Problem while varying the size of the particle

Dear LAMMPS Users,
I'm using atom_style "Bond" and Units "lj" in my simulation. In the
system, I have polymers and tracers. Polymer beads are connected through
FENE potential. In first case the polymer beads and the tracers have the
same diameter (sigma_P = Sigma_T) of sigma=1.0 and having lj repulsive
(WCA) interaction between two tracers and between two polymer beads itself
using r_cut=1.12 and the interaction between tracers and polymer beads is
set to be lj attractive using r_cut=2.5. Then I have tried to change the
size of the tracers by changing the sigma and r_cut in such a way that if
my sigma_T=5 then my r_cut=1.12*sigma(1.12*5=5.50) for repulsive
interaction between tracers and the attractive interaction between tracers
and polymer beads is defined as sigma_P=1,
r_cut=2.5*sigma+delta_ij(2.5*1+2=4.5), where delta_ij =
{(sigma_T−sigma_P)/2} in order to account for the size asymmetry (ref.
DOI: 10.1021/acs.macromol.7b02441). So is my approach is fine to account
for the change in tracer dynamics due to change in tracer size?

The usual trend in MSD is that when the size of the tracer is increased
then the diffusion of tracer become slower compare to the small tracers.
But in the above case when I am plotting the MSD the trend is reversed. So
am I missing something in my model which can cause this...

Thanks in advance

-Praveen

Dear LAMMPS Users,
I'm using atom_style "Bond" and Units "lj" in my simulation. In the
system, I have polymers and tracers. Polymer beads are connected through
FENE potential. In first case the polymer beads and the tracers have the
same diameter (sigma_P = Sigma_T) of sigma=1.0 and having lj repulsive
(WCA) interaction between two tracers and between two polymer beads itself
using r_cut=1.12 and the interaction between tracers and polymer beads is
set to be lj attractive using r_cut=2.5. Then I have tried to change the
size of the tracers by changing the sigma and r_cut in such a way that if
my sigma_T=5 then my r_cut=1.12*sigma(1.12*5=5.50) for repulsive
interaction between tracers and the attractive interaction between tracers
and polymer beads is defined as sigma_P=1,
r_cut=2.5*sigma+delta_ij(2.5*1+2=4.5), where delta_ij =
{(sigma_T−sigma_P)/2} in order to account for the size asymmetry (ref.
DOI: 10.1021/acs.macromol.7b02441). So is my approach is fine to account
for the change in tracer dynamics due to change in tracer size?

The usual trend in MSD is that when the size of the tracer is increased
then the diffusion of tracer become slower compare to the small tracers.
But in the above case when I am plotting the MSD the trend is reversed. So
am I missing something in my model which can cause this...

you change the effective size with changing sigma. what about the mass?

axel.

Thank you.
I have performed the simulation in three conditions
(i) Initially, I have varied the sigma by keeping mass constant
(ii) next, the mass is varied by keeping sigma constant
(iii) finally I have varied both mass and sigma simultaneously

the first case already discussed in previous mail. In second case the msd
shows a slower diffusion for higher mass particle. But when I used the
third case the MSD shows reverse trend as compared to second case. So My
query is to change the size of the particle and to see its effect in the
simulation which parameters are I suppose to change? Just mass and sigma
one at a time or both simultaneously...

Thank you.
I have performed the simulation in three conditions
(i) Initially, I have varied the sigma by keeping mass constant
(ii) next, the mass is varied by keeping sigma constant
(iii) finally I have varied both mass and sigma simultaneously

how did you change the mass? i assume, that you want to model finite
size particles of the same material, i.e. the same density. have you
taken that into account?

the first case already discussed in previous mail. In second case the msd
shows a slower diffusion for higher mass particle. But when I used the
third case the MSD shows reverse trend as compared to second case. So My
query is to change the size of the particle and to see its effect in the
simulation which parameters are I suppose to change? Just mass and sigma
one at a time or both simultaneously...

sorry, but what you are asking about is not about LAMMPS but what kind
of model you are simulating and thus it is off-topic for this mailing
list.
that is a discussion that you should have with your adviser/supervisor
or colleagues. i don't have the time to fill in for them and advise
you on how to do meaningful research. i will not further comment on
this topic.

axel.

how did you change the mass? i assume, that you want to model finite
size particles of the same material, i.e. the same density. have you
taken that into account?

Initially, I have kept the mass as constant. Because I'm using atom_style
'Bond', that means we are dealing with point particles. So, I have varied
the sigma to account for change in the size but the change is not
reflected in simulations.
So, my question is how can i vary the size of particles when i'm using
atom_style 'bond' and how can i set the lj interaction (repulsive as well
as attractive) between them.

You did not answer my question, and I already answered yours.

Axel