Dear lammps users,
I have simulated the adsorption between a nanoparticle and a protein. What I need is that the bond inside particles be free in both particles to break during the adsorption. I have used the pair style hybrid “tersoff lj/charmm/coul/long”. I also have used these below commannds.
Bond style harmonic
Angle style charmm
Dihedral style charmm
Improper style harmonic
Special bonds charmm
I have three questions.
- Are these commands lead to a well defined free adsorption and bonds can break and create truly during the adsorption as the response of pair styles and interactions?
- Do the special bonds charmm command lead to a permanent bond? As I know form the manual it is for permanent bonds, but what can I do to not force the system any bond but the strength bonds remain in force during the adsorption?
3.Creating and breaking the bonds is important for me. Do you have any advice for me to study them the best?
Best regards
Runak
You have some more fundamental problems than you think: adsorption is governed by nonbonded interactions. To form bonds you need a chemical reaction.
Before you continue with your simulations, I strongly suggest you read up on the modeling schemes and study the physics of adsorption in more detail. Also you should get tutoring from a person competent in these matters.
Thanks for you reply. I know adsorption is about nonbonded interactions. I just need to let the bonds to break. This is my only problem I think. I just wonder about the special bonds command that remains in force bonds in every situation. Do you think I should use it or not?
Best regards,
Sorry, but let me repeat: there are no bonds that should be broken, if your simulation setup is correct. Experience tells me that there is a finite chance that you may be seeing bonds being drawn by your visualization software, but those showing connections between your nanoparticle and your protein are most likely bogus.
The special_bonds command has nothing to do with adsorption. It manages how 1-2, 1-3, and 1-4 exclusions are handled and its setting depends on the force field you are using. You are obviously not trained to understand the kind of simulation setup you have and need to seek in-person tutoring/advising assistance.
Axel.
I think I didn’t explain well. I mean the bonds of each particle. For example the bonds of protein individually. I want to let them free if they break down as a result of clashes and adsorption. This sentence in special command means that for bonds that conforms and breaks repetitively don’t use the special commands.
" These weighting factors are NOT used by pair styles that compute many-body interactions, since the “bonds” that result from such interactions are not permanent, but are created and broken dynamically as atom conformations change"
There is nobody expert known unfortunately. I have to think and conclude myself.
Best regards,
I think I didn’t explain well. I mean the bonds of each particle. For example the bonds of protein individually. I want to let them free if they break down as a result of clashes and adsorption. This sentence in special command means that for bonds that conforms and breaks repetitively don’t use the special commands.
" These weighting factors are NOT used by pair styles that compute many-body interactions, since the “bonds” that result from such interactions are not permanent, but are created and broken dynamically as atom conformations change"
but you are using the CHARMM force field which definitely does not fall into the “manybody” category and requires very specific handling of the special_bonds setting (and the entire force field definition).
also, when people talk about adsorption, they usually refer to “physisorption”. what you are talking about would be called “chemisorption” or “catalysis” or “mechanochemistry”, i.e. processes that change the bonding pattern through causing chemical reactions. that you simply cannot model with a setup you have. most of the time, some level of quantum chemistry is needed to correctly represent the “active” parts of your system with sufficient accuracy.
so at the very least you need to use a specific force field that has been designed for studying chemical reactions. for which you usually also need specific parameterizations. there is for example ReaxFF, but I am not aware of any ReaxFF parameterization that is suitable to simulate full proteins with sufficient accuracy. and then again, proteins usually don’t easily undergo chemical reactions on the conditions where they are stable (which is a narrow window) and if you go beyond that you would “destroy” them anyway.
There is nobody expert known unfortunately. I have to think and conclude myself.
then you should be looking for a research topic for which you can find somebody with expertise to guide you.
in my personal opinion, starting research on a topic with so little initial knowledge and no expert guidance is doomed to fail or be a major waste of your time. you most certainly cannot learn what you need to learn from emails.
there is a lot more to doing good and meaningful MD simulations than having a few keywords adjusted, stitching together some geometry and force field setting and hoping for the best.
sorry for the bad news
axel.
That is because I want to explain which bonds in the protein breaks down after clashes. Do you know how can I visualise the protein bonds loss? Actually I can see them in VMD. But I want to have a diagram. Some softwares use the residue loss and creation but lammps don’t have this option.
Best regards,