[gmx-users] creating a larger lipid membrane

[Justin A. Lemkul]

Amit Choubey wrote:
> Hi Justin,
> 
> Yes you are right. I didnt fix the periodicity to start with. Could you 
> tell me how to do that, which command to work with?
> Thanks.
> 

Periodicity is corrected using trjconv.  This involves creating a .tpr file of 
to represent the system and using trjconv -pbc mol -ur compact, or some such 
equivalent.

My tutorial gives some information on doing this.  Please see:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

-Justin

> amit
> 
> On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amit Choubey wrote:
> 
>         Dear Gromacs Users,
> 
>         I have been trying to generate a larger lipid system but am
>         running into troubles due to improper initial co-ordinates set
>         up. Following are the steps i am trying to follow.
> 
>         1. I start with a 128 dppc membrane and use genconf to create a
>         larger system. I got the dppc128.pdb from Dr. Peter Tieleman's
>         website.
> 
> 
>     Did you correct for periodicity before you extended the system?  The
>     files distributed by Tieleman are compact representations.
> 
> 
>         2. I changed my topology file accordingly (change the number of
>         DPPC and Water molecules)
> 
>         3. I move on to energy minimization. During the mdrun i see the
>         following message :-
> 
>         Warning: 1-4 interaction between 1854 and 1857 at distance 6.249
>         which is larger than the 1-4 table size 2.800 nm
>         These are ignored for the rest of the simulation
>         This usually means your system is exploding,
>         if not, you should increase table-extension in your mdp file
>         or with user tables increase the table size
> 
> 
>     Looks to me like two bonded atoms are across the box from each
>     other, which seems to answer my question above :)
> 
> 
>         I also notice that the max force does not converge to less than
>         2000 rather its of the order of 2e+06 .
> 
>         4. I tried to do energy minimization again on the above system
>         but the steepest descent could not change the potential energy
>         substantially and terminated after less that 20 steps. I again
>         noticed the following warning
>         Warning: 1-4 interaction between 1854 and 1857 at distance 5.269
>         which is larger than the 1-4 table size 2.800 nm
>         These are ignored for the rest of the simulation
>         This usually means your system is exploding,
>         if not, you should increase table-extension in your mdp file
>         or with user tables increase the table size
> 
>         5. Now i changed my mdp files to do periodic_molecules = yes .
>         Note pbc = xyz has been used as default.
> 
> 
>     Bad idea.  This option is for "infinite" molecules, like nanotubes
>     or graphene sheets that are supposed to extend across the simulation
>     box.
> 
> 
>         Same warnings were printed out during energy minimization.
> 
>         6. I also tried to use the table-extension option and increased
>         its value to 10 nm but later the LINCS printed out too many
>         warnings and MD could not be done. I know that its not at all a
>         good idea to increase the 1-4 cut off.
> 
> 
>     The standard advice is to fix the problem with the system, not
>     change the table-extension.
> 
> 
>         By the way to be specific the system size was 12 x 12 x 6 in
>         nm3. I had 256 lipids and about 7300 water molecules.
>          
>         I believe that this might not be the best way to create a larger
>         bilayer system. Could somebody suggest me other ways of doing this?
> 
> 
>     Fix periodicity, then use genconf.
> 
>     -Justin
> 
>         Any help will be appreciated thank you
> 
>         Amit
> 
> 
> 
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> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================