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. 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) Thank you again for your help. Caleb Carlin
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