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

Stéphane Téletchéa steletch at jouy.inra.fr
Thu Nov 30 12:04:46 CET 2006

David van der Spoel a écrit :
> Stéphane Téletchéa wrote:
>> 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
> are you sure all the lipids are in one piece?
> if not you will have very large bond energies in the minimization

No, unfortunately, they are not ...

I should have mentionned this first.
I took the dppc64.pdb for Dr Tieleman's site, and then imaged it using 

editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc

But unfortunately, some lipids are not imaged (at least 18, 25 and 53). 
I tried using trjconv but it needs a topol.tpr that i don't have :-(

Any hint ?


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

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