[gmx-users] Spacing

[P.R.Anand Narayanan]

Dear gromacs users,
I've been using gromacs to run a simulation of  a protein with a cofactor and a ligand. i had a problem while running the simulation; the cofactor, ligand and the substrate molecule were spaced away from the protein in the solvent box., thereby creating literally zero interaction energy.
How do I solve this problem and place all the molecules together in the solvent box?
Thanking you,.
Anand.




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