[gmx-users] a snapshot of NVT

[Tsjerk Wassenaar]

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.

Cheers,

Tsjerk


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
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.