Whew.
Thanks Callum!
On Aug 1, 2014 7:51 AM, "Dickson, Callum J" <callum.dickson09.imperial.ac.uk>
wrote:
> Hi Jonathan,
>
> That is normal behaviour and is due to the use of periodic boundary
> conditions, you can use ptraj/cpptraj to image everything back into the
> unit cell. Something like:
>
> trajin traj.nc
> center origin :1-384 mass
> image center origin
> trajout image.nc
>
> Cheers,
> Callum
> ________________________________________
> From: Jonathan Gough [jonathan.d.gough.gmail.com]
> Sent: 31 July 2014 21:15
> To: AMBER Mailing List
> Subject: [AMBER] question about lipid tutorial
>
> Hi everyone,
>
> I was working through the lipid tutorial and I had a question. During the
> 04_hold portion of the simulation does the water expand? and spread out?
> Is the system in a periodic box and the water/system would stay together.
> I'm just trying to see if there is something I am doing wrong.
>
> Thanks,
> Jonathan
>
> screenshots below showing the system at the beginning of the simulation and
> then part way along.
>
> https://www.dropbox.co
> m/s/5e2zgnxi413okm4/Screenshot%202014-07-31%2016.03.54.png
>
>
> https://www.dropbox.com/s/dn7xc93klne4hks/Screenshot%202014-07-31%2016.04.15.png
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Received on Fri Aug 01 2014 - 07:30:02 PDT
