For example i want to create atomic bond between nano-particle atoms and thiol molecule , also i want to model bbb with endothelial cells membrane and nano particles crossing through bbb that i have modeled.

Thanks

For example i want to create atomic bond between nano-particle atoms and thiol molecule , also i want to model bbb with endothelial cells membrane and nano particles crossing through bbb that i have modeled.

this is just a more detailed version of the same question, so i have to give you a more detailed version of the same answer.

you need to decide what kind of model you want to use, i.e. if this is an atomic level calculation, you need to decide, whether this is supposed to be a reactive model or a simple classical model or even a simplified coarse grained model and then you also need to figure out how and at what level of detail you want to model the cell membrane (and what size, and what parameterizations).

unless you can answer these questions, it is impossible to give an answer. you need to know the model, the parameters, the length scale, the time scale, how large/parallel a computer you have and then, maybe, somebody can point you into the right direction. but with just the phenomenological description of the application, and not knowing any details about models and parameters and length and time scale, it is impossible to give a meaningful answer to your questions.

axel.