Re: amber-developers: problems with iwrap2, molecule.f, etc in amber11?

From: Gustavo Seabra <>
Date: Tue, 7 Oct 2008 09:24:23 -0400

On Tue, Oct 7, 2008 at 7:10 AM, David A. Case <> wrote:
> (Mainly for Gustavo, but also everyone:)
> There appears to be serious problems with the recent iwrap2() stuff in
> amber11: in sander.f, the allocate_molecule() routine only seems to be called
> by master nodes (which seems wrong), and is deallocated by all nodes. The
> code then tries to broadcast the atom_to_resid_map to nodes where this space
> has never been allocated.

I'm looking into it right now, sorry!

> Also, do we really need an iwrap2() funtion and all the complexity it entails?
> I would prefer to remove all wrapping from sander (if possible), not to make
> it yet more complex. I know it's a losing battle to keep sander as simple as
> we can, but it's still should be a design criterion.

we are actually working on a different problem: being able to have a
variable QM zone, where a constant number of the closest solvent
molecules will always be treated as QM, and the 'iwrap2' functionality
was actually developed for that. Since it was already there, I thought
I might just as well make it available to everyone, instead of just
keeping it in one code. I also noticed that other routines (hybrid
remd comes to mind) also use similar code, so I considered that having
this functionality around just may come in handy for others later. (Of
course that's assuming it works...)

I'll fix it now.

Received on Wed Oct 08 2008 - 05:10:23 PDT
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