[gmx-users] Oh topology .. go away ...

[Berk Hess]

>As I have my Fe bonded to the oxygens, they are now in a 1-3
>position with respect to each other and thus have no LJ
>interaction ! The result is a perfectly planar coordination
>environment of the Fe, which is wrong for this particular
>molecule.
>So how can I INCLUDE LJ and electrostatic terms for these
>"1-3 bonded" oxygens only  ?

There are two ways of doing this:

1) Add the 1-3 interactions in the [ pairs ] section in the topology.
   You have to make sure that the pair LJ parameters are set
   correctly. You can also add the parameters to the pairs in the
   topology.

2) Use a harmonic potential (bonds type 6) instead of a normal bond
   for the bonds with the iron. For this bond type grompp does not
   generate exclusions. Any 1-4 exclusions that you do want can be
   added in the [ exclusions ] section.

Berk.



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