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

Deron Johnson deronj at comcast.net
Fri Oct 20 06:06:48 CEST 2017

I am new to gromacs. I followed the steps of the lysozyme tutorial
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).

More information about the gromacs.org_gmx-users mailing list