[lammps-users] deleting bonds

Dear all,

I have a specific question this time and would be grateful if somebody could possibly suggest what is going wrong:

I have 7 spools (polymer chains) in a sphere, and because the spools are separated and
bonds between them are deleted by a command "delete_bonds", and I have
also attempted to delete angles using a similar command, my simulation
can only function when the angle coefficient is<= 5 (should be higher ideally, when I have 1 spool, persistence length of 50 works well).
  Otherwise, LAMMPS is unhappy because atoms are lost in the process of simulation or FENE
bonds are too long. Do You think this is caused by the fact that the
interactions (angles) are not properly deleted?
Thank you very much in advance!
Anna
I use the following commands:

delete_bonds deletedgroup multi remove
delete_bonds deletedgroup angle remove

dear anna,

Dear all,

I have a specific question this time and would be grateful if somebody could possibly suggest what is going wrong:

I have 7 spools (polymer chains) in a sphere, and because the spools are separated and
bonds between them are deleted by a command "delete_bonds", and I have
also attempted to delete angles using a similar command, my simulation
can only function when the angle coefficient is<= 5 (should be higher ideally, when I have 1 spool, persistence length of 50 works well).

personally, i always prefer to do this kind of manipulations with
a tool before even starting a LAMMPS simulation, e.g. VMD.
there is much more control and flexibility.

Otherwise, LAMMPS is unhappy because atoms are lost in the process of simulation or FENE
bonds are too long. Do You think this is caused by the fact that the
interactions (angles) are not properly deleted?

there is a simple way to check this. use write_restart to write a restart
straight away and then convert the resulting restart with restart2data
into a data file and then check the result.

if you see a discrepancy between what should be there and what you
get instead, please provide an example so that it can be debugged.

axel.

Dear all,

I have a specific question this time and would be grateful if somebody could possibly suggest what is going wrong:

I have 7 spools (polymer chains) in a sphere, and because the spools are separated and
bonds between them are deleted by a command "delete_bonds", and I have
also attempted to delete angles using a similar command, my simulation
can only function when the angle coefficient is<= 5 (should be higher ideally, when I have 1 spool, persistence length of 50 works well).
Otherwise, LAMMPS is unhappy because atoms are lost in the process of simulation or FENE
bonds are too long. Do You think this is caused by the fact that the

one more comment.

if you have previously equilibrated the system before deleting the bonds,
then you have to factor in, that you are suddenly cutting away something
that had been in balance. if the bonds/angles that you delete had been under
considerable tension, then the system may "snap back" and thus can lead
to high atom velocities, long bonds and "lost" atoms. so it is advisable to
run some minimization steps, or otherwise "quench" the excess local potential
energy.

cheers,
    axel.

Dear Dr Axel,

Thank You very much for Your help again. I am slightly confused because now I have tried to do minimisation steps and (using the minimize command), however, I do not get the simulation to run for 25460 monomers (20 chains). Works fine without minimisation until 8911 monomers (7 chains), but when I increase the number of chains, I cannot get it to work…
Do You think that my code (please see below) has something catastrophically wrong with it or should I add something else to minimise the local potential energies?

Thank You very much for Your time again!

Sincerely Yours,
Anna

units lj
atom_style angle #with stiffness
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 10000 9_chain.dump.* id x y z ix iy iz
dump_modify 1 format "%d %.5f %.5f %.5f %d %d %d"
restart 1000 9_chain.restart
read_data 9_chains_new.dat
thermo 1000
thermo_style custom step temp epair emol press pxx pyy pzz pxy pxz pyz vol
angle_style cosine
angle_coeff 1 5
pair_style lj/cut 1.12246152962189
#pair_style soft 1.12246152962189
pair_modify shift yes
pair_coeff 1 1 1.0 1.0
bond_style fene
bond_coeff 1 30.0 1.0 15.0 1.0
group all type 1
group deletedgroup id 1273
group deletedgroup id 1274
group deletedgroup id 2546
group deletedgroup id 2547
group deletedgroup id 3819
group deletedgroup id 3820
group deletedgroup id 5092
group deletedgroup id 5093
group deletedgroup id 6365
group deletedgroup id 6366
group deletedgroup id 7638
group deletedgroup id 7639
group deletedgroup id 8911
group deletedgroup id 8912
group deletedgroup id 10184
group deletedgroup id 10185
group deletedgroup id 11457
group deletedgroup id 11458
group deletedgroup id 12730
group deletedgroup id 12731
group deletedgroup id 14003
group deletedgroup id 14004
group deletedgroup id 15276
group deletedgroup id 15277
group deletedgroup id 16549
group deletedgroup id 16550
group deletedgroup id 17822
group deletedgroup id 17823
group deletedgroup id 19095
group deletedgroup id 19096
group deletedgroup id 20368
group deletedgroup id 20369
group deletedgroup id 21641
group deletedgroup id 21642
group deletedgroup id 22914
group deletedgroup id 22915
group deletedgroup id 24187
group deletedgroup id 24188
delete_bonds deletedgroup multi remove
#delete_bonds deletedgroup angle remove
`

minimize 0.0 1.0e-8 1000 100000

``fix 1 all nve fix 2 all indent 10.0 sphere 0.0 0.0 0.0 40 units box side in fix 3 all langevin 1.0 1.0 2.0 424242 timestep 0.012 reset_timestep 0 run 100000`