The potential of mean force (PMF) can be used to calculate the free energy landscape with principal components. The PMF along the coordinate is computed from the average distribution function (see below equation).
∆G=-kB*T*lnρ(x,y)
Where T and kB is the temperature and Boltzmann constant, respectively. The x and y represent two principal components. In this tutorial, the molecular dynamics (MD) simulated results of glucagon receptor (GCGR) are selected for this example (Front Chem. 2019 Dec 17;7:851.) [1]. Here, MolAICal (https://doi.org/10.1093/bib/bbaa161) is employed for this tutorial.
2. Materials
2.1. Software requirement
1) MolAICal: https://molaical.github.io
2.2. Example files
1) All the necessary tutorial files are downloaded from:
https://github.com/MolAICal/tutorials/tree/master/007-PMF
For more detailed procedures, please go to https://molaical.github.io, and click the section named "Tutorials" in the left part of webpage. Once "Tutorials" open, you can freely find pdf file about PMF tutorial (see Figure 1):
You can repeat this tutorial according to the content of pdf file.
References
1 Bai, Q. et al. Conformation Transition of Intracellular Part of Glucagon Receptor in Complex With Agonist Glucagon by Conventional and Accelerated Molecular Dynamics Simulations. Front Chem 7, 851 (2019).
