water-modeling

Hi
I simulate a system with a explicit solution to see the ion exchange between polymer and electrolyte , but water molecules prevent of the ion exchange . I don’t want to use implicit solution for my system. please let me know, how can I model the water molecules , not to prevent the ion exchange.

thanks in advance
ramin



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There is a CHARMM-related pair style in LAMMPS that
has the word “implicit” in its name - it just reduces
the strength of the Coulomb interaction and is designed
to use without water. Other LAMMPS potentials
are for coarse-grained systems where assumptions
are made about implicit solvent effects.

You’d have to provide more details about how
you intend to see/model ion exchange, to give
a better answer.

Steve

I do not want to use implicit solution , because of water in my system. I have a membrane that include polymer + water + ions and a bulk of water( electrolyte ) beside it that have water molecules + ions. my main is to see the exchange of ions of membrane and electroyle .but water molecules prevent the motion of ions to exchange.

LTA

units real
boundary p p p
atom_style full

pair_style lj/cut/coul/long/tip4p/omp 7 8 6 8 0.1250 12.0
kspace_style pppm/tip4p 1.0e-4
special_bonds lj 0.0 0.0 0.0 coul 0.0 0.0 0.0
bond_style harmonic/omp
angle_style harmonic/omp
dihedral_style none

read_data 15NaLTA2AgClallhyd.lammps05

#GROUP

group oxygen type 7
group water type 7 8
group mobile type 3 5 6 7 8 9 10
group zeolite type 1 2 4
group sodium type 6
group chlorine type 10
group silver type 9
group agna type 6 9

neighbor 2.0 bin
neigh_modify every 2 delay 10 check yes page 100000

#FIX

compute myTemp mobile temp

thermo_style multi
thermo_modify temp myTemp
thermo 10000

fix 2 zeolite setforce 0.0 0.0 0.0

minimize 1.0e-4 1.0e-6 100 1000

fix 1 mobile nvt temp 370 370 50

fix 3 water shake 0.0001 20 0 b 6 a 8

fix 4 water ave/spatial 1 100000 100000 z lower 1 density/mass file water_mass370.profile units box
fix 5 sodium ave/spatial 1 100000 100000 z lower 1 density/mass file sodium_mass370.profile units box
fix 6 chlorine ave/spatial 1 100000 100000 z lower 1 density/mass file chlorine_mass370.profile units box
fix 7 silver ave/spatial 1 100000 100000 z lower 1 density/mass file silver_mass370.profile units box

#DUMP

dump 1 all custom 100000 equilib-0.lammpstrj id type xs ys zs ix iy iz vx vy vz

restart 100000 15lta.restart

timestep 1

run 10000000

thanks
ramin

I think your description is

You have a polymer with ions in it and the polymer is solvated by an electrolyte that has different ions than the ones already in the membrane. [You also provided (redundant) information that you are not dealing with an implicit solvent.]. You would like to see the exchange of the different kinds of ions in the polymer and water. With your current settings, you don’t observe the exchange of ions and you think the problem is caused by water which prevents the exchange from happening.

Hi
I simulate a system with a explicit solution to see the ion exchange between polymer and electrolyte , but water molecules prevent of the ion exchange . I don’t want to use implicit solution for my system. please let me know, how can I model the water molecules , not to prevent the ion exchange.
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  • |

you are asking the wrong question.

if you just want LAMMPS to do what you say,
then you are not looking for a simulation
program, but an animation program. of course
the scientific value of that will be next to nothing.

the question that you should ask and try to
answer is: why does this happen?

there are two possible explanations:

  1. it is energetically unfavorable
  2. it is kinetically hindered
    of course, a combination of both is possible, too.

in the first case, you’ll have to look into whether
your parameters that describe the mutual
interactions are correct.

in the second case, you have to determine the
(free) energy barrier for an ion being solvated in
water going into being adsorbed in your polymer.
if that barrier is high, then the exchange will happen,
but it is just very improbable.

as mentioned above, this barrier height is affected
negatively by bad potential parameters.

i find it quite likely that you are underestimating
the difference between a macroscopic process
and its atomistic scale representation and the
time scales.

just forcing the system to do what you want to do
is not giving you a useful answer; for the most part,
you’ll just massively increase the entropy of the
universe.

cheers,
axel.

Yes of course!! the ion exchange between membrane and electrolyte becuase of the difference of chemical potential , that my electrolyet have a high chcmical potential because of low entropy . when I use implicit solution ( without water ) I see the ion exchange but in explicit solution not. I think it is because of lacking enough force in my electrolyte .

best
ramin

Yes of course!! the ion exchange between membrane and electrolyte becuase of the difference of chemical potential , that my electrolyet have a high chcmical potential because of low entropy . when I use implicit solution ( without water ) I see the ion exchange but in explicit solution not. I think it is because of lacking enough force in my electrolyte .
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  • |

what force?

i think you have not really understood the implications
of free energy barriers and activated processes
or “rare events” in atomistic simulations.

assuming that you’ll get the same exchange rates
than in an implicit solvent description is plain ignorance.

what you have to do is to validate your potential parameters
independently and whether they are compatible to each other.
just saying “it doesn’t do what i want it to do” and asking
“how can i change it so i does what i want?” is looking at
the situation from the wrong perspective and will lead to
a lot of wasted time on your side.

axel.

my mean by force is the difference of pressure
in electrolyte and membrane to have
ion exchange that hydrated by water molecules.

ramin

I validate potential parameters in my other simulation ( diffusion constant ) with comparing by experimental data.

ramin

I would try to validate you are using the right parameters by first comparing against simulation data that use the same potential. A simulation is rarely exact and your match for the experimental diffusion constant may just be a coincidence.