[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

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://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

========================================