بسم الله الرحمن الرحيم
*First, please see the attached article (especially the part of the
Dendrimer model and simulation).*
please note, that a) by posting this article in a public forum, you
probably violated the licensing/redistribution terms under which you got
access to it, and b) i have no time to learn, study and review your
research. that is your job or something you need to discuss with your
adviser. i can tell you what i know to be incorrect or unusual. it is
ultimately your choice whether you stick with your settings or change them,
and it is going to be ultimately you that has to justify your choices when
you present your work.
*Second, the geometry should be a 3-D shape as in the article.*
it *very* obviously is not. just visualize it and look at the data file,
it is *obvious* to see, that there are many lines with the exact same
this is easily proven by adding the following command to your input:
delete_atoms overlap 0.01 all all
this will delete all atoms that have a distance of less than 0.01 \AA.
you'll see in the output that this deletes the number of atoms that i
claimed are redundant.
* The article method has no simulation boundaries, so no periodic bc, but I
chose this as a test.*
as mentioned before, if you do not want periodic interactions, don't use
periodic boundaries. shrinkwrap boundaries in LAMMPS are specifically
designed to set this up in the most effective way.
* The coul/debye potential in the article has no cutoff radius, so I chose
this cutoff which is equal to the length of the box of simulation.*
that makes no sense at all. just make some simple back-of-the-envelope
considerations: a) if you don't want interactions with periodic images of
your base molecule, your cutoff *MUST NOT* be longer than *HALF* the
shortest end-to-end length of your box. it is a *RADIUS*. b) however, if
you do want all interactions *within* your molecule, your cutoff needs to
be *at most* the maximum possible *extent of your molecule*.
* As for morse potential I chose the same cutoff as in the article. I
chose lj/coul 1.0 1.0 1.0 for special bond because I need to calculate all
interaction as in this article.*
* I chose the dielectric constant of the water which is the implicit
solvent and coul/debye for pair style as in the article.*
this makes no sense at all. this way you are include the screening effect
from the solvent *TWICE*.
* The choice of nsq came from a problem faced and this choice solved it,
but I made some changes so I think the default one will work fine now. (I
forgot return it to default one).*
this is a very bad approach to problem solving. you cannot just change
options without understanding what they do until your input runs. what if
it will run only for the wrong reasons? and thus result in a bogus
trajectories. please keep in mind, that a input that does not crash is a
necessary condition for a correct simulation, but not a sufficient one.
*I hope that I help you guess the situation.*
i have summarized what i think. it is now your job to turn this into a
meaningful simulation. it looks to me, you should seek some proper tutoring
from a local person, that has experience in MD simulations and statistical
mechanics. if you struggle as much with such basic issues, you will be in
deep trouble, if you actually move on to something more complex.