Re: [AMBER] regarding sqm

From: Jason Swails <>
Date: Thu, 22 Apr 2010 08:15:26 -0400


On Thu, Apr 22, 2010 at 2:51 AM, Asfa Ali <> wrote:

> Hi,
> I wanted to ask why has mopac been replaced by sqm in AmberTools 1.3 ? Is
> sqm better than mopac, if so, how? Moreover sqm calculation takes a much

It's not that sqm is better than mopac, per se, but sqm is better for amber
than mopac I would argue. It was written by amber developers and provides a
unified QM engine for the whole package (i.e. the same QM engine used for
sander's QM/MM is used for all other amber-related QM calculations) which
avoids duplication of code and makes the quantum calculations more
consistent. It also prevents us from having to change programs that used
mopac every time mopac output format changed (by making Amber less dependent
on external programs).

longer time to finish that required by mopac fot the same ligand.

I believe this is due to a stricter default convergence criteria for sqm
than that found in mopac. This causes sqm to require more SCF iterations
(which, in turn, increases the computational cost), but also increases the
reproducibility of numbers across different platforms. You can probably
reduce this value to the one used by mopac and recover comparable timings.
If I'm wrong, someone please correct me, I'm not an sqm-guru.

All the best,
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Apr 22 2010 - 05:30:02 PDT
Custom Search