[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 12 14:01:09 CET 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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