Hi everyone
I need some help about clustsizing in course grained MD simulation. I am using martini methods CG simulation and want to do clustsizing analysis on my system composing of self-assembled peptides. What is the optimal cut off value for clustsizing?
Thank you in advance
Havva Mehralitabar
You can potentially find a useful value from a radial-pair-distribution function as obtainable in VMD f.i. There you would see peaks at corresponding distances, that you can assign to intramolecular and intermolecular (the latter is the one you're interested in). We have used a "h-bond" equivalent cutoff for CG being 5.9 in the past to analyze protein-protein interactions.
That depends on your system and the size of the clusters that you can see visually (or analyze the rdf, as Norman suggest). Nevertheless, it would be interesting to have an atomistic comparison or at least from a united atom approach, since the Martini force field has a slightly higher tendency to aggregate peptides, than what happens in atomistic systems.
I imagine that your system was validated with some kind of experimental data, or with some smaller atomistic system. But execute at least a pair of ns of the complete system at atomistic level, will allow to see if the aggregation in Martini is superior.
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