[gmx-users] creating a larger lipid membrane

[Amit Choubey]

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.

amit

On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul <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
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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
>
> ========================================
> _______________________________________________
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091009/22b1b627/attachment.html>