Dear gromacs users, Thanks for your previous guidance. I used Drug/Enzyme complex solvation tutorial to run my simulation in nitrogen box. It finally worked.
But I think that the *.gro coordination file of my solvent has problem beacuse when I run it, in my _b4ion.gro file the nitrogen molecules have overlapped and created connected triangles near the protein where they are more dense. Since nitrogen is gas, I can not make a dense box. If the nitrogen molecules in my gro file be more than 60, the protein structure breaks and energy minimization can't take place. If it be few I'll confront this error when I type mdrun_d -s a_pr.tpr -o a_pr.trr -c a_b4md.gro -g pr.log -e pr.edr &: 2 particles communicated to PME node 1 are more than a cell length of their charge group. (I've optimized the #solvent molecules and I guess 49 is the best.) If I define a larger box of 2.1 the error changes to: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated. Thus, I think that all the problem is the coordination file of nitrogen. I need a nitrogen box with its coordinations and pre-equilibrating it. Is it really my problem? Can someone explain how I can generate a pre-equilibrated coordination file similar to spc216.gro but with nitrogen? Thanks. Cheers, Sarah K. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
