[gmx-users] membrane-protein tutorial

[mohsen ramezanpour]

Dear Dr.justin
Thank you.You are right.
I did what you said.

please let me know the answer of my other question in first email:
I am doing iteration more than 26 times that you said in your tutorial.
I am in 28th step now and my area per lipid is 63 and I think it is lowering
everytimes I do iteration.
In the other words it seems it dosen't converge!!
What do you think?
Thanks in advance

On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>> Yes,I know,it deleted some lipids according to inflateGRO script in the
>> first timethat I used perl command.
>> Besides:
>> I did iteration 25 times correctly,and no addition or doubling was
>> occured.
>> I used the same commands of  25th iteration.of course I changed numberes
>> from 25 to 26 in commands.
>> I think it is because I have compacted my lipids more than it is required.
>>
>>
> Over-packing your lipids will not cause your coordinate file to magically
> be doubled.
>
>
>  my commands are as below:
>> after doing EM for output of 25th iteration(its output were
>> EM-inflate-26.*) I entered :
>>
>> trjconv     -f  EM-inflate-26.trr       -s  EM-inflate-26.tpr      -o
>> EM-inflate-26-trj.gro       -pbc   mol     -ur   compact
>>
>
> Here's the problem.  You're converting a .trr (which presumably has 2
> frames) and converting it to a multi-frame .gro file.  All you need is to
> fix the PBC on the final frame, i.e. the .gro file that mdrun writes.
>
> -Justin
>
>  perl     inflategro        EM-inflate-26-trj.gro      0.95         DPPC
>>    0        system_shrink26.gro      5        area_shrink26.dat
>> grompp      -f      minim-strong.mdp       -c        system_shrink26.gro
>>      -p    topol.top         -o   EM-inflate-27.tpr
>>
>> thanks in advance for your reply
>>
>>
>> On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    mohsen ramezanpour wrote:
>>
>>        Dear all
>>
>>        I am doing Membrane -protein tutorial.
>>        Actually I did each step carefully,I could score down my lipids
>>        26 times.
>>        But there were two problems:
>>        1-I get ~77 A for area per lipid in 26th step not 71 as
>>        Dr.Justin has said
>>        2-I tried to do more iteration to make closer my area per lipid
>>        to 71,But I get the following error:
>>        Program grompp, VERSION 4.0.7
>>        Source code file: ../../../../src/kernel/grompp.c, line: 362
>>
>>        Fatal error:
>>        number of coordinates in coordinate file (system_shrink26.gro,
>>        12876)
>>                    does not match topology (topol.top, 6438)
>>
>>        I checked and I found program has added some additional DPPC
>>        molecules to my system!!
>>
>>
>>    InflateGRO does not add lipids, it deletes them.  Whatever you've
>>    done has exactly doubled the system.  You've managed to concatenate
>>    coordinate files or otherwise manipulate it in some nonsensical way.
>>     Without seeing the command you used it's impossible to say.
>>
>>    -Justin
>>
>>
>>        Besides I get 32 A area per lipid for this step!!!
>>
>>        Please let me know what is the reason.
>>        Thanks in advance
>>        Mohsen
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    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
> MILES-IGERT Trainee
> 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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