[gmx-users] puzzling about ffnonbonded.itp

[Mark Abraham]

On 3/09/2012 6:02 PM, Wu Chaofu wrote:
> Dear gmxers,
> While I try to make one customed force field by studying some existing
> force fields, I find that bond_type and at.num defining [atomtypes ]
> in the ffnonbonded.itp are included in some force fields (i.e.
> oplsaa), but not in other force fields (i.e gmx). I wonder how gmx
> identifies the difference and choose the correct parameters from them.
> Could you please expain this in details? Thank you very much for any

Not sure which part of these issues you're concerned about. Different 
force fields work differently. Few of these fields are actually relevant 
(e.g. charge never is, in practice), some get over-ridden some times. 
grompp has a bunch of magic scanf() format strings that work out what is 
in each field and dispatches the information to the data structure 
correctly. In practice, you should probably pick an existing force field 
as a model and follow its format.

Mark