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

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 30 11:53:38 CET 2006

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

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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