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

Wes Barnett w.barnett at columbia.edu
Tue Oct 17 17:37:33 CEST 2017


On Sun, Oct 15, 2017 at 3:13 PM, Deron Johnson <deronj at comcast.net> wrote:

> 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>
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


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-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us


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