[gmx-users] How to put more solutes into the system ?

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> 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.

Mark