[gmx-users] I need 256 lipids ...

[Stéphane Téletchéa]

Hello,

I'm willing to simulate a membrane protein, and to gain lipid 
equilibration time, i'm using either Dr Tieleman's lipids or Dr 
Vattulainen's lipids (dppc 128 / dppc64).

In order to fully surround my protein, i need to enlarge those boxes to 
get at least 256 lipids (thus multiply the 64 lipids by 4).

To perform the enlargment, i used genconf:
genconf -f dppc64.pdb -o dppc256.pdb -nbox 2 2 1

But when i try to use the resulting dppc256.pdb, the system crashes 
(even if i try to fully minimize it first). I assume the problem arises 
from overlapping atoms while doing genconf but i thought this was the 
goal of the tool to be carefull about this.

I've been able to perform some dynamics (1 ns test systems) without 
problems if i do not use genconf ...

Is there any problem in my methodology ?
Is there a clever way to duplicate the starting lipids ?

I'm willing to do a full automated process for the lipids, this is why i 
did use genconf. I'm actually trying to build manually the lipid 
bilayer, but since i'm not sure whether i'll use dppc, dmpc, popc, i'm 
still searching for an automated method.

Thanks a lot in avdance for your answers,

Stéphane Téletchéa

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901