Re: [AMBER] question about lipid tutorial

From: Dickson, Callum J <>
Date: Fri, 1 Aug 2014 11:49:09 +0000

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:

center origin :1-384 mass
image center origin

From: Jonathan Gough []
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.


screenshots below showing the system at the beginning of the simulation and
then part way along.
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Received on Fri Aug 01 2014 - 05:00:03 PDT
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