AMBER Archive (2007)

Subject: AMBER: Extra points... virial computation

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Sun Apr 08 2007 - 01:48:11 CDT

If anyone on the listserv has worked with the AMBER extra points
implementation, could you please privately email me?

Those who have been on this listserv for awhile will recall my troubles
with virial computations in the past.

Well, in the past, I've gotten through them with some help from listserv
contributors, some elbow grease, and some help from collaborators.

Now, I'm trying to implement a virial computation using "extra points" as
seen in TIP5P. My thought is that I should be able to simply place the
lone pairs in the proper positions, i.e. after using SETTLE to work out
the constraints of the TIP5P water and just before a non-bonded force
computation, then compute forces as normal and tally the non-bonded virial
contributions as I do so, then transmute the forces on each water molecule
due to the extra points so that they act on the massive atoms only, with
no virial contributions from the transmutation of forces. The constraints
and constraint virial are computed as normal, once the transmuted forces
are calculated, of course.

But, I'm getting the familiar problem where my system blows up
again--clearly, my virial computation is wrong somewhere. Things are fine
if I do TIP3P water with constraints, so the constraint virial is not the
problem per se, nor is the non-bonded virial if I don't have these extra
points flying around.

Thanks!

Dave
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