Translocation code in LAMMPS

Sir,
I have obtained an input file (attached below) for the coordinates of polymer and an atom thick wall through moltemplate. I want to translocate the polymer through entropic force only, my question is that can we proceed further by writing codes in LAMMPS.
Thankyou
Andri Sharma

system1.data (3.39 KB)

Sir,
I have obtained an input file (attached below) for the coordinates of polymer and an atom thick wall through moltemplate.

you data file is incorrect (there is no Boundary1 section in LAMMPS)
and does not represent what you say it does.
have you tried to visualize it (after removing the bogus section)?

I want to translocate the polymer through entropic force only, my question is that can we proceed further by writing codes in LAMMPS.

this input is obviously not suitable, but there are many open
questions. should there be solvent? what kind of force field are you
planning to use? is this supported by LAMMPS? where would you find
suitable parameters? how would you equilibrate your system? is the
system of suitable size for your needs?

it looks like you have limited experience in MD. so here is some
unsolicited piece of advice from somebody who has seen a lot of people
struggling to get started because they tried to move too fast with too
little experience.

before continuing with setting up your research project, you should do
two things:

a) you need to do some literature research and review what kind of
simulations people have done on this topic and particularly whether it
is at all possible to simulate the entropy driven translocation at the
MD time scales and what kind of setups people were using for that, in
case people actually did this. i have a suspicion, that you may easily
run into time and size scale issues.

b) you need to learn simulation basics first and that can only be done
by simulating simpler systems and particularly by reproducing results
from tutorials/publications of simulations of simple polymer systems
*without* the translocation part. only after you are confident with
those kinds of simulations to reliably reproduce published results
from multiple research groups, you should proceed to study your
translocation project. by that time you will likely see immediately,
that you have to start over.

axel.