Re: [AMBER] Queries about QM/MM

From: Jason Swails <>
Date: Wed, 18 Jun 2014 08:41:31 -0400

On Wed, 2014-06-18 at 12:06 +0530, Tanmoy Paul wrote:
> Dear amber users,
> Sorry to disturb you again. I need some
> clarifications about qm/mm. All my jobs are running quite well . There is
> no problem with that . But the point is while running these simulations in
> amber I just have to specify the QM -zone and that's it . I don't have any
> control over my simulation as I am relying on some parameters for each
> atoms downloaded from the DFTB -website and hopping that everything will go
> fine .
> I have run the simulations for quite a long time but it seems nothing is
> happening . Now my questions are........
> 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) ?

It doesn't. Simulations are dumb -- you tell it the potential energy
function to use (QM, MM, QM/MM, etc.), and it will run the simulation.

If the potential energy function dictates that a reaction should happen,
that reaction happens. If it doesn't, no reaction happens.

> 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 on the (free) energy barrier of the process you are trying
to model. Basically, you won't know how long it will take until you see
how long it takes or how high the energy barrier is. Some reactions
happen incredibly rapidly, some happen over eons (think diamond
reverting to graphite).

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

Watch the trajectory that is generated by sander. You will need to play
with the visual representations of the quantum region to see bonds
breaking and forming (look at "dynamic bonds", for instance, which draws
bonds based on a simple distance criteria).

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

See my answer to #2.

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

People typically do biased sampling, like steered MD or umbrella
sampling, to drive the reaction to occur. You can remove the bias
post-hoc to recover the original free energy surface without the bias.

There are different families of enhanced sampling techniques. There are
those that construct a so-called PMF (potential of mean force) which is
basically a projection of the free energy function in a reduced
dimensional space (e.g., a reaction coordinate). Examples are steered
MD and umbrella sampling.

Other enhanced sampling methods, like accelerated MD, do not require a
reaction coordinate to accelerate sampling. The method you should use
depends on what you already know about your system and what you wish to


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 18 2014 - 06:00:03 PDT
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