AMBER Archive (2008)

Subject: RE: AMBER: Protein rotating out of box

From: Steve Spronk (
Date: Tue Apr 01 2008 - 09:55:20 CDT

Hi Lars,

I know that using an octahedral box would waste waters, but this is
definitely the preferable method. It's better to have slower simulations
with an octahedral box than fast simulations that give you junk, like a
protein interacting with its own image.

The only other method that I can think of is using a rectangular box as
before, but you could place very weak restraints on a couple of atoms that
lie along the long axis (preferably on opposite sides of the protein). That
way the protein couldn't rotate except around the long axis. However, this
is nonphysical and may introduce other problems--you'll have to investigate.
I've never heard of this before, but perhaps you could get away with it.

People do simulations with long straight structures like DNA or fibrous
proteins. You could see if there are any tricks mentioned in those papers.


-----Original Message-----
From: [] On Behalf Of
Lars Skjærven
Sent: Thursday, March 27, 2008 5:35 PM
Subject: AMBER: Protein rotating out of box

Dear all,

I am simulating a very nice little protein in a rectangular box with
different dimensions. Unluckily for me, the solute rotates within its
box during the simulation such that the longest dimension of the
solute no longer coincides with the longest dimension of the box.
Thus, it now spans the whole box, and interacting with its image. Some
atoms are actually out of the box on both ends. I use default values
of NSCM. I would avoid using a octahedral box since there will be a
lot of wasted waters.

Any tips on how to tackle the rotation will be greatly appreciated.
Have a pleasant day :-)

Best regards,
Lars Skjærven
Department of Biomedicine
Universitetet i Bergen
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