[gmx-users] I need 256 lipids ...
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 30 12:39:40 CET 2006
Stéphane Téletchéa wrote:
> David van der Spoel a écrit :
>> Stéphane Téletchéa wrote:
>>> 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 ?
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 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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