[gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)
anoddlad at yahoo.com
Mon Mar 31 11:40:43 CEST 2008
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?)
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 ?
Technical University of Denmark
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