[gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)

[Alan Dodd]

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 <mariagoranovic at gmail.com>
To: Discussion list for GROMACS users <gmx-users at 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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