I think this is way too broad of a question (and therefore answer) to be particularly useful. It's also not clear what you're asking.
to explain the interaction between my aptamers and specific target to my audience
Are you just looking for a visualisation/animation? or do you want to run proper analyses?
Molecular Dynamics is a huge field in and of itself, so you've got a lot of learning ahead to achieve even basic proficiency.
I'm no expert, though I've done some courses so perhaps the following very general pointers might help:
Force Fields
MD simulations are all about force fields (essentially the equations that govern the behaviour of the system). If you want to study effects in solution for instance, force field choice can be very important - especially since we don't have a completely perfect model of water. If I recall, AMBER is one of the most popular. I can't offer you any more information than this though really, it's often a case of optimising your set up, and/or picking a forcefield etc. with some kind of justification as to why).
Building Models
You'll need 3D models (accurate ones) of all of your structures to feed in to the scenes you simulate. I believe Avogadro is very good for structure editing/building.
Docking/Interactions
You probably don't need to delve 'fully' in to the world of MD to achieve interaction/docking simulations. From what I know of this area, AutoDock Vina is a very popular tool for docking studies, and has a comparatively low barrier to entry I think. It's usually intended for small molecule ligand - protein docking, but might work for your aptamers.
Viz
If you are just looking to visualise the docking/interactions or to create an animation and not actually do 'rigorous analysis', you might want to look in to Molecular Flipbook (for very rough approximations) or UCSF Chimera/PyMOL
Thank you so much Healey for your response. I do not want to go too deep and just need visualization to show the interaction between my aptamers and the target molecules. Im not sure I want to go deep into all the math. I will see if I can make 3D of all my molecules and try one of the tools you provided. Its just an idea I am trying to build on and I feel for my up coming presentation, the audience would appreciate something like that. Thank you
I would start off with something like UCSF Chimera in that case. It has plugins for MD and Docking studies, whilst also being a 'self-contained' and fairly user-friendly package.
At the absolute simplest level, you can manipulate molecule models individually, so you could position them by hand if you just wanted to give your audience an idea without actually worrying about the 'science' too much.
Yes. This sounds exactly right. Thanks for understanding what Im trying to do. I will get back you on the results I get.
Thanks. I was able to get something to include in my slides and it really helped. I am now looking to try different studies on binding energies etc, I need this so that when i try to publish, I won't have much worries. Once again, Thanks
Ok, great. Remember to accept the answer if it solved your problem so that the thread doesn't stay marked as unanswered for others.