It sounds like you have it pretty clear already. A point to note, in GROMACS
the origin coordinate 0,0,0 is at a corner of the box, not the centre. This
could be what caused such a big (apparent) shift.
----- Original Message ----
From: maria goranovic <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Monday, March 31, 2008 10:32:28 AM
Subject: [gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes
2 monolayers (shift in box center?)
Hello Folks,
I am simulations a lipid bilayer. After minimization, the output .gro file
contains a bilayer that is a layer of water sandwiched between 2 monolayers of
lipids (instead of being the other way around). I guess this has something to
do with the periodic shift in boxes or something. Can someone please clarify
this for me ?
Thank you
-Maria
--
Maria G.
Technical University of Denmark
Copenhagen
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