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

[David van der Spoel]

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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++