[gmx-users] a few detailed questions about the topology file format

[Eric Smoll]

Hello Gromacs users,


As far as I understand, values listed in the top file override any
information pulled from share/gromacs/top. However, ff an atom type (e.g.,
"opls_100") serves as a references to information contained in the
share/gromacs/top directory, is it necessary to include a value for the
charge in a itp/top file? It seems that the corresponding entry in
ffnonbonded should supply this information. Going further, what is the
minimal amount of information necessary in the atoms directive?

The gromacs manual includes an example topology for urea. The bonds
directive only lists pairs of atom indices. When the function type is not
listed, does it default to "1"?

Best,
Eric