[gmx-users] help with creating membrane

Dinesh Pinisetty dpinis1 at lsu.edu
Tue Sep 14 18:03:37 CEST 2004

From:gmx-users-bounces at gromacs.org on 09/14/2004 04:01 PM ZE2

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Subject:    [gmx-users] help with creating membrane

Hi all
I have to create a lipid membrane but I have this problem. I have bilayer
lipids with something bigger 'area per lipid' parameter cause I want to
laterally compress them. But these lipids are just settled by genconf
program. I've tried to make the sd energy minimisation but when I used
periodic boundaries, the membrane exploded (or something like that), and if
not, whole membrane collapsed into a sphere. So if somebody has any
experiences with constructing membranes, I will be pleased if he/she will
share them. Especially I will be pleased by example .mdp files.


What you do is start of with low values of box size for a single
molecule.Before using genconf itself you try to have a lower box size and
see that when multiplied it is accoeding to the area per
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