[gmx-users] dmso+water

[Dinesh Pinisetty]

Hello everybody,
         I did an MD simulation with water and dmso for 4 ns.
    I created a dppc bilayer with water on either side.I pickes up the
molecules from the upper side of bilayer(i.e. I had water z-direction
vectors high).Then I added dmso molecules in a seperate box and then
translated it nearer to the water and started the simulation with gap
between them.
    But the interesting thing I observed was that for 1-2 lakh steps out of
20 lakh steps it looked as if it was circle in front view when I rotated it
around it looked as a cylinder but afetr few more steps it automatically
changed to a rectangle from front view then again it changed to rectangle
from side view.but I desired the box to be less in z direction which is not
so after simulation.How is it possible to see that z vector is less when
compared to that of x & y directions.
  By the way why did it happen in that manner.
Any suggestion would be greatly appreciated..............
Thanking you,
Dinesh............