Box preparation in gromac?

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Satnam Singh

gmx insert-molecules -f firstmolecule.gro -ci secondmolecule.gro -nmol 10(numberof molecule e.g 10) -box 5 5 5(means 5nm cube) -o finalbox.gro -try 10

Arpit Jain

Generate urea topology with pdb2gmx or ACPYPE.
Create the box: gmx editconf -f urea.pdb -o urea_box.gro -c -d 1.0 -bt cubic.
Solvate: gmx solvate -cp urea_box.gro -cs urea.gro -o urea_solv.gro -p topol.top.
Adjust MDP: Set urea concentration and parameters.
Minimize/Equilibrate: Use gmx mdrun as usual.

all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.