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

Deron Johnson deronj at comcast.net
Tue Oct 17 17:30:16 CEST 2017

BTW: I’m using 

gromacs 5.1.4
VMD 1.9.3

on a Macbook Pro with macOS 10.12.3 (Sierra).

> On Oct 15, 2017, at 12:08 PM, 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 <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! (I've attached an image of the display window, using CPK representation).
> Does anyone know how I can fix this? Did something get messed up during solvation?
> <lyzozyme_tut_vmd_display.png>

More information about the gromacs.org_gmx-users mailing list