Re: [AMBER] Amber QM/MM

From: Gustavo Seabra <>
Date: Wed, 11 Dec 2013 12:57:02 -0200

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 <>
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 <> 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!
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Received on Wed Dec 11 2013 - 07:30:02 PST
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