Can someone help me? The authors have extracted the conformations of different free energy states and compared the motions....I know it's a Free energy landscape and how to generate it through sham module of gromacs...but how to extract a conformation of particular energy state and how to know their timeframe in the trajectory?
Hi, I believe you need to extract the values of the corresponding PC1 and PC2. Subsequently, you should identify the frame that corresponds to those specific PC1 and PC2 values. This will give you an idea of the structure and the corresponding timeframe. You can refer to the following link for more information: http://www.strodel.de/index_files/lecture/html/analysis-10.html. This resource might provide you with some helpful insights.
Dear Abhik
Thank you for your reply....I found a comment where the author mentioned about a "PC vs time plot"....and he extracted the time range of particular PC coordinate form this plot...how to generate this plot?
Certainly, I can help you with that. To extract conformations of a particular energy state and determine their timeframe in a trajectory during a molecular dynamics (MD) simulation, you can follow these steps using GROMACS:
Remember to replace placeholders like your_trajectory_file.xtc, your_topology_file.tpr, lower_energy_bound, and upper_energy_bound with your specific file names and energy values. This process will allow you to extract and analyze conformations from specific energy states in your MD trajectory.
You can use the *.log file to extract the structures. This file contains all the data.
Hi Sanjay Kumar Paul the method below is well described on github, I think it can help you get your respects. It was made completely in Python and is very intuitive to understand!
Free Energy Landscape GitHub: https://github.com/sulfierry/free_energy_landscape
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA