<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>

CC BY-SA 4.0
2019-04-15T18:49:48.407Z
@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?).
aerijman
CC BY-SA 4.0
2020-04-22T16:26:50.533Z
@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
aerijman
<rna><rna-structure><thermodynamics>
How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA
# 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  

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## 0 answers

