[gmx-users] Lyzosyme with ligand tutorial

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 25 10:58:26 CEST 2011

On 25/10/2011 5:29 PM, James Starlight wrote:
> This was due to that in .gro file corresponded to the end of 
> productive MD I've found this 
> http://i1209.photobucket.com/albums/cc394/own11/mdL.png
> It's looks like the protein moved out from box so I've thought that 
> some error occured during stimulation

There's no outside to a periodic cell - you will find a matching cavity 
on the other side of the triclinic periodic cell, where some of the 
solute atoms actually are also....

GROMACS uses the triclinic representation internally for efficiency - a 
2D analogy is that a hexagon tiling a plane can be converted to a 
rhombus tiling the plane. It doesn't bother wasting your valuable 
computing cluster time converting back to the initial representation, 
which probably wasn't wanted. That is, mdrun makes no attempt to guess 
how you would like your output to appear.  See 
for ideas about how to make your output look as you would like.


>     I don't understand this statement.  You should also note that a
>     periodic box has no "outside."  Perhaps it would be useful to post
>     images online.  If you choose to do so, please follow bullet point
>     #4 here:
>     http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
>     -Justin
>     -- 
>     ========================================
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>     ========================================
>     -- 
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