[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

Chih-Ying Lin chihying2008 at gmail.com
Mon Jan 4 21:07:40 CET 2010

Thanks a lot, Tsjerk ! My simulation is running.
I never knew that a discrepancy between the the .top file and .gro,  grompp
uses the topology information in stead of
the coordinate file information.

What does issue a set of warnings by grompp ?
How do you know the discrepancy between the the .top file and .gro will make
simulation wrong?

Thank you

> Tsjerk gave me suggestion to check the .tpr file created by the command
> grompp.
I also suggested to try and find out why the water molecules got garbled.
Between adding solvent and energy minimization, you also added
chloride to counter the net positive charge. I assume you used genion
for that, which is the most sensible way to do so. Genion typically
adds the ions at the end of the topology. I further assume that you
manually updated the topology by adding a line 'CL-   26' under [
system ]. But if you inserted that line _before_ the line specifying
the number of solvent molecules, whereas in your .gro the chloride
ions were at the end of it, then you had a discrepancy between the
two. In such cases, grompp uses the topology information in stead of
the coordinate file information, but does issue a set of warnings. If
my assumptions are correct, then if you had sent the grompp output at
first instance, we would have been immediately able to pinpoint your
error. Besides, if you had looked at the output from grompp yourself,
you would (should) have noticed that something was wrong there.

Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
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