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

Chih-Ying Lin chihying2008 at gmail.com
Thu Dec 24 04:58:51 CET 2009

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

7. Relaxation of solvent and hydrogen atom positions
   Run => Position restrained MD
   => simulation break

What is wrong here?
How to put another 10 ligands into the simulation box correctly?

Thank you

Chih-Ying Lin wrote:
> Hi
> I have a system -  solutes with water.
> The system has been under MD simulation for 100 ns.
> Now, I want to put more solutes in it.
> Would you please tell me which command can make it ?

Go back to the start, take a coordinate file with a suitable periodic
box defined (editconf), and replicate it suitably (genconf), then
solvate that (genbox), then equilibrate.

You could replicate the solvated box, but it's more trouble than it is


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