Re: [AMBER] Queries about QM/MM

From: David A Case <>
Date: Wed, 18 Jun 2014 06:54:51 -0600

On Wed, Jun 18, 2014, Tanmoy Paul wrote:
> 1) How the program recognize the atoms which are supposed to take part in
> the reaction ( because there are lots of other atoms in the qm -zone) ?

Amber doesn't know that any reaction is "supposed" to take place. In the
setup you describe, that would have to take place spontaneously.

> 2) Is there any average time limit for any reaction to occur ( like in my
> case the proton transfer ) because it will give me some idea about how long
> I have to continue ?

This depends *very* strongly on the type of reaction you are studying. If you
can estimate the reaction barrier, you could use transition state theory to
get a rough estimate of the time scale.

> 3) Can I see the reaction happening in VMD ?


> 4) What is the time scale for a reaction to happen ( is it in atosec or
> femtosec time scale?) ?

See item 2) above. Proton transfer reactions are usually on the microsecond
or slower time scale, and you will essentially never see them happen
spontaneously in an MD simulation.

> 5) Can I do something more meaningful than just waiting for this reaction
> to happen ?

Yes. Things like umbrella sampling along the reaction coordinate are usually
required. I'd recommend finding a research paper that describes a reaction
similar to the one you are interested in, and seeing what sorts of approaches
were used. Amber's tutorial A10 walks you through one approach to a proton
transfer reaction.


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Received on Wed Jun 18 2014 - 06:00:05 PDT
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