[gmx-users] How to put more solutes into the system ?
Mark.Abraham at anu.edu.au
Wed Dec 23 23:27:31 CET 2009
Chih-Ying Lin wrote:
> The system = one protein molecule + 10 ligands + water molecules in 6
> x 6 x 6 box.
> after 100 ns simulatin, 10 ligands have attached on the protein.
> Now, I tried to put another 10 ligands into the system.
> The steps are as follows.
> 1. Take one coordinate file and remove all the coordinates of the
> water molecules.
> 2. Center the protein with the attached 10 ligands
> 3. With "genbox" command, to put another 10 ligands into the simulation box.
> 4. Solvate the system, with "genbox" command
> 5. Add ions, with "genion" command
> 6. Energy minimization of the solvated system
> pbc = xyz (minim.mdp)
> => the system is crystallized with visualization
What's the energy and maximum force?
> 7. Relaxation of solvent and hydrogen atom positions
> Run => Position restrained MD
> => simulation break
Check the box size at each step makes sense. Load the structure at each
step into a visualization program and check that it makes sense with the
box. I'm expecting you've got some molecule clashing with another. If
everything's OK, trying a smaller integration time step can sometimes help.
Otherwise, the procedure looks good.
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