Modelling temperature dependent RNA structures

[Anonymous]

Hi to all,

I am really new to rosetta. I am using rna_denovo to generate 3D structures of RNA. I believe the default tempertaure used for modelling is 300K. I want to know if we can set our own temperature  for modelling RNA ? I did saw the option of temperature in the -help, written as 2 in the settings option, but I am not sure how to use it. Can we just define the temperature that we want, after writing this option? I am not sure how to go about this.

Please let me know the best way to go about this. And many thanks.

[Anonymous]

Rosetta simulations of RNA structure are Monte Carlo simulations; the temperature parameter you’ve found is not a physiological temperature (as in molecular dynamics) but rather reflects how readily moves are accepted even if they make the energy worse.

I might suggest you change the temperature of your secondary structure prediction, and then use that higher or lower temperature secondary structure as an input to the algorithm

[Anonymous]

That make sense, I did not think about changing the temperature  during the secondary structure prediction. I will try that.  Many thanks for your help.

[Author]

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