Re: [AMBER] is iwrap=1 a key parameter?

From: Ben Roberts <>
Date: Mon, 29 Mar 2010 09:40:06 -0400

Hi Jianing,

In my response to you, I'm going to assume you're familiar with the role of periodic boundary conditions, which your simulation is making use of.

As you say, iwrap=1 doesn't change the energy and forces. Its sole function is to wrap atoms into the primary unit cell. Thus, if you were to compare the energies of your two simulations, you would find that they are very similar. (Bear in mind, however, that because simulations are chaotic, very small differences in initial conditions - like a different random number sequence - can cause two otherwise identical simulations to rapidly become somewhat different.)

The error you describe is likely because, if atoms are not wrapped, they may move very far from their original positions. All atoms start off near [0, 0, 0]. It seems there is some kind of limit as to how large the x-, y- and z-coordinates of the atoms may be. By using iwrap=1, you will force the atoms back towards zero now and again (really, replacing atoms that have wandered out of the box with their periodic images that have moved into it from the other side), and your "coordinates too large" problem shouldn't occur.

I hope that helps.

Best regards,

Ben Roberts

On 29/3/2010, at 8:49 a.m., Nancy wrote:

> hi,
> I am confused about the role of iwrap=1 played in MD simulation.
> Recently, I've performed two kilnds of MD simultion on villin headpiece with explicite water TIP3P using AMBER FF03 force field.
> One was without iwrap=1 and the system stopped at 4ns with error info: coordinates of the atoms are too large,
> so MD exited.
> For the other, with iwrap=1, the system now is at 8ns ,and the simulation structure is still similar to the XRD structure of villin headpiece.
> Both the two MD share the same input files except the key word "iwrap"
> I searched iwrap in the AMBER 10 user guide, it seemed iwrap=1 did't change the engery and forces during MD , so it could not be so important in MD, but what I obtained was opposite.
> Can someone help me out of this trouble?
> Thanks in advance for your reply.
> sincerely
> Jianing Song

Dr. Benjamin P. Roberts
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Received on Mon Mar 29 2010 - 07:00:03 PDT
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