Body: <p>In the <a href="https://www.tbi.univie.ac.at/RNA/tutorial/" rel="nofollow noreferrer">tutorial</a> of RNAfold it states,  </p>
  
  <p><code>RNAfold</code> reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in dot-bracket notation and its free energy to stdout.   </p>
  
  <p>In the example using the <code>-p --MEA</code> options, the </p>
  
  <ul>
  <li><strong>MFE = -5.00</strong> and the </li>
  <li><strong>ensemble Free Energy = -5.72</strong>. </li>
  </ul>
  
  <p>How can the free energy of the ensemble be lower than the minimum free energy?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-15T18:49:48.407Z
Comments.Text: @MichaelG. First, thank you. I read and learn from your comments and answers. Second: I tried with __CUACGGCGCGGCGC__ and I get: structure=.....(((...))) with -0.40 kcal/mol for the MFE and for the probab. representation of the ensemble, structu=.....,,,...)), with -1.10 kcal/mol. 
  I don't see pseudoknots there (should I?).
Comments.UserDisplayName: aerijman
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-22T16:26:50.533Z
Comments.Text: @MichaelG. 1st: Thank you! I feel honored!! 2nd: I think (and I could be wrong) that the only tool in Vienna that predicts pseudoknots is RNAPKplex (I am too far from being expert in the topic, I just googled it -couldn't find that info as fast in Vienna documentation-).  3rd: I am perplexed... I don't know how is this possible
Comments.UserDisplayName: aerijman
Tags: <rna><rna-structure><thermodynamics>
Title: How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA
ThreadText: # How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA
  
  (Asked by: username_0 on 2019-04-15)
  
  In the [tutorial](https://www.tbi.univie.ac.at/RNA/tutorial/) of RNAfold it states,
  
  `RNAfold` reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in dot-bracket notation and its free energy to stdout.
  
  In the example using the `-p --MEA` options, the
  
  * **MFE = -5.00** and the
  * **ensemble Free Energy = -5.72**.
  
  How can the free energy of the ensemble be lower than the minimum free energy?
  
  **Tags:** rna, rna-structure, thermodynamics
  
  > **Comments:**
  > **username_0**: @MichaelG. First, thank you. I read and learn from your comments and answers. Second: I tried with __CUACGGCGCGGCGC__ and I get: structure=.....(((...))) with -0.40 kcal/mol for the MFE and for the probab. representation of the ensemble, structu=.....,,,...)), with -1.10 kcal/mol.  I don't see pseudoknots there (should I?).  
  > **username_0**: @MichaelG. 1st: Thank you! I feel honored!! 2nd: I think (and I could be wrong) that the only tool in Vienna that predicts pseudoknots is RNAPKplex (I am too far from being expert in the topic, I just googled it -couldn't find that info as fast in Vienna documentation-).  3rd: I am perplexed... I don't know how is this possible  
  
  ---
  
  ## 0 answers
  
  