Re: [AMBER-Developers] sqm/sander shared files

From: Scott Brozell <>
Date: Mon, 11 Oct 2010 21:10:04 -0400


On Mon, Oct 11, 2010 at 08:22:53PM -0400, case wrote:
> On Mon, Oct 11, 2010, Jason Swails wrote:
> >
> > I'd say it's probably fine to make sander's md.h/memory.h a (soft, hard?)
> > link to sqm's since Amber is dependent on tools.
> I don't think links are the way to go here. There already is an
> However, the better solution is to not have sqm referring to
> sander-specific files like memory.h or md.h at all. This is really a

You betcha.

> limitation of the current abstraction: after all, if we want to claim
> that sqm is general, and could be linke to other codes (like CHARMM or
> pmemd), it cannot depend on files that are really sander files. At some
> point, a brave soul needs to figure out which variables are actually
> needed by sqm, and get them into an appropriate module that would be
> stored in $AMBERHOME/AmberTools/src/sqm, but imported by the code in
> $AMBERHOME/src/sander.

>From my roof, I can see all the way to the pacific ocean, but what are
those islands ? I need a map, and that's what the brave soul needs.
So the brave soul should figure out how to get the compiler to
list unused variables. Ive done this, but need to find a cheat sheet
to make it easy to re-do it; contact me if you, brave soul, need help.


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Received on Mon Oct 11 2010 - 18:30:02 PDT
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