> On Feb 8, 2015, at 11:02 PM, Robert Molt <rwmolt07.gmail.com> wrote:
>
> Sirs and Madames:
>
> I am inexperienced in MD calculations and most certainly am making an
> elementary mistake. I was attempting to do a pedagogical calculation for
> my own welfare and encountered problems. I attempted to simulate a
> methanol molecule in a box of water; the water box blows up (V-->
> infinity). Here are the details of the protocol I followed:
Your mistake is a common one. You assume that the only particles present in your simulation are the ones for which you have coordinates and can see when you load it into VMD.
If you use periodic boundary conditions, this is simply not the case. Bear in mind that every particle has an infinite number of periodic ‘images’ tessellated through space. So while some of the water seems to be ‘evaporating’ away from the methanol (as you would *expect* it to do in a microscopic droplet), a periodic image of the water that is leaving in one direction is actually approaching from the opposite (i.e., as one image leaves one unit cell, one of its periodic images enters from the other side).
Long story short, what you’re seeing is an imaging, or visualization, artifact. Trajectory files only ever store one image of each particle, and it just so happens that (unless you set iwrap=1 in the input file), the images that it tracks move to different unit cells.
Try loading your trajectory into cpptraj and using the command “autoimage”, which will image all water molecules back into a “central” unit cell surrounding the solute (in this case, a methanol molecule).
In many cases, you can actually use cpptraj to do some direct analyses without imaging, since those analyses respect periodic boundary conditions and will use the minimum image convention (like, for instance, the radial distribution function).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 08 2015 - 20:30:03 PST
