Isn't there some way to turn down the VdW via a distance cutoff or so?
(EnableCutOff and SetVdWCutoff) I've never used these but hopefully they
will prevent the pairwise generation of all of the VdW terms.
- Noel
On 15 May 2012 22:40, Tom Daff <td...@uottawa.ca> wrote:
> I work with molecular crystals and was very interested in the UFF
> implementation in OpenBabel. Unfortunately, it seems that periodic
> boundaries are not used for any of the atom typing, bond calculation or
> force field calculations. I noticed that periodic boundaries are one of the
> version 3 goals; is this something that is underway? Looking at the code
> this seems far from trivial to implement.
>
> As an alternative, I decided to just use the powerful atom and bond typing
> systems from my Python code to setup UFF calculations elsewhere, but have
> encountered another problem. I can extract the types and bonds using pybel
> after feeding the OBMol to a Setup() of OBForceField etc. however, in order
> to ensure that the atoms at the edge of the cell are typed correctly, I
> generate a 3x3x3 supercell with the idea to take the atoms from the centre.
> This generates about 8000 atoms in my test system and during the setup of
> the forcefield the memory shoots up and crashes the python process (usually
> without any explicit error). After some digging and using obenergy etc., I
> see that the atom typing works as they are printed and the vdW setup step
> is
> using all the memory and causing the crashing. As far as I can tell there
> is
> no way to decouple the individual parts of the setup using the python
> bindings: .SetTypes() only works if ._mol has been set, but _mol is only
> set
> through .Setup() from the bindings. I could probably hack together a c++
> tool or modify my compile to get the required result but would prefer a
> simple way to achieve this with the python bindings alone. Is there
> something I'm missing, or a better way to get the UFF atom types?
>
> Many thanks,
>
> Tom
>
>
>
>
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