AMBER Archive (2007)

Subject: AMBER: Extra Points... How to Deal with Them

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Tue Apr 03 2007 - 01:39:23 CDT

Realizing I've been scooped like a quart of ice-cream by that very fine
researcher Bertrand Guillot (well, I'm sure there's room for both of us
like there was room for SPC and TIP3P), I want to add some originality to
this water model I was working on.

I think there's a real possibility of improving something like TIP5P with
diffuse charges, and I don't see too many obstacles to getting my code to
run TIP5P, so long as I can get the extra points figured out right.

My understanding of extra points implementation is that the ONLY thing I'd
have to do is to transfer the forces on the massless extra points to
equivalent forces on the massive atoms of the parent molecule in
preparation for SETTLE or SHAKE. The computation of the non-bonded virial
is unchanged--I simply fold in the contribution from

f_ij \dot r_ij$

where f_ij is the force, r_ij is the distance between atoms i and j, and
one or both of atoms i and j could be massless extra points. The SHAKE /
SETTLE protocol for the massive atoms is similarly unchanged once the
forces on the extra points have been turned into equivalent forces acting
on the massive atoms. And, all I need to do is then re-compute the
positions of the extra points based on some geometric rules about where
they go with respect to massive atoms, right before I compute non-bonded
forces to make sure they're in the right spots.

Is that true?

Thanks!

Dave
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