P water model; it is considered one of the better ones as far as reproduction of typical water properties goes. (It is also the water model to be used together with the OPLS-AA force field.)
Setup Gromacs by sourcing GMXRC.
Generate a small (2.5 nm) water box with genbox:
genbox -cs tip4p.gro -box 2.5 2.5 2.5 -o water.pdb
Note the number of SOL molecules (or count them, e.g. with egrep '^ATOM.*OW' water.pdb | wc -l).
Edit the topology (water.top file) and enter the number of waters in the [ molecules ] section.
You can also try using a different water model (such as TIP3P, SPC, SPC/E) by selecting a different itp file to be included in the topology file. For these “three point water models” use genbox -cs spc216.gro ....
Use the em_opls.mdp parameter file to set up an energy minimization
grompp -f em_opls.mdp -c ../top/water.pdb -p ../top/water.top -o em.tpr
and run it:
mdrun -v -deffnm em
Use the energy minimized system em.gro as input for the MD simulations.