[gmx-users] Protein coming out of the box

[Mark Abraham]

gtroiano at if.usp.br wrote:
>  Hi all
> 
>  I'm simulating a helical protein in a water box, neutralized with Na and Cl to
> a 0.2M comcentration. I had to pick the smallest box I could (in editconf,
> rectangular, with -d 0.1, and -princ to align the box with the helix). But in
> the MD trajectory I see the protein coming out of the box, most of the time. I
> know that it uses PBC, and I'm seeing just 1 image, but does it mean that
> there's something wrong with the MD?

http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

Mark