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 - 05:00:03 PDT
