[gmx-users] Errant hydrogen bonds in the Lysozyme tutorial -- Please advise

[Mark Abraham]

Hi,

That's normal. Please see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Fri, 20 Oct 2017 06:07 Deron Johnson <deronj at comcast.net> wrote:

> I am new to gromacs. I followed the steps of the lysozyme tutorial
> (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> )
> All the analysis checked out, so I believe I followed the steps correctly.
>
> I then tried to visualize the results in VMD (by first loading npt.gro and
> then loading
> md_0_1.xtc) I got a strange result: the hydrogen atoms for several water
> molecules near
> the boundaries appear on the OTHER side of the box, and there are bonds
> between these
> hydrogens and their associated oxygen molecules which stretch the entire
> length of
> the box!
>
> Does anyone know how I can fix this? Did something get messed up during
> solvation?
>
> BTW: I’m using
>
> gromacs 5.1.4
> VMD 1.9.3
>
> on a Macbook Pro with macOS 10.12.3 (Sierra).
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