Problem in deleting overlapping polymer atoms and their entire chains using delete_atoms overlap in LAMMPS

[tami]

Hi everyone,

I have a simulation box filled with polymer molecules. However, I placed/fixed a ZnO nanoparticle at the center of the box, which overlaps with several polymer atoms. Naturally, when I run the simulation using this data file, the NPT run terminates. I suspect this is due to overlapping atomic coordinates.

Now, I want to remove the polymer atoms - and their entire corresponding polymer chain - if they overlap with the ZnO nanoparticle. Is there a LAMMPS command, such as delete_atoms, that can help with this? This would create a void in the polymer matrix for the ZnO nanoparticle (which is kept fixed at that position in the box) so that its atoms do not overlap with those of the polymer.
Additionally, I want to print out the polymer atoms that remain after removal and verify that the ZnO nanoparticle atoms are still intact by printing their atom indices. I want to understand what’s going wrong.

ERROR: Velocity command with no atoms existing (src/velocity.cpp:57)
Last command: velocity nanoparticle set 0.0 0.0 0.0

---

Below is my Lammps script
echo screen
variable dcdfreq index 500
variable outputname index step5_production_npt

units real
boundary p p p
newton off

pair_style lj/charmmfsw/coul/long 10 12
pair_modify mix arithmetic
kspace_style pppm 1e-6

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
improper_style harmonic
special_bonds charmm
timestep 1.0

=== Read initial data ===

read_data merged.data

=== Define ZnO nanoparticle group ===

group nanoparticle id 14289:14462

=== Define polymer group before deletion ===

group polymer subtract all nanoparticle

variable zno_before equal count(nanoparticle)
print “ZnO atom count before deletion: ${zno_before}”

variable polymer_before equal count(polymer)
print “Polymer atom count before deletion: ${polymer_before}”

=== Delete overlapping polymer atoms and their molecules ===

delete_atoms overlap 2.5 polymer nanoparticle mol yes

=== Redefine polymer group after deletion ===

group polymer subtract all nanoparticle

variable polymer_after equal count(polymer)
print “Polymer atom count after deletion: ${polymer_after}”

variable zno_check equal count(nanoparticle)
print “ZnO atom count after deletion: ${zno_check}”

=== Output groups for verification ===

group polymer_left union polymer
group zno_left union nanoparticle

dump dump_polymer polymer_left custom 1 polymer_left.dump id mol type x y z
dump dump_zno zno_left custom 1 zno_left.dump id mol type x y z

=== Neighbor and force settings ===

neighbor 2 bin
neigh_modify delay 5 every 1 check yes
comm_modify vel yes

=== Apply fixes ===

velocity nanoparticle set 0.0 0.0 0.0
fix freezeZnO nanoparticle setforce 0.0 0.0 0.0

velocity polymer create 500 12345 dist gaussian
fix 1 polymer npt temp 500 500 100.0 iso 1.0 1.0 1000.0

=== Output ===

thermo ${dcdfreq}
thermo_style custom step time xlo xhi ylo yhi zlo zhi etotal pe ke temp press ebond eangle edihed eimp evdwl ecoul elong temp vol
dump 1 all atom 100 step5_production_npt.lammpstrj
dump 7 all custom 1000 step5_production_npt.xyz id mol type x y z xu yu zu
dump_modify 7 sort id

run 400000

=== Save final output ===

write_dump all custom {outputname}.dump id type x y z vx vy vz ix iy iz write_data {outputname}.data

---

My input merged.data file is in the following format: it contains 94 polymer chains, each consisting of 152 atoms (corresponding to 10 monomers), with atom IDs ranging from 1 to 14,288. Atom IDs from 14,289 to 14,462 correspond to the ZnO nanoparticle atoms.

Atoms

       1           1           8 -0.27000000000000002        19.674173733527343        49.352861146467873        16.510434323073341     
       2           1           3   8.9999999999999997E-002   19.699819226427344        50.161802107967873        15.708286921073340     
       3           1           3   8.9999999999999997E-002   18.871962013827343        48.586732839067871        16.248055911973339     
       4           1           3   8.9999999999999997E-002   19.437190105227344        49.815609037867873        17.524461173973339     
       5           1           5 -0.10000000000000001        21.162531118327344        48.584779338767873        16.580801409573340     
       6           1           4  0.95999999999999996        21.130728204727344        47.564439013967871        17.925608866873340     
       7           1          10 -0.48999999999999999        20.811489601727345        48.316466442767869        19.101638965173340     
       8           1           9 -0.63000000000000000        21.361255338427341        46.355758414567873        17.914511984873339     
       9           1           8  -1.0000000000000000E-002   20.727895422127343        47.691409607167870        20.457747986873340     
      10           1           3   8.9999999999999997E-002   21.779368768727345        47.435173055767869        20.840942243473339     
      11           1           3   8.9999999999999997E-002   20.230666354927344        48.415315704167874        21.196930774973339     
      12           1           3   8.9999999999999997E-002   20.106042460827343        46.727155182367873        20.411126344873338     
      13           1           8 -0.27000000000000002        21.440079202427341        47.601058922667875        15.244064764273340     
      14           1           3   8.9999999999999997E-002   21.373752719627344        48.210561138567869        14.286441598873340     
      15           1           3   8.9999999999999997E-002   22.472547738727343        47.126745228067868        15.336962043673340     
      16           1           3   8.9999999999999997E-002   20.642451314227344        46.784232908567873        15.227309628873339     
      17           2           7 -0.17999999999999999        22.450417253327345        49.626608111867874        16.895569199373341     
      18           2           2   8.9999999999999997E-002   22.359280119527345        49.960300429567873        17.988808675873340     
      19           2           2   8.9999999999999997E-002   23.403642292027342        48.994989323867870        16.763757655173340     
      20           2           5 -0.10000000000000001        22.638663139527345        51.007629491367872        15.965023520873340     
      21           2           4  0.95999999999999996        21.526847115127346        52.183815471767872        16.409929305273341     
      22           2          10 -0.48999999999999999        20.868294078427343        51.850708632467871        17.632167493273339     
      23           2           9 -0.63000000000000000        21.303915798127342        53.207895125967873        15.760656617773339     

.
.
.
14288 10 3 8.9999999999999997E-002 52.869834549927347 23.968732724467870 59.978864738973343
14289 1 11 1.2170000000000001 35.250000000000000 33.876359447479246 34.600458110809328
14290 1 11 1.2170000000000001 35.250000000000000 32.000359447479248 37.200458110809329
14291 1 12 -1.2170000000000001 35.250000000000000 33.876359447479246 37.822458110809329
14292 1 11 1.2170000000000001 35.250000000000000 33.876359447479246 39.800458110809323
.
.
.
14460 1 11 1.2170000000000001 41.750000000000000 45.134359447479248 39.800458110809323
14461 1 12 -1.2170000000000001 41.750000000000000 43.258359447479251 40.422458110809330
14462 1 11 1.2170000000000001 41.750000000000000 43.258359447479251 42.400458110809325

[akohlmey]

@tami

I want to remove the polymer atoms - and their entire corresponding polymer chain - if they overlap with the ZnO nanoparticle. Is there a LAMMPS command, such as delete_atoms, that can help with this?

delete_atoms is the command.

@tami

I want to print out the polymer atoms that remain after removal and verify that the ZnO nanoparticle atoms are still intact by printing their atom indices.

You can just dump the coordinates and visualize them.

@tami

ERROR: Velocity command with no atoms existing (src/velocity.cpp:57)
Last command: velocity nanoparticle set 0.0 0.0 0.0

The error message is self-explanatory: there are no atoms in the “nanoparticle” group. Check your log file and input.

@tami

This would create a void in the polymer matrix for the ZnO nanoparticle

Another option to create a void would be using fix indent sphere with a variable radius. You can create and equal-style variable that uses the “ramp()” function to have a spherical indenter placed into your polymer that will slowly grow over time during a run. You will need to continue with the desired radius fixed for a while until there is sufficient space (and overestimate the radius somewhat). And then you could insert the nanoparticle.

@tami

Below is my Lammps script

This is badly formatted and near unreadable. Please see the “guidelines” post on how to properly format text files in the forum and also what other information you should provide.

@tami

My input merged.data file is in the following

Incomplete files are close to useless.

[tami]

Thanks, now I’m able to run the lammps script using NPT successfully.
In this case, what I can see is that the polymer matrix has shrunk in size inside the previously defined box. The figure is attached below. So, I tried to get the correct box dimensions using vmd, we loaded data file " topo readlammpsdata step4.0_minimization_shifted.data full "

1. Select all atoms

set sel [atomselect top all]

2. Get min and max coordinates of atoms

set minmax [measure minmax $sel]
set min [lindex $minmax 0]
set max [lindex $minmax 1]

3. Compute box lengths

set lx [expr {[lindex $max 0] - [lindex $min 0]}]
set ly [expr {[lindex $max 1] - [lindex $min 1]}]
set lz [expr {[lindex $max 2] - [lindex $min 2]}]

“68.53632354736328 68.14553833007813 69.75263214111328”

however in the figure you can see there is still an empty space in the box and the polymer matrix is residing along one side of the box. Pls help! Couldn’t understand what could be going wrong in correctly estimating the box size.

[akohlmey]

@tami

what I can see is that the polymer matrix has shrunk in size inside the previously defined box.

What do you mean by that? It is not at all clear what you have done and what you are looking at.

@tami

Couldn’t understand what could be going wrong in correctly estimating the box size.

What you did is not getting the box size, but rather determining the maximum extent of the atoms in each direction. That is quite a different thing, especially when you have “long” molecules. Anyway, this whole procedure makes no sense at all, after you have already equilibrated your system with fix npt.