Caleb Carlin wrote:
First, thank you to everyone that responded. The suggestions for
viewing the output of grompp worked.
Grompp was changing the configuration file because of the order of the
molecules in the .top file. The initial .gro file listed the silicon
first and the water second, while the .top listed them the other way
around. Reversing these in the [molecules] section resolved the issue.
The ordering in the itp file may have affected this as well.
Atom ordering within molecules needs to correspond between structure
file and topology file, and order of molecules in the [ molecules ]
section also needs to correspond. I've just looked in Chapter 5 of the
manual and can't find anywhere that specifies this, and it should be
there. Any ideas, people?
The symptoms were a reordering of atoms in the .gro file and the
following error in the grompp output:
Warning: atom names in topol.top and Config.GRO don't
match (O - SI)
Ah, some useful information. Telling the people you're asking for help
about the warning messages you were getting would have been a way to get
your problem solved more quickly using less of their time.
Mark
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