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
methods).
Regards,
Brian
On Wed, Dec 11, 2013 at 8:54 AM, Fengxue Li <lifx916.126.com> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 11 2013 - 07:00:02 PST
