[gmx-users] creating a larger lipid membrane

[Justin A. Lemkul]

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
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

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

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