PS
I just thought of another way of doing this, which wouldn't require changing
the code:
I could introduce "bonds" (with zero force constants) between all the
hypothetical particles, so they would be in the exclusion list.
If there are a lot of particles, however, this would lead to a whole load of
bonds (i.e. between all possible particle-particle pairs), and this may
affect performance quite drastically...
So it would probably still be better to modify the exclusion list by
changing the code.
--Marc
On 11 October 2011 09:42, 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.
>
> Probably the cleanest way to change the code is to modify the non-bond
> exclusion list (or perhaps introduce an inclusion list).
> I guess this is quite similar to what happens in QM/MM, where all the MM
> VdW and electrostatic interactions between the QM atoms are turned off. (So
> perhaps an alternative would be to introduce an MM force field as a "QM
> method" and put the particles in the qmmask, but I think this may be quite
> tricky to change in the code...)
>
> 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.
>
> 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 between the particles and the solute), but that may well be outdated as it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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Received on Tue Oct 11 2011 - 02:00:03 PDT
