Hi Fengxue,
Note the internal diagonalizer in sander is only really efficient for up
to 60 QM atoms or so. For larger systems I suggest compiling using MKL -
You'll need to obtain and install MKL and then set the MKL_HOME
environment variable to point to it's location. Then recompile. Once that
is done set diag_routine=0 in the qmmm namelist and this will
automatically benchmark all the diagonalization options and choose the
most efficient one.
Good luck,
Ross
On 12/11/13 6:57 AM, "Gustavo Seabra" <gustavo.seabra.gmail.com> wrote:
>Hi Fengxue Li,
>
>What do you mean by "spends too much time"? QM calculations will normally
>take a lot longer than regular MM calculations, so the QM/MM calculation
>is
>expected to take longer than regular MM.
>
>Also, if you are using sander for the QM part, it probably means you are
>already using a semi-empirical QM method - the fastest QM you can do.
>
>My only suggestions by now would be:
>
>1. Check to see if you are having convergence problems. This could make
>the
>calculations even longer than usual for QM, and the results could be
>meaningless. (Sander will print warnings if this is the case.)
>
>2. If the time is still above what you can manage, would you consider
>reducing the QM zone?
>
>
>Gustavo Seabra <http://goo.gl/7Cphf>
>Professor Adjunto, Departamento de Química Fundamental
>Coordenador, CENAPAD-PE
>Universidade Federal de Pernambuco
>Fone: +55-81-2126-7450
>
>
>On Wed, Dec 11, 2013 at 10:54 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
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 12 2013 - 08:00:02 PST
