Hi,
I am using martini force field and Coarse-Grained simulations to calculate the salvation energy of alanine in water in the form of decoupling. I have previously followed Justin Lemkul's tutorial on free energy calculations and trying to implement the same method with coarse grained simulations but I am getting a positive value in the case of coarse-grained simulations. Which I think I is unlikely. I have made changes in some of the parameters in order to make it compatible with coarse grained simulations. I am attaching my mdp file for production run. If someone can help finding the problem. I will be grateful.
Thanks,
Just some thoughts:
1) Alanine isn't actually very soluble, solvation energy will be relatively small. If you have uncapped termini then it should definitely be negative, but I'm not sure martini even has special bead types for termini.
2) One residue? With Martini? This is basically a single bead, CG forcefields like martini are for studying collective behaviour of many residues. My analogy is that you can treat a million water molecules as LJ spheres, but you can't usefully treat three water molecules as LJ spheres.
3) Perturbing dialanine to nothing is a pretty standard example for atomistic calculations. Try one one of the many worked examples for atomistic dialanine that are out there and then see if you still want to move to CG monoalanine once you have that sorted.
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