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

Berk Hess gmx3 at hotmail.com
Thu Apr 4 10:43:56 CEST 2002

>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
>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

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.


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