On Thu, Oct 15, 2015 at 10:02 AM, Khabiri, Morteza <khabiri.med.umich.edu>
wrote:
> Dear Jason
> If iwrap= 1, the coordinates written to the restart and trajectory files
> will be "wrapped" into a primary box. This means that for each molecule,
> its periodic image closest to the middle of the "primary box" (with x
> coordinates between 0 and a, y coordinates between 0 and b, and z
> coordinates between 0 and c) will be the one written to the output file.
>
The *center of mass* (or maybe center of geometry, I'm not sure) of each
molecule will be wrapped into a central unit cell. For a large protein,
this still means that a large portion (up to ~half) of the protein may be
sticking out of the unit cell.
So I repeat, why do you say your system is not getting wrapped? What does
it look like? An image is far better than a description here.
Also, use the "autoimage" command in cpptraj -- does it look a lot better?
Also, look at your unit cell dimensions and simulation density (should be
printed to the output file). It could be that your box is a lot bigger
than you thought it was and your simulation is evaporating or boiling...
Of course this is all speculation. I've never seen iwrap=1 *fail* to wrap
molecules, so my guesses right now are centered on what could make your
system *appear* unwrapped when it is really being wrapped.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 15 2015 - 07:30:05 PDT
