[gmx-users] Simulation of membrane protein

[James Starlight]

Ok, James thank you

It seems that I should to wite some script for too many iterations e.g

perl inflategro.pl minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr

mdrun -v -deffnm minimized2

perl inflategro.pl minimized2.gro 0.95 DPPC 0 shrinked2.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr

mdrun -v -deffnm minimized2

......

perl inflategro.pl minimized20.gro 0.95 DPPC 0 shrinked20.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr

mdrun -v -deffnm minimized21

Does this action sequence correct? So as the consequence I need to
find operator wich stop the script untill defined value of S per lipid
will be reached



Thanks again

James

2011/10/17 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>>
>> James,
>>
>> As the consequence the correct orientation of the peptide in the membrane
>> as well as futher solvation are caused many questions :)
>>
>>
>> Firsly, following by tutorial guide I've done orientation of KALP peptide
>> in the membrane by
>>
>> 1- perl inflategro.pl <http://inflategro.pl/> confout.gro 0.95 DPPC 0
>> system_shrink1.gro 5 area_shrink1.dat
>> 2- minimization
>> 3- perl inflategro.pl <http://inflategro.pl/> system.gro 4 DPPC 14
>> system_inflated.gro 5 area.dat
>>
>>
>>
>>
>> 4- minimization
>>
>> after six iterations of the  3rd and 4th steps I've obtained 6,5 nm^2
>> value for the area per lipid
>>
>>
> The tutorial suggests at least 26 or so iterations.  Your APL value is 100
> times larger than it should be.
>
>
>  Next I've done solvation of my protein ( including big vdv radii for
>> carbons )
>>
>>
>>
>> Finally my sytem is consisted of 70000 atoms. I think that it's too big
>> ammount of water molecules for such small protein like KALP
>>
>>
> Yes, because your membrane is not correctly packed.
>
>
>  so its seems that i've done some mistakes-
>> 1- During shrinking of my peptide- I think that obtained structure (
>> http://www.sendspace.com/**file/wenkf4<http://www.sendspace.com/file/wenkf4>)
>> consist of too big distances beetween peptides so it should be futher
>> shrinked.
>>
>>
> Correct.
>
>
>
>>
>> But how many iterations must be? I've found in the tutorial that 65 A^2 is
>> good value for that system. But maybe I've used wrong parametries in the pl
>> program?
>>
>>
> No, you just haven't done enough iterations.  See above.  Your value is 6.5
> nm^2 , which is 6500 A^2.
>
>
>  2- Or maybe too many waters are moved within the membrane in spite of
>> increased VDV radius for carbon atoms. So what I should do for the excluding
>> all unnecessary water from my structure?
>>
>>
>>
> Ignore this for now.  Your system simply isn't built correctly.
>
>
>
>> E.g I want to simulate hydrophobic effect. What length of that simulation
>> must be ?
>>
>
> Perhaps tens of ns.
>
>
>  How I can evaluate the ammount of water before and after simulations?
>>
>
> Visualization.
>
>
>  Finally, What other options of Genbox could I use for preventing insertion
>> of water into my membrane ?
>>
>>
>>
> None.  A better starting model is required.
>
> -Justin
>
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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