[gmx-users] genbox - Umbrella Sampling

Steven Neumann s.neumann08 at gmail.com
Fri Feb 10 15:54:45 CET 2012

Dear Gmx Users,

I am preparing my protein-ligand complex system for Umbrella Sampling (free
binding energy of ligand) and I set
 up the box (Pulling with Z coordinate):

editconf -f Protein10LIGrot.pdb -o ProteinLIGbox.pdb -box 12 7 13

Then using VMD I placed my Protein-Lig complex to on the right side, saved
coordinates of the system

 and tried to add water:

genbox -cp ProteinLIGbox.pdb -cs spc216.gro -o Solv.gro -p topol.top

The problem is that after adding water gromacs move my Protein-Lig complex
in the center of the the Z coordinate - center my complex... Why? I want it
as it was just before adding water. Do you have any clue what is happening?

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