Re: [AMBER-Developers] sqm and AmberTools 1.5

From: David A Case <>
Date: Thu, 10 Mar 2011 14:32:54 -0500

On Thu, Mar 10, 2011, Jason Swails wrote:

> Not upgrading sqm will
> certainly fix QM/MM in sander, but then the sqm documentation and such will
> have to be rolled back to an earlier date...

A key question here is: how much has really been updated in the stand-alone
sqm since last April? Is the problem that Jason identifies (documentation
changes) a serious one? Is there a reason to want to get version 1.5 of
the stand-alone code out there in a more timely fashion (i.e. before the next
release of sander)?

My feeling from the meetings (and from monitoring code going into git) is that
almost all recent development has been on the QM/MM side (e.g. getting various
ab-initio codes hooked in, either directly or through PUPIL, having adaptive
QM/MM boundaries, etc.) But if I am missing things, then Jason's suggestion
(below) is probably the way to go. So, the sqm people need to chime in here.

> To avoid having to sit on sqm 1.5 for another year until Amber12 is
> released, we can ... package sqm1.4 into a
> different directory that won't cause confusion (for example sander11_qm, or
> something of the like). The only thing that would need to change is where
> sander's Makefile has to go to build libsqm. This is a very fast, easy
> change to the script to get this to work.


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Received on Thu Mar 10 2011 - 12:00:04 PST
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