[gmx-users] creating a larger lipid membrane

[Amit Choubey]

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.

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

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.

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.

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?

Any help will be appreciated thank you

Amit
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091009/dc9ab91b/attachment.html>