I'd like to add something in addition to Jason's comments.
Even the repeated center/image commands Jason suggested sometimes fail to
place your solute molecules next to each other.
If the solute molecule is intact in your first frame (of the trajectory),
you can try
unwrap :1-100
center :1-100 mass origin
image origin center familiar
Here, :1-100 is your solute mask. As far as your trajectories are
continuous, this will not fail.
On Thu, May 5, 2011 at 5:10 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, May 5, 2011 at 9:03 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>
> > Hi all,
> > I'm running simulations of small proteins in mixed solvent. The very
> > common problem I'm seeing is the protein being out of the solvent box
> > after the post-simulation image operation. Since I'm looking for protein
> > surface solvation patterns, this makes life somewhat difficult.
> >
>
> Centering and imaging *can* be a tricky business in some cases. Here is a
> (as I've seen so far) sure way to image "properly". sander/pmemd do
> pressure scaling/wrapping on a per-molecule basis, which means that only
> whole molecules get imaged. Molecules are assigned by leap as any entity
> in
> which all atoms in that molecule are covalently bonded to at least one
> other
> atom in the molecule, and NOT covalently bonded to any atom that is in a
> different molecule. Keeping this in mind, simply center each solute
> "molecule" and image everything around it sequentially.
>
> That is -- suppose we have 4 solute molecules surrounded by solvent, each
> molecule is 25 residues large. The center/image ptraj script will look
> like
> this (using familiar for truncated octahedrons and omitting it for
> rectangular cells):
>
> center :1-25 mass origin
> image origin mass (familiar)
> center :1-50 mass origin
> image origin mass (familiar)
> center :1-75 mass origin
> image origin mass (familiar)
> center :1-100 mass origin
> image origin mass (familiar)
>
> Note that the :1- is intentional in each case. The first one will center
> the first solvent molecule and image everything around it. What this
> assumes is that it images the second molecule (residues 26-50)
> appropriately
> next to the first molecule if it had been wrapped during the course of the
> simulation (or leaves it alone if it didn't change boxes). Now that the
> first 2 molecules are in the same box, we center the first 2 molecules and
> image everything around them, then use the same reasoning for the remaining
> molecules we want at the center of the box.
>
> Note that in most cases only the first 2 center and image commands will
> give
> you the desired behavior, but better safe than sorry :).
>
> Is there a way to stack several of these unit cells to get a complete
> > solvation picture for the protein?
>
>
> Yes. In VMD, open up the Graphical Representations tk window, then click
> on
> the "periodic" tab. The rest should be self-explanatory.
>
>
> > Alternatively, is there a way to keep
> > the protein within the bounds of the box.
> >
>
> Yes, 2 ways, but there are problems with both. Run with iwrap=0. Then,
> imaging is as easy as
>
> center :1-100 mass origin
> image origin mass familiar
>
> I can provide a more detailed explanation of why this is the case if it's
> not that clear (but I'm lazy now :)). However, iwrap=0 has problems (at
> least as long as we have ASCII formatted restarts) for long simulations.
> The other way is hacking the prmtop file. If you figure out how to combine
> all solute molecules into a single molecule definition (see the sections
> ATOMS_PER_MOLECULE and SOLVENT_POINTERS and their descriptions on
> http://ambermd.org/formats.html for details), then pmemd and sander will
> *never* image them separately. However -- if you do this wrong, you will
> pay for it (with segfaults and other difficult-to-trace errors -- I just
> recently spent ~1 hr determining that a segfault thrown by pmemd was caused
> because the ATOMS_PER_MOLECULE section of the sample prmtop was wrong,
> though I was not the one to modify it).
>
> And this concludes more than you probably ever wanted to know about
> imaging,
> wrapping, and molecules in the amber topology.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
InSuk Joung
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Received on Sat May 07 2011 - 21:30:02 PDT
