AMBER Archive (2008)

Subject: AMBER: Protein rotating out of box

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Thu Mar 27 2008 - 16:34:48 CDT

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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