[gmx-users] creating a larger lipid membrane

Amit Choubey kgp.amit at gmail.com
Sat Oct 10 03:17:58 CEST 2009 

Thank you for the tip. I will try to use it.
Amit

On Fri, Oct 9, 2009 at 6:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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>>
>>    --    ========================================
>>
>>    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
>
> ========================================
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