[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> 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?

grompp is warning you that it is impossible to exclude long-range (reciprocal 
space) interactions calculated with PME.  Whatever you're trying to exclude 
cannot be completely excluded.

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

I don't know what you're asking here.  g_membed has no need of APL information; 
it grows the protein into the membrane, a process that removes lipids but does 
not attempt to converge APL data in any way.

-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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