[gmx-users] creating a larger lipid membrane

[Amit Choubey]

Hi Mark,
Yes i checked the procedure on the original structure. It woks fine. As for
genconf i used the following

genconf -f dppc128.pdb -o out.gro -nbox 2 2 1

As Justin pointed out, I did not correct the periodicity of original
structure before using genconf .

Thank you,
Amit

On Fri, Oct 9, 2009 at 5:44 PM, Mark Abraham <Mark.Abraham at anu.edu.au>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.
>>
>
> What command line did you use?
>
>  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 :-
>>
>
> Test your protocol on the original coordinate file. It needs to work for
>  your procedure to be sound.
>
>  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.
>>
>
> You don't have periodic molecules. Changing mdp options haphazardly is a
> recipe for problems. Read 7.3 about them in the first instance, and then
> look up in the table of contents for more background.
>
>  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.
>>
>
> Yup, bad idea. Fix the underlying problem, not the symptoms.
>
> Mark
>
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