Sorry, I did it using VMD using these codes:

set aml [atomselect top protein]

$aml writepdb aml.pdb

in vmd.. you can also write .gro file directly

I am using Roshan's example:

set aml [atomselect top protein]

$aml writepdb aml.pdb

animate write gro aml.gro sel $aml

Dear Roshan,

To remove water molecules from a .gro file in gromacs, simply use the following command.

editconf -ndef -f Orignal.gro -o selected_structure.gro