Hi,
It looks like the the problem is the asymmetry in ion distribution. I have
seen from the literature that such ion asymmetry can be maintain by
implementing slab geometry. Can anybody provide me some information of how
to build vacuum slab above and below the membrane ( ie in Z direction).
What all modification I should make in mdp input file to take care of the
slab geometry?
Many thanks in advance
Anu
On Tue, Jul 14, 2015 at 3:57 PM, anu chandra anu80...@gmail.com wrote:
Thanks for the reply Mark. Yes, its a periodic box. Below is the input mdp
I have used for minimization.
define = -DREST_ON -DSTEP6_0
integrator = steep
emtol = 1000.0
nsteps = 5000
nstlist = 10
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
coulombtype = pme
rcoulomb= 1.2
;
constraints = h-bonds
constraint_algorithm= LINCS
**
Please find attached the snapshot of the system before (initial.png) and
after minimization (min1.png). Green is the calcium ions and blue is the
chloride ions. All I have done is adding calcium ions to one side of the
membrane. It looks to me like calcium ions enetering from the opposite side
of the box ( ie from its image box). Hope I am taking care of the periodic
condition. Please have a look and help me to figure out the problem.
On Tue, Jul 14, 2015 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
It's a periodic box, right? There is only one water region. You can't get
steady-state non-equilibrium ion distribution without forcing it, e.g.
https://www.mpibpc.mpg.de/grubmueller/compel
Mark
On Tue, Jul 14, 2015 at 12:42 PM anu chandra anu80...@gmail.com wrote:
Dear Gromacs users,
I am working with membrane proteins. The system contains CaCl2 ions
and I
build the system with calcium ions on one side of the membrane (here,
upper
layer) and chloride ions distributed on both side of the membrane, in
order
to maintain the physiological condition. Unfortunately, after the very
first minimization, when I visualize the gro file in VMD I have noticed
that the calcium ions entered the opposite side of the membrane (ie,
lower layer) and subsequently get distributed in the lower layer during
the
equilibration process. Though I have tried with varying Z-dimension
values
of the box size, the same has been noticed when visualizing the output
gro
file with VMD.
Please help me to figure out what is wrong with my simulation box.
Many thanks
Anu
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