protein interact with its image

From: Shunzhou Wan (
Date: Tue Apr 19 2005 - 10:23:58 CDT


I am running a NPT simulation with PBC. The protein rotates during a
long simulation (25ns). The longest axis of protein deviates from the
longest axis of the box. The other two dimensions are not long enough
when the longest axis of protein is in these direction (protein is too
close to its image in one dimension). It is very computational expensive
to use a cubic box.

Would there be a way of suppressing the rotation of protein, or resizing
the waterbox? Any help/suggestions would be appreciated. Thanks!



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