Re: amber-developers: PIMD, NEB, LES - request for code inspection and tests

From: David A. Case <>
Date: Tue, 24 Jul 2007 08:34:43 -0700

On Tue, Jul 24, 2007, Wei Zhang wrote:
> Carlos Simmerling wrote:
> > yes, it is just that there is a huge amount of unnecessary communication
> > for NEB, not sure if that' true for PIMD also. for example, in NEB all
> > beads share coordinates with all other beads. I've changed my version so
> > that only neighbors communicate. I've also gotten rid of the extra
> > velocity communication and I think we can get rid of the extra force
> > communication with a little work.
> For primary PIMD, it could be true, you just need change the code to
> estimate the kenetic energy.
> For Normal Mode PIMD and CMD, it is not true, since both requires the
> coordinates and velocities to do the transformation.

Wei, Francesco:

For normal mode PIMD, do all beads need to know all coordinates and
velocities? Are we sure we are doing the minimum amount of communication

Received on Wed Jul 25 2007 - 06:07:35 PDT
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