switching off intrachian lj interaction in polymer chain

Hi all,
I am trying to simulate a multiple polymer chain using harmonic bond potential and lj potential , I want to switch off the LJ potential between the intrachain beads, while not affecting the potential between the beads of different molecules, Is there any method in laamps, for switching off the intramolecular lj interaction.

Thanks

Hi all,
I am trying to simulate a multiple polymer chain using harmonic bond
potential and lj potential , I want to switch off the LJ potential between
the intrachain beads, while not affecting the potential between the beads of
different molecules, Is there any method in laamps, for switching off the
intramolecular lj interaction.

try:

neigh_modify exclude molecule all

and check out the docs at:
http://lammps.sandia.gov/doc/neigh_modify.html

Wow, Axel, that's cool. (I did not know about that feature.)
I would worry that if you switch the interactions off between atoms in
the same molecule, they could pass through each other. If the
polymers are short and rigid, it does not matter.

In any case, I've attached a preliminary version of the code to for a
new pair style named
"lj/charmm/coul/charmm/inter"
We are using this pair style in several projects in our lab (and in
several upcoming moltemplate examples).

This pair style is (nearly) identical to "lj/charmm/coul/charmm".
The main new feature of this pair style is that it allows you to
select different Lennard-Jones parameters between atoms in the same or
different molecules. (The code looks complicated because it also has
several other features you probably don't care about, such as
repulsive mixing rules, and soft-core repulsion. This code works with
the 2012-7-1 version of lammps.)

To use the new pair style, copy the attached .cpp and.h files to your
LAMMPS "src" directory, recompile LAMMPS. A simple usage example is
attached (In two different formats. Run lammps using "lmp_binary -i
run.in.nvt") Some more detailed documentation is included below.

(To people browsing the mailing list archives: If the attachments to
this message become unavailable in the future, email me or check at
moltemplate.org for them.)

-- Documentation--

Here is a quick rough draft of the documentation for this pair style.

General Formula used:
U(r) = e * (Ca*K*(s/r)^12 + Cb*L*(s/r)^6 )

   (where "Ca" and "Cb" depend on coeff_style such as "eskl" or
"es4k4l" as shown below. "Ca" and "Cb" are usually +/- 4, 1, or 2)

Suppose you want to customise the interaction between atoms in
different molecules. You would use:

pair_style lj/charmm/coul/charmm/inter 7.5 8.0
pair_coeff 1 1 0.40 3.6 0 0 0.8 3.6

In this example, the epsilon value for atoms in the same molecule is
0.4. For atoms in different molecules it is 0.8. NOTE: If you want
to customise the interactions between atoms in different molecules,
then you must specify the 1-4 interactions as well for this pair
style, even if they are the same or zero.

Examples:

pair_style lj/charmm/coul/charmm/inter 7.5 8.0
pair_style lj/charmm/coul/charmm/inter 7.5 8.0 eskl maxmax
pair_style lj/charmm/coul/charmm/inter 7.5 8.0 es4k4l maxmax rsoftcore 1.0

pair_coeff 1 1 0.40 3.6
pair_coeff 1 1 0.40 3.6 1.0 -0.5
pair_coeff 1 1 0.40 3.6 1 -1 0.0 0.0 0 0 0.8 3.6 1 0

In the last example, the user also turned OFF the attractive part of
the interaction between atoms in different molecules (by switching the
"L" parameter to zero), while leaving the repulsive steric interaction
in place. (In your case, you might want to do the opposite.)

pair_lj_charmm_coul_charmm_inter.cpp (36.3 KB)

pair_lj_charmm_coul_charmm_inter.h (3.55 KB)

pair_lj_softcore2.cpp (9.06 KB)

pair_lj_softcore2.h (2.61 KB)

pair_lj_remix.cpp (15.9 KB)

pair_lj_remix.h (8.98 KB)

test_system_2bead.tar.gz (23.1 KB)

test_system_2bead_moltemplate_files.tar.gz (122 KB)