I have computed a representation of the free energy landscape (FEL) sampled by my trajectories of MD following the tutorial as attaching . I would like to know if there is one specific reason as to why they used the rmsd to the average structure?
Could someone suggest a good paper to analyze the results of the FEL?
http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
Dear Nubia,
the choice of so called reaction coordinate to generate and analyze any kind of free-energy related problem is in most cases pretty arbitrary, but in this case better choice would be probably dihedral PCA based FELs - there's a lot of papers which prove that this kind of conformational space probing leads to best results - they are pretty easy to find in google. RMSD here is just an example.
You should keep in mind that to calculate the free energy landscape from MD simulations related to any chosen reaction coordinate may need long time simulations or use of enhanced sampling techniques to accelerate MD simulations.
You can also have a look at this recent paper:
Miao, Nichols, McCammon, Phys Chem Chem Phys. 2014, 16:6398-406
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