[gmx-users] how to create a dummy atom in the oplsaa force field?

[leafyoung81-group at yahoo.com]

Yes. It was a bit complicated to define dummy atoms
when I did it.

Here is my advices.

1. Add user-defined atoms in the bottom of
ffoplsaanb.itp. E.g.
opls_O      O      0.0        -0.198148148 D    xxx  
xxx
opls_C      C      0.0         0.0         D    xxx  
xxx
opls_O and opls_C are defined name, variable according
to your preference. Just remember to set mass to 0.0
and atom type as D(for dummy)

2. In the topology, use your defined type where you
want to be.
[ atoms ] 
    1 opls_O     1       SPD     O1      0
...
   11 opls_C     1       SPD     O1      12

Don't put any bonded interaction to dummies. Dummy
atoms only have non-bonded interaction with others.

3. In [ dummiesX ] section, set the parameters for the
positioning of the dummies (refer to manual)

4. There are other things needs to taken care,
non-bonded interaction is the most important one (at
least, for me). Do you want that dummy atom to have
interaction with others, or with specific ones? This
will be set according to nrexcl in [ moleculetype ]
section and [ exclusions ] section in the topology.
Check this with the output of gmxdump and quick MD
tests. Until you have been sure everything is in
control, you may start the simulation.

Good luck!

Yang Ye

--- nanyu101 at sina.com wrote:

> Dear gmx-users,
> 
>    I am trying to find a right way to simulate my
> zinc enzyme. There are several methods found in the
> references and mailing lists, such as cationic dummy
>  atom approach. But how to create a dummy atom in
> the parameter files? The munaul is very compact, I
> can\\\'t understand it clearly. Thanks a lot.
> 
> all your bests,
> ______________________________________
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