[gmx-users] walls and E-z

Alex nedomacho at gmail.com
Fri Nov 3 07:43:25 CET 2017

Hi all,

It appears that the external field is refusing to move the ions when 
walls are present. I am comparing two setups of a system that has an 
aqueous bath (1M KCl) split by a semi-porous (infinitely selective for 
cations) membrane in XY. The only difference between them is that one is 
periodic in XYZ and the other has two walls. The difference isn't minor 
-- consider K+ fluxes with and without walls: 

Initially, ionic populations in each case are homogeneous. I realize 
that with walls the process will stop when all cations end up at the top 
of the box (and that's the goal). However, there is no flux right from 
the start. Relevant portion of the mdp with walls below (not sure if 
this is important, but 'ewald-geometry' directive isn't in the mdp 
without walls):

pbc                 = xy
nwall               = 2
wall-type           = 12-6
wall-r-linpot       = 0.25
wall_atomtype       = opls_996 opls_996
wall-ewald-zfac     = 3
periodic_molecules  = yes
ns_type             =  grid
rlist               =  1.0
coulombtype         =  pme
ewald-geometry      =  3dc
fourierspacing      =  0.135
rcoulomb            =  1.0
rvdw                =  1.0
vdwtype             =  cut-off
cutoff-scheme   = Verlet

Any ideas?



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