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<blockquote type=cite class=cite cite>I just simulated a 5ns MD by
GROMACS FF for a small system containing 160<br>
amino acid residues in a water box. The thing confused me was that
the<br>
protein started to close one edge of the water box around 2ns and part of
it<br>
movedout of the box later. At the end of the 5ns calculation, most
of<br>
protein was out of the box, while water molecules were still in the
box.</blockquote><br>
That is just the PBC acting. The water molecules are so small that,
pretty much as soon as they wander out of the box visually, they then
reappear on the opposite side. However, with something as large as
a protein, as it moves out the side of the box, to visually keep it
within the rest of the water, you would have to break the molecule.
And that isn't done, so it seems that the protein is sticking out into a
"vacuum". But if you check the opposite side of the box,
there will be a hole in the water where the protein molecule is
inserted. Using VMD you can easily turn on the boxes in each
periodic direction, so that you can easily see that happening.<br><br>
Just used trjconv to center the protein back in the simulation box if you
want to.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Lecturer<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9574<br>
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