From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Fri Apr 27 2018 - 17:51:39 CDT
I ran ~12ns NPT equilibration of a spherical protein in a water box with 5A
padding with NaCl and my simulation cell tilted during equilibration by
about 5-8 degrees by the end of this run. The size of the box did not
change and rmsd of the protein is about ~1.5A, the protein seems to be
stable, i.e. not falling apart. The center of mass of the protein is at the
origin and cell center is very close, within 0.5-1A on each axis. In the
end of this run one of the residues partially sticks out of the box, but
the structural integrity of that subunit is preserved.
What could be the reason for water box tilting? Can I still use this
equilibrated structure for further calculations (such as ABF)?
Thanks in advance,
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