[gmx-users] Errant hydrogen bonds in the Lysozyme tutorial -- Please advise
mark.j.abraham at gmail.com
Fri Oct 20 07:15:53 CEST 2017
That's normal. Please see
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
> 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
> BTW: I’m using
> gromacs 5.1.4
> VMD 1.9.3
> on a Macbook Pro with macOS 10.12.3 (Sierra).
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users