AMBER Archive (2006)

Subject: Re: AMBER: simulate a self-assemble process in vacuum

From: Gustavo Seabra (
Date: Thu Jul 13 2006 - 08:22:15 CDT

Hi Eric,

In princliple, I don't see anything wrong with that. However, in
practice, things are a bit different...

For one, what is the timescale of this process? Most "long" MD
simulations go up to the nanoseconds timescale (someone please correct
me if I'm wrong). If the self-assembly process happens in the
miliseconds timescale, your calculation may take forever (and a bit
more!) to see eomething happening.

Second, does that self-assembly process involve bonde
breaking/forming? If so, you will need some sort of QM/MM calculation.
Amber 9 can do that, but now the timescale you can reach with the
calculation is even shorter. (Or you'll need "more forevers" to see
anything happening :-) )

But there is still hope... You may be able to get around this by using
some steered molecular dynamics, where you give the atoms a little
push in the right direction, and that can get around the timescale
problem. However, now you have to be careful because you'll be
introducing a bias in your system, and you may end up making happen
things that wouldn't happen otherwise, so a closer understanding of
what you're trying to simulate becomes even more important.

Another possibility is by using replica exchage MD, which will help
your system overcome barriers. Amber can do that as well. But in this
case, depending on your system's size, you may need a large number of
processors and maybe even some special techniques.

In summary, simulating what you want is not impossible, just involves
a bit more work than just "putting-all-in-one-pot-and-wait".

I hope that helps. (Also, I hope someone here will correct me if I
said something wrong.)

Best wishes,


On 7/12/06, Eric Hu <> wrote:
> Hi, I am trying to simulate a self-assemble process of an organic
> molecule. My logic is to prepare a series of molecules that have
> random orientations in high concentration in a limited space. I wonder
> if AMBER can help achieve this goal. The reason I ask is that in my
> mind this is a very similar way as creating periodic boundary
> conditions for your own solvent which some people might already
> encounter. Thanks!
> Eric
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