[gmx-users] see some line in vmd

[Morteza Khabiri]

Dear gmx user

I have a box which contain protein and solution. Before running I
minimized it very well and also system is running. After 2 ns when I saw
the trajectory in vmd I saw that ther is some lines like bondes in the
system. eg, between oxygen group of one water molecule in one part of box
with hydrogen atom of other water molecule in opposite part.

what do you think about this event?

thanks