Re: [AMBER] Amber QM/MM

From: Brian Radak <>
Date: Wed, 11 Dec 2013 09:55:31 -0500

The various QM/MM models in sander all have quite different efficiency and
scaling behavior. Broadly speaking the following is true in terms of
efficiency, especially for large atom counts (say > 40):

                                                  time per MD step/chemical
accuracy -->
sp NDDO (AM1, PM3, *etc.*) ~= SCC-DFTB < spd NDDO (AM1D, PM6, *etc.*) <<
external *ab initio*

The first 2 sets of methods can also, in general, be successfully scaled up
to a full compute node (8 processors maybe?) with near linear gains in
efficiency. However, due to the nature of the algorithm, the d-orbital
methods have *very* small gains (anecdotal tests of 2 and 4 processors got
about 10% and 20% gains). The external methods generally scale a bit better
(depending on the program), but the timing prefactors are about (this is a
*wild* guess) 1000 times larger.

The link atom methods are described in detail in the manual. You may also
want to look in the AmberTools manual for a description of SQM. The default
method is simple hydrogen capping, although a pseudoatom approach should be
possible using the "parameter_file" option (at least with the SQM internal


On Wed, Dec 11, 2013 at 8:54 AM, Fengxue Li <> wrote:

> Hi,all
> I want to use the AMBER software suite to carry out QM/MM simulations,My
> system include 150 atoms in QM part ,When I used Sander order,it spends too
> much time ,I want to how to improve the computational efficiency?at the
> same time ,I want to know how to add link atoms and the type of link atoms。
> Can anyone help me?
> Thank you advance!
> _______________________________________________
> AMBER mailing list

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 Brian Radak                                             :     BioMaPS
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Received on Wed Dec 11 2013 - 07:00:02 PST
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