On Tue, Oct 11, 2011 at 4:42 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Hi all,
>
> For a future project, I am thinking of using hypothetical particles (with a
> VdW radius and partial charge) that interact with a solute, but NOT (or
> perhaps very little) with each other. The particles would have their own
> atom types.
> I don't think this would be possible without changing the code (i.e. by
> hacking the prmtop or so), but please chime in if this is not the case.
>
The exclusion list will only allow you to omit non-bonded interactions
between those atoms. If this is what you want to do, then editing the
exclusion list should suffice. However, this requires an understanding of
the topology file and knowledge of how to modify it properly (and how the
exclusion list is constructed specifically in this case).
I've actually written a topology file editing program specifically designed
to make hacking the topology file easier that has the ability to modify the
exclusion list in the way you describe. I'm hoping this will be released
with the next version of AmberTools some time early next year.
>
> [snip]
>
> To start, I probably won't try using PME as this may make things more
> complicated. I also don't care too much about affecting performance at this
> stage.
> As I am pretty much a novice when it comes to the AMBER code, it would be
> great if someone could point me to where I could think of making changes.
> Also, any ideas about different ways of doing this will be highly
> appreciated.
>
True... If you wanted to use PME, then the exclusion list approach wouldn't
work. The exclusion list only applies to the primary cell (or the
direct-space part), which means that your long-range electrostatics will
include unwanted contributions from your mystery-particles from different
periodic boxes.
If you want to get this behavior across periodic boxes, you'd have to modify
the sander source code itself to get the desired behavior.
HTH,
Jason
>
> BTW, I did find an old thread in the archive that has some relevance
> (although not quite the same, as I do want full non-bonded interactions
> between the particles and the solute), but that may well be outdated as it
> is from 2004:
> http://archive.ambermd.org/200404/0263.html
>
> Many thanks,
> Marc
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 11 2011 - 18:30:02 PDT
