Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visualized the " Simulation-System-EM-solvated.gro " after the energy minimization. Then, I found that the Simulation Sysmtem is devided into 16 domains very clearly and the molecules (protein, ligand, and water) break into atoms in the boundaries. I have checked that the 20 ligands are not overlapped each other and are not overlapped with protein from the beginning.
More, i have created 10 alike system and each is with "one protein + 20 ligand + water molecules" Two of them get the "minus potential energy" after energy minimization and I can continue running the MD simulation successfully. Others of them get the "extreme high positive potential energy" and the system is devided into 16 domains after energy minimization and the simulation broke afterall. With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 ) There is no problems like that. Please give me your ideas to solve the problem. Thank you Lin
-- 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
