Jason, thank you for the detailed reply.
I'll experiment with the options you suggested - hopefully will get it
to work.
Cheers
Sasha
Jason Swails 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
>
>
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Received on Thu May 05 2011 - 15:00:09 PDT
