[gmx-users] regarding .gro file

[Ananya Debnath]

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.

Thanks,
Ananya.



> Message: 4
> Date: Sat, 24 Nov 2007 01:15:02 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] regarding .gro file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4746E066.6020801 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

> > Ananya Debnath wrote:
> > Hi,
> >
> > Can anyone tell me whether gromacs writes coordinate in  .gro file
> > with periodic boundary condition?

> The coordinates are the coordinates. Whether you choose to interpret
> them modulo some box is up to you and the software. Is this really the
> question you meant to ask?

> Mark