Chih-Ying Lin wrote:
HiSorry that i have posted the same message for several times.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.
Chih-Ying sent me before and after .gro files off-list, and the structure really has done something like this (pic attached). After EM, the cubic simulation cell has partitioned four times along each side, and within each small cube, the waters have contracted as if to minimize surface area. The result is as if each small cube did an EM in isolation of any other such cube. Are you sure you are using a 3.3.3 mdrun? Consult the top part of the log file. I'd guess the most likely problem is that you're seeing some bizarre artefact of your MPI or installation. How was GROMACS configured? Did you use shared libraries? Try a version without. Try single-processor grompp+mdrun. If there's no light shed by the above, please send me your input protein and ligand structure files, and your pre-EM .tpr and I'll see if I can reproduce your workflow or result. Mark
<<inline: weird EM.JPG>>
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