[gmx-users] protein wandering away

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Mar 23 23:16:51 CET 2005

>I just simulated a 5ns MD by GROMACS FF for a small system containing 160
>amino acid residues in a water box. The thing confused me was that the
>protein started to close one edge of the water box around 2ns and part of it
>movedout of the box later. At the end of the 5ns calculation, most of
>protein was out of the box, while water molecules were still in the box.

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.

Just used trjconv to center the protein back in the simulation box if you 
want to.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9574
When the only tool you own is a hammer, every problem begins to resemble a nail.
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