Answers.Body: <p>You would need to calculate the free energy along a trajectory and the rmsd along that trajectory and then cross-correlate/eliminate variables.  There may be a utility which does this but I am not ware of it.
  <a href="https://manual.gromacs.org/current/user-guide/cmdline.html" rel="nofollow noreferrer">https://manual.gromacs.org/current/user-guide/cmdline.html</a>
  There are two utilities of interest for doing just that.  See gmx_energy and gmx-rmsd.  Then you can plot one against the other by elimination of the time/space variables. Check out other calculations you can do with GROMACS:
  <a href="https://manual.gromacs.org/current/user-guide/cmdline.html" rel="nofollow noreferrer">https://manual.gromacs.org/current/user-guide/cmdline.html</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-28T19:01:21.697Z
Answers.LastActivityDate: 2022-12-28T19:01:21.697Z
Answers.UserDisplayName: Guy Francis Mongelli
Body: <p>how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
  <a href="https://i.sstatic.net/0495U.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0495U.jpg" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-18T12:00:15.873Z
Comments.Text: I look at that graph and I note the high ∆G at 0 Ångström and wonder if the reference pose for the RMSD was not energy minimised correctly... so maybe not the best reference. http://prody.csb.pitt.edu/ is a helpful toolkit for this kind of analysis. Is Python an option and what is your reference? (If any user knowledgeable about peptides sees this please step in as I doubt I can help —NMR works by magic, right?)
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-18T14:06:30.250Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-18T19:42:57.650Z
Comments.Text: Thanks for the comment .. i'm trying to use the tool but couldn't .. in which part please i can plot RMSD with energy surface ?
Comments.UserDisplayName: sam
Tags: <proteins><gromacs><peptide-shaker>
Title: plot the relation between RMSD and free energy
ThreadText: # plot the relation between RMSD and free energy
  
  (Asked by: username_0 on 2022-02-18)
  
  how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
  [![enter image description here](https://i.sstatic.net/0495U.jpg)](https://i.sstatic.net/0495U.jpg)
  
  **Tags:** proteins, gromacs, peptide-shaker
  
  > **Comments:**
  > **username_1**: I look at that graph and I note the high ∆G at 0 Ångström and wonder if the reference pose for the RMSD was not energy minimised correctly... so maybe not the best reference. http://prody.csb.pitt.edu/ is a helpful toolkit for this kind of analysis. Is Python an option and what is your reference? (If any user knowledgeable about peptides sees this please step in as I doubt I can help —NMR works by magic, right?)  
  > **username_2**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_0**: Thanks for the comment .. i'm trying to use the tool but couldn't .. in which part please i can plot RMSD with energy surface ?  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2022-12-28. Score: 0
  
  You would need to calculate the free energy along a trajectory and the rmsd along that trajectory and then cross-correlate/eliminate variables. There may be a utility which does this but I am not ware of it.
  <https://manual.gromacs.org/current/user-guide/cmdline.html>
  There are two utilities of interest for doing just that. See gmx\_energy and gmx-rmsd. Then you can plot one against the other by elimination of the time/space variables. Check out other calculations you can do with GROMACS:
  <https://manual.gromacs.org/current/user-guide/cmdline.html>.
  
  
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