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between the particles and the solute), but that may well be outdated as it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 - 02:00:02 PDT
