Molecular Dynamics vs Rigid Body Dynamics

[alpha_wolf]

How different/similar is molecular dynamics from rigid body dynamics? Could I use RBD software such as ODE to simulate MD? What assumptions/modifications would I need to make for this to work (e.g. treat atoms as rigid spheres connected through some special type of joints)?

 

[baffledMatt]

If all you want to do is simulate molecules as spheres connected together by rods (I assume that's what you are thinking about) then there are some clever ways to get MD alone to do it. I think it's covered in D C Rapaport's "The Art of Molecular Dynamics Simulation".

Matt

 

[Gokul43201]

Remember, bond angles are not perfectly "rigid". And rotations are often allowed in molecules lacking a large steric asymmetry.

 

[JohnDubYa]

I think many of the effects translate fairly well. Consider the coriolis effect in regards to molecular rotation, such as CO2. (Atkins discusses this phenomenon in his book on quantum chemistry.)

 

[alpha_wolf]

Remember, bond angles are not perfectly "rigid". And rotations are often allowed in molecules lacking a large steric asymmetry.

Yes, I know. Generally, I want to simulate all the major effects such as vibrations, rotations, etc. The reason I was asking about similarity to RBD, is because I am not familiar with any free software that is specifically designed for MD simulation. Come to think of it, I should do a search.