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I used Amber's solvatebox function with a small polypeptide and tip3p water with a distance of 15 angstroms between the molecule and the edge of the box.

After I ran dynamics, I tried to view the output by removing water from view in Jmol, but I had a really hard time rotating the polypeptide. When I viewed it with water, I found that the difficulty in rotating was because the radius of rotation (are those the right words?) was extremely large because some waters floated off in the distance.

enter image description here

I want to remove these stray waters. How would I go about doing that? Would I just crack open the output and remove those waters by deleting lines that contain information for those particular waters?

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  • $\begingroup$ That looks pretty peculiar. I've had similar things happen when trying to visualize a large system using jmol, and it usually is a problem with going from the MD to jmol and not actually a problem with the simulation itself. It usually has something to do with periodic boundary conditions... I would maybe try using solvateShell instead of solvateBox which creates a shell around the peptide of some specified thickness which will probably avoid problems with the boundaries that solvateBox might create. $\endgroup$ – jheindel Nov 21 '16 at 1:29
  • $\begingroup$ If you use solvateShell, you can use a harmonic restraining potential to keep your solvent from flying off, but if I remember correctly the simulation is no longer periodic. $\endgroup$ – pentavalentcarbon Nov 21 '16 at 13:33
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This has nothing to do with box walls (there are no walls!) or restraining the waters. You do not want to do that!

Do not confuse periodic boundary conditions with wrapping to the central cell. Look at the amber tutorials, it is all explained there.

You either need to set iwrap=1 in your amber minor put your trajectory trough cpptraj and use autoimage.

Again, all in the tutorial and manuals.

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    $\begingroup$ Sounds like you know what you're talking about here. Can you expand on how one would use the iwrap, cpptraj, and autoimage keywords, perhaps by mocking up an input file containing them? See here for a tutorial on Markdown formatting to aid comprehensibility. Welcome to Chem.SE -- thanks for posting! $\endgroup$ – hBy2Py Nov 21 '16 at 18:52
  • $\begingroup$ Could you tell me a bit more about what iwrap and autoimage do? $\endgroup$ – Melanie♦ Nov 25 '16 at 17:34

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