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

[David van der Spoel]

Stéphane Téletchéa wrote:
> 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:
> 
> 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
> 
It requires some manual work, but with editconf you can translate a 
subset of atoms, so you have to find out which atoms they are, and then 
write an index file, and then translate them by one box.

-- 
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
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