[gmx-users] a snapshot of NVT

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jun 17 07:55:49 CEST 2013

Hi Maggin,

Okay, this image may require a bit of explanation :p VMD has drawn bonds
according to the bondedness in a reference file. But the atoms have moved,
and some went over the box boundaries. So they show up with long bonds
crossing the whole box. It's not a problem, just a visualization artefact.



On Mon, Jun 17, 2013 at 7:52 AM, maggin <maggin.chen at gmail.com> wrote:

> Hi, all
> When I run a small peptide at NVT stage, I get a snapshot like this:
> <http://gromacs.5086.x6.nabble.com/file/n5009206/next6_gro2.bmp>
> I am not sure if it right, and can I use it for NPT ?
> Thank you very much!
> maggin
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Tsjerk A. Wassenaar, Ph.D.

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