request

[Pooja_Sahu]

Hi,

I have made a surface of crownether embedded poly-styrene, i want to adsorb ions (from its aqueous solution) on this surface, solution (solvent+ion mixture) size is smaller than surface , now when i put solution on surface and give setforce 0.0 0.0 0.0 for surface , water (or any solvent) expands in whole space available in the box.
And if i put setforce NULL NULL NULL for surface, solution above surface does not expands but surface in z direction gets distort , (crown-ether from surface comes forward to capture the ions) .

My Lammps input file is as follows –

dimension 3
units real
boundary p p p
kspace_style pppm/tip4p 1.0e-4
kspace_modify order 3.0
atom_style full
pair_style lj/cut/coul/long/tip4p 15 16 12 21 0.1546 9.0 #1st bond then angle
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_modify mix arithmetic
read_data JoinOutput.data
group surface type 1 2 3 4 5 6 7 8 9 10 11 12 13
group wtr type 15 16
group ion type 14

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes one 10000 page 1000000
minimize 1.0e-4 1.0e-6 10000 100000
fix 3 surface setforce 0.0 0.0 0.0
fix 1 wtr shake 0.0001 20 0 t 15 16 a 21 b 12
fix 2 all nvt temp 298.0 298.0 100.0 # iso 1.00 1.00 1000.0 # dilate partial
timestep 1.0
thermo 1000
thermo_style custom step temp press vol pe evdwl
restart 20000 adsorb2
dump 6 all custom 1000 adsorb_confine.dump id mol type x y z
run 1000000

please help me. I will be very thankful to you all.

With Regards,
Pooja sahu

[akohlmey]

Hi,
    I have made a surface of crownether embedded poly-styrene, i want to
adsorb ions (from its aqueous solution) on this surface, solution
(solvent+ion mixture) size is smaller than surface , now when i put
solution on surface and give setforce 0.0 0.0 0.0 for surface , water (or
any solvent) expands in whole space available in the box.

             And if i put setforce NULL NULL NULL for surface, solution

above surface does not expands but surface in z direction gets distort ,
(crown-ether from surface comes forward to capture the ions) .

it is very difficult to comment on simulations without
any tangible knowledge of how they came to be and
how you prepared the system.

has it been properly equilibrated?
what is the behavior of the total/potential energy?
have the potential parameters been used
successfully for similar systems?

that a simulation doesn't quite do what you
expect it to do can have many reasons, and
most of them have nothing to do with the
simulation software but rather are due to
bad "preparation" or a bad model and will
happen even if you use reasonable parameters
in your input file.

axel.

[Andrew_Jewett]

it is very difficult to comment on simulations without
any tangible knowledge of how they came to be and
how you prepared the system.

It's true, but I'll make an attempt to add a comment.
I also think including including pictures which show visually what
went wrong, and what you expected to happen would also help.

Hi,
    I have made a surface of crownether embedded poly-styrene, i want to
adsorb ions (from its aqueous solution) on this surface, solution
(solvent+ion mixture) size is smaller than surface , now when i put
solution on surface and give setforce 0.0 0.0 0.0 for surface , water (or
any solvent) expands in whole space available in the box.

I assume this is good. Is this what you wanted to happen?

             And if i put setforce NULL NULL NULL for surface, solution
above surface does not expands but surface in z direction gets distort ,
(crown-ether from surface comes forward to capture the ions)

I assume this is not what you wanted to happen?
If you allow the atoms in the surface to move, they might not do what
you expected them to do. If you are certain that this behaviour is
not correct, then unfortunately you will have to fix your force-field.

If you have not done this, I would also check your periodic boundary
conditions visually. (If you use, VMD, then click on the
"Graphics->Representations" menu, and select the "Periodic" tab.)
Hopefully the atoms in the surface are not overlapping with atoms in
the neighboring cell.

I have some comments about your script.

     Try replacing:

fix 3 surface setforce 0.0 0.0 0.0
fix 2 all nvt temp 298.0 298.0 100.0 # iso 1.00 1.00 1000.0

     with:

group mobile subtract all surface
fix 2 mobile nvt temp 298.0 298.0 100.0 # iso 1.00 1.00 1000.0

This is the standard way to immobilize an object in LAMMPS (at constant volume).

(Incidentally I see some left over script debris from when tried to
run a constant-pressure simulation. Perhaps anticipating your next
question, if you do intend to run an NPT simulation, I would use
something like "aniso" instead of "iso" . If you plane to immobilize
the surface, then replace "dilate partial" with "dilate GROUPNAME", in
this case "dilate mobile". There are some other changes you would
have to make, such as "neigh_modify exclude surface surface", and
maybe "fix rigid". Running NPT simulations with large immobilized
objects is tricky and is discussed frequently. If you plan to do
this, have a look at these threads:
http://sourceforge.net/mailarchive/message.php?msg_id=30056113
http://sourceforge.net/mailarchive/message.php?msg_id=30018547)