[gmx-users] How to put more solutes into the system ?
chihying2008 at gmail.com
Wed Dec 23 17:10:50 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
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?
Chih-Ying Lin wrote:
> 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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