[gmx-users] Simulation of membrane protein

[James Starlight]

Justin,


Indeed GenBox added insufficien of the SOL to my system due to the ussage
of increased vdvdat ( I've used 0.350 value for the c atoms only but the
were alot of void beetwen water and bilayer )

lipid_posres in Z directions have prevented the displacement of the bilayer
but the water were distruibuted irregular on the bilayer surface  at the
end of NVT phase

By the way in Gmembed system I have no such problems because the were no
need to use genbox but during processing of the system I've obtain warning

WARNING 1 [file membed.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups



What does it mean?

By the way could I indicate Area per lipid during processing of my system
with the G_membed?


James




2011/11/11 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> The system was compact after inserting protein into bilayer (I've obtain
>> Area per lipid in accordanc with experimental reference) and futher
>> minimization (only some llipid tails on the border of the system were
>> distorded alittle)
>> But after  nvt simulation this discrepancy occured :)
>>
>> I've used pbc size like in the KALP simulation because I have bilayer  (
>> 128 lipids) and the protein (38 a.a) of the same size.
>>
>
> KALP-15 has only 15 residues; your peptide is significantly longer.
>
>
>  My box vectors were 6.500 6.500 6.500
>>
>> Do you think that I should use smaller pbc? How I could define pbc on the
>> right size for my purely bilayer system?
>>
>>
> You shouldn't use the box vectors I did in the tutorial - use the
> dimensions present in the actual membrane you're using.  I still see no
> conceivable way that the bilayer separated that much during NVT without
> significant empty space in the unit cell to start.  In NVT, the volume is
> constant, so if there are voids, the lipids will fill to expand them.  I've
> seen it countless times, so please be sure you're actually providing
> sufficient solvent and an appropriate location for all your components
> within the unit cell.
>
> -Justin
>
>  I've used
>>
>> trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact
>>
>> at the preequilibrated bilayer and than done anything in accordance to
>> the KALP tutorial
>>
>>
>> James
>>
>>
>> 2011/11/11 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>    How large of a void exists between your lipids and water prior to
>>    starting the simulation?  I'm almost certain that you built the unit
>>    cell incorrectly - there should never be that much free space.
>>
>>
>>
>>        By the way I'ts intresting that Gmembed has removed 6 lipids in
>>        comparison to the inflateglo ( althought I've done all things in
>>        accordance to the KALP tutorial because my protein is the same).
>>
>>
>>    Different algorithms, different results.  Nothing odd about that to me.
>>
>>    -Justin
>>
>>
>>    --     ==============================**__==========
>>
>>
>>    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<http://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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