[gmx-users] regarding .gro file

[Mark Abraham]

> Hi,
>
> Actually I started a simulation with bilayer. After energy
> minimization I could see in ngmx the bilayer was at the middle of a
> box and two layers of water are on both sides of it  and that was my
> initial structure. After simulation of 1.5 ps the bilayer has moved to
> one side of the box, with a thin layer of water in one side and
> maximum number of water on another side of bilayer.  I want to
> understand whether the whole bilayer is diffusing to one side of the
> box or it is due to imaging problem. So I wanted to know the technical
> way of writing .gro file by gromcas.

The system's periodic, so there are an infinite number of equivalent
representations. There is no "side" to the box. You can use trjconv to
generate an acceptable look. See
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

Mark