I have performed MD simulation using Desmond and converted the CMS file to DCD and PDB formats using VMD. Then, I carried out PCA analysis using Bio3D on the Galaxy server. Now, I would like to know how to calculate the energy and proceed with generating the free energy landscape (FEL) diagram using the Galaxy server.
Welcome @Srimari_S
We have a tutorial here with some of the basics you are working through. At the very end is an advanced workflow that is close to what you want to do. It is missing one of the data points you are asking about, but that could be added in! So, please consider the workflow a template that you can build on or use as an example not as a static artifact.
- Hands-on: Analysis of molecular dynamics simulations / Analysis of molecular dynamics simulations / Computational chemistry (scroll down to Further analysis)
- Workflows / Analysis of molecular dynamics simulations / Computational chemistry (simple + advanced)
From what I understand, you’ll need to pull in more raw data for the energy calculations. Or, maybe you have those already?
I’ve asked our computational chemistry experts to help out with what I may have missed or stated in an incomplete or wrong way. This is the chat, and feel free to join! 
You're invited to talk on Matrix
Hope this helps to get you oriented and we can certainly follow up more until you have an action plan. 
Dear Jennifer Hillman,
Thank you for your kind response.
I used a PDB file and DCD trajectory file as input for PCA analysis in Bio3D via Galaxy, which provided the raw data for PC1, PC2, and PC3.
However, for constructing a 3D Free Energy Landscape (FEL) diagram, I understand that energy values are required.
Could you please clarify where or how I can obtain these energy values from the PCA results and generate the FEL diagram using Galaxy.
Hi @Srimari_S
The underlying data comes from the simulation tool as another output which is why I included this in my other reply. The PCA results themselves do not include the data directly, or enough data to derive this other data from it alone. If I am wrong, someone can correct me!
So, if you are not sure where to get that data from the files generated by the tool you used, this forum is not be the best resource for general proteomics help for your other tool. Maybe review some published protocols? Or a scientific forum?
The alternative to use GROMACS in Galaxy. These have good documentation – scroll down to the bottom of the tool forms to get started.
Hi @Srimari_S
We don’t have a tool in Galaxy to do that. I guess you have some energies as output from Desmond. If you have an energy value per MD frame, and you can project the frame to a point in PCA space (I think the PCA ‘raw data’ output should have this information), you could perhaps generate a plot yourself.
Kind regards
Simon
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Thanks @simonbray and I’m going to add in a few more comments from the Comp-Chem matrix from another of our scientists.
as Simon suggested in the thread, we don’t have a tool to do that. However what she can do is generate a Radius of gyration using this tool Galaxy
and then an RMSD using this Bio3D tool toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3.4 or another GROMACS tool Galaxy?
Both of these would involve using her Desmond trajectory (perhaps some conversion of formats may be needed before going further). Once she has these two data sets, and her PDB file, she can use this tool outside of galaxy, to generate the free energy landscapes MD DaVis — MD DaVis 0.4.1 documentation
Hope this works out for you @Srimari_S 