Re: Half of the structure goes out of the simulation box!

From: Richard Overstreet (
Date: Fri Sep 30 2016 - 06:25:19 CDT

Nothing is wrong check out the Wrap commands.

On 09/30/2016 05:18 AM, faride badalkhani wrote:
> Dear NAMD experts,
> I have performed a simulation on a nanostructure in a water box and I
> did not get any errors. However, when I load the dcd file in VMD I see
> that almost half of the structure remains in the water box and the
> remain part of the molecule is out of the box. Could you tell me what
> is wrong with the simulation, please?
> regards,
> Farideh

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:30 CST