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 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 Lin 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 worth. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
