[gmx-users] coordination file

sarah k dailycolors at gmail.com
Mon Apr 18 19:58:23 CEST 2011

Dear gromacs users,

Thanks for your previous guidance. I used Drug/Enzyme complex
solvation tutorial to run my simulation in nitrogen box. It finally

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.

Sarah K.

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