Is it possible to study the interaction of bio molecules with DEFECTIVE nano tubes with MD simulation by using GROMACS ? does is make a sense? any DFT or quantum calculation should be used or just MD calculation would be enough?
Well you can check what people do nowadays do with GROMACS.
If the dimensions are way larger than what you have in mind, you've got your answer. It really depends on the size of your molecules, but I would guess that in principle it should work.
What do you mean by defective? If I understand you correctly than you asking boundary conditions?
Best
Thank you stefan
I mean point defect, stone-wales defect,...is it possible to study it with MD properly?
Nanotube with 550 molecules+amino acid+solvent
Thank you so much
Thank you so much stephane, if nanotube waa not parametrized before, what should I do! It's ZnS nanotube.
i did this for ZnS nanosheet but I don't have parameters for its nanotube.
best regards
If no parameters are available, you have to either make one by your own, or use semi-empirical methods, such DFTB to do the simulation.
If you want to make your own parameters, you can take advantage of VMD force field toolkit (http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/). For DFTB, look at this website (https://www.dftb.org/).
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