On Tue, Oct 7, 2008 at 7:10 AM, David A. Case <case.biomaps.rutgers.edu> 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.
Gustavo.
Received on Wed Oct 08 2008 - 05:10:23 PDT
