Is 100Ps Of Small Molecular Dynamics Run Is Valid Enough To Judge The Stability Of A Rna Molecule?

Question

[grosy]

Hello friends,

I don't highly sophisticated computational power to do a MD run in nanoseconds scale. So, i have done a molecular dynamics simulation for 100 ps through which i am able to see which molecule is stable enough and which is not.

But Can i say that 100 ps of small MD run is valid enough to see that the RNA structure i am simulating is stable enough?

Any advise or suggestion?

NOTE: the RNA molecule is 33 nucleotides length

Please help!

[Pappu]

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Answer 1

[João Rodrigues]

I would say that 100ps is definitely not enough for a RNA molecules of 33 bases. If you don't have access to a local server to run the MD, look for alternatives: WeNMR or Xsede. For more details, look for papers where they describe the simulation of RNA molecules and check their stability and see which parameters were used. This is also the best way of 'validating' your approach, knowing that it's not something you thought of out of the blue but something that others have also used and that passed peer-review.

Answer 2

[quentin.delettre]

I am not an expert but i would say 100ps is not enough. If you found a protocol in the litterature for the rna molecule you use or very similar, try to fit to it.

Also you can have a look to this tutorial for amber simulation, for example.