[lammps-users] How to calculate effective interaction of two charged molecules in aqueous solution, again.

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1

Dear,

I want to calculate effective interaction between two charged molecules in aqueous solution. The simulation system include two molecules(including 50 LJ atoms, respectively), 3000 water(LJ liquid),and counterions( 100 anion). There are mainly three interactions in my system, U_LJ(Lennard Jones potential) and U_coulomb (Coulomb potential), and U_FENE bond.

Firstly, the pair of molecules are placed symmetrically along the body diagonal of the cubic simulation box ( I used fix spring command with tether keyword in LAMMPS). The distance R of two molecules acts as a parameter and could be varied.
Next, I want to calculate the effective force F_i acting on each molecule i (i = 1,2) . The force F_i( i = 1,2) would be due to the other molecule, solution and counterions. How Can I calculate the force F_i with LAMMPS command or how can I dump all pair force as data for postprocessing when running LAMMPS in code?

Any sugesstions is highly appreciated.

2

See the compute group/group command.

Steve

3

Thanks for your reply

But the compute group/group command does not include long-range interactions due to a kspace_style command . Any other suggestions?

Thanks in advance.

Redram

2008/12/4 Steve Plimpton <[email protected]>

4

I don't know how to compute that contribution. Does anyone?

Steve

5

Redram,

You wrote: How Can I calculate the force F_i with LAMMPS command or how can I dump all pair force as data for postprocessing when running LAMMPS in code?

Can you try something like “dump [id] atoms-in-molecules custom N dump.out tag mol x y z fx fy fz” and then use this information to calculate a center-of-mass force for each molecule in post-processing? That should include the long range interactions on each atom without needing a special handling of the kspace portion.
Joanne

6

Dear Joanne,

Thanks for your suggestion. I guess that your idea could be equivalent to two commands like this:
compute 1 mol_one reduce sum fx fy fz
compute 2 mol_two reduce sum fx fy fz

Isn’t it? The above commands can calculate composition of forces of each molecule. Is IT equal to all pair force due to the other molecule, solution and counterions?

I am considering whether the force due to fix spring command is the force I want to get or not according as the third law of Newton.

Any idea?

Thanks in advance.

Redream.

2008/12/6 Budzien, Joanne Louise <jlbudzi@…3…>

7

I'm confused by this thread. If you have 3 groups of atoms: A,B,C,
and they all interact with each other. And you want the summed force
on all atoms in A, due to all the B atoms, but not the C atoms.
E.g. A and B are 2 molecules and C is the solvent.

Then you cannot get the force you want from the dump file. The per-atom
forces on A atoms will include C atoms. You can
get the force you want via compute group/group. But it will not
include long-range Coulombics. I don't know how (or even what it
means) to talk about the long-range Coulombic force on an A atom
due to all the B atoms, but not the C atoms.

Steve