Example Protein in water box

Load the psf file to vmd using the selection File> New Molecule, then pdb file using File $>$ Load Data Into Molecule in VMD Main window.Source the script by using selection Extensions $>$ tkcon inVMD Main window

solvate myo.psf myo.pdb -b 2.4 -t 5 -o myo_wb

This will place the protein in a box of water with a layer of water of dimension 5 $\AA$ in all directions. The output psf file will be named as myo_wb.psf and pdb myo_wb.pdb. The water layer will be 2.4 $\AA$ from the protein.

At the end the script prints the minimum and maximum coordinates of water.Below given is the vmd snap shot of water box.

solvate has also got some other options.For eg

solvate myo.psf myo.pdb -b 2.4 -minmax { {-30 -30 -30} {30 30 30}}

creates a water box with minimum(-30,-30,-30) and maximum (30,30,30) coordinates(in $\AA$) of water with water layer 2.4 $\AA$ from the protein.