Problem with visualising dipoles in vmd

Dear lammps users and developers,

I am trying to visualize the trajectory consisting of dipoles. As instructed, I have used

global env

set env(LAMMPSDIPOLE2ATOMS) 0.5

Then to see it with cpk:

set sel1 [atomselect top {type 1}]

set sel2 [atomselect top {type 2}]

$sel2 set radius 0.4

$sel1 set radius 0.4

mol bondsrecalc top

set tip [atomselect top {index % 2 == 1}]

$tip set radius 0.6

$sel1 set name C

$sel2 set name N

$tip set name S

but Dipoles are not created properly. I am getting two different atoms as LAMMPSDIPOLES2ATOMS created. But they

are not joined. One this I want to ask, after LAMMPSDIPOLES2ATOMS can I expect two types of atoms in

the system? But, in my vmd it is always one type of atom. and after “$tip set name S” it is showing only C and S.

I am attaching the snapshots.

Can you please help me with this?

With regards,
Puja

initial.jpeg

final.jpeg

Dear lammps users and developers,

I am trying to visualize the trajectory consisting of dipoles. As
instructed, I have used

global env

set env(LAMMPSDIPOLE2ATOMS) 0.5

Then to see it with cpk:

set sel1 [atomselect top {type 1}]

set sel2 [atomselect top {type 2}]

$sel2 set radius 0.4

$sel1 set radius 0.4

mol bondsrecalc top

set tip [atomselect top {index % 2 == 1}]

$tip set radius 0.6

$sel1 set name C

$sel2 set name N

$tip set name S

but Dipoles are not created properly. I am getting two different atoms as
LAMMPSDIPOLES2ATOMS created. But they

are not joined.

​whether VMD will create a bond between those atoms depends on the
parameters you choose. if your radius is too small, or the dipole scaling
factor too large, the "mol bondsrecalc" command will not detect those as
(new) bonds.​

One this I want to ask, after LAMMPSDIPOLES2ATOMS can I expect two types
of atoms in

the system?

​the option will double the number of atoms, but those should be of the
same time.​

But, in my vmd it is always one type of atom. and after "$tip set name S"
it is showing only C and S.

I am attaching the snapshots.

​these are useless.

Can you please help me with this?

​this is really a VMD problem and not a LAMMPS problem. the only
LAMMPS-specific thing is that you are reading a file generated by LAMMPS.
the rest of the issue is VMD scripting. you should study the VMD user's
guide to learn more about VMD scripting.

axel.​