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
--
========================================
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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