SiO2 Nanocluster formation inside a carbonate simulation box

Hello all,
I am attaching two images. One show’s the SiO2 cluster I am trying to make. and the other is the entire simulation box along with the cluster at the center. Its a amorphous alpha crystal of SiO2.
I ll give you a brief idea about what I am trying to do.
First there is a pure eutectic of Li2CO3 and K2CO3. Then we add 1% SiO2 nano particles in this pure mixture and see its effect on the structural changes.
I am not able to create the nanocluster in moltemplate. I do not have enough knowledge of how to make it.
Also, I wanted to mention the issue with the material studio. The data file that I get from msi2lmp tool has repeated molecules of Si and O. I mean in atom type there are 2 types of Si and O. With this all the other types, viz bond-coeffs, angle coeffs etc increases where as actually I should have only single types of Si and O, two band coeffs and two angle co-effs. I cannot just manually remove the extra ones, because its hard to figure out which refers to which molecule.
FYI, I am attaching the nanocluster data file which will make you understand my issue more clearly.
I really need help with all this. I ll be glad, if anyone could help me out.

sio2before.jpg

Impure Box.png

nano2 (3.41 KB)

For starters, why in the world would you keep record of all previous posting with issues completely alien to yours instead of just focusing on the one that concerns you?

As to making the nano-cluster, why not using the BKS potential for SiO2 so that you don’t have to worry about bonded and angular terms in the FF? The BKS potential has been tested quite a bit in the quartz system. However, keep in mind that unless you know the initial cluster structure from Xtalography, a few steps may be required to create the initial cluster shape (some annealing of the bulk lattice or some PES search to identify low-energy cluster configurations). The last comment applies to any FF you decide to use when modeling the cluster geometry.

Carlos

Hello all,
I am attaching two images. One show's the SiO2 cluster I am trying to make.
and the other is the entire simulation box along with the cluster at the
center. Its a amorphous alpha crystal of SiO2.
I ll give you a brief idea about what I am trying to do.
First there is a pure eutectic of Li2CO3 and K2CO3. Then we add 1% SiO2 nano
particles in this pure mixture and see its effect on the structural changes.
I am not able to create the nanocluster in moltemplate. I do not have
enough knowledge of how to make it.
Also, I wanted to mention the issue with the material studio. The data file
that I get from msi2lmp tool has repeated molecules of Si and O. I mean in
atom type there are 2 types of Si and O. With this all the other types, viz
bond-coeffs, angle coeffs etc increases where as actually I should have only
single types of Si and O, two band coeffs and two angle co-effs. I cannot
just manually remove the extra ones, because its hard to figure out which
refers to which molecule.
FYI, I am attaching the nanocluster data file which will make you
understand my issue more clearly.
I really need help with all this. I ll be glad, if anyone could help me
out.

the primary source of help with these kind of problems should be your
(senior) colleagues and your adviser. if you don't know how to set up
a system (regardless of what kind of tools you are using), you cannot
do any kind of serious simulations, so this should be part of your
basic training. pleading for help on a mailing list, is not likely to
provide much help unless you have a problem that is of specific
interest for somebody so that he is willing to do the work that is
ultimately your responsibility. but the usual case is that this is
only of interest for you (and/or your adviser) and somebody working on
something similar would likely be competing with you and thus even
less inclined to help you.

axel.