I have obtained a number of trajectories of various systems. I've observed that the solute tends to form some micro-clusters at certain concentrations, so I'd like to know how much time these clusters lives, a sort of a dimer lifetime function but for much more molecules than two (about 50-60). I've tried TRAVIS "aggregation functions" but it really does not help. Any idea?
Dear Alessandro,
the easiest way is to perform cluster analysis, for example using PCA-based clustering (but I don't claim it's best solution) and check the population of setten cluster. You can easily do it using for example CARMA tool from N. Glykos.
Good luck :)
Thank you, but I do not have the .PSF and .DCD files. I'm using AMBER11 with GAFF and I'm not simulating proteins but Ionic Liquid mixtures
I believe you can still apply some clusterization methods. It shouldn't be vary difficult to generate some kind of pair-relationship, for example. I haven't used AMBER output files so far, but for sure you could convert your trajectory to multiframe pdb or xyz and preprocess your output using geometrical criteria in python.
What have you tried so far?
Yes, I have converted the AMBER output in an xyz trajectory so that I've processed it with TRAVIS. If you don't know it, is a powerful trajectory analyzer that perform various kind of observations. Among them there are, as I said, the "aggregation functions" that compute the lifetime of a dimer that satisfy certain conditions od distance and/or angle. Nevertheless it is a powerful analysis, it isn't what I need
So the next question would be: is it possible to describe what you need in any form of equation or equations set?
And in addition: are you keen on any programming language?
- Badges
- Science topic
- Similar topics
- Chemistry
- Biochemistry
- Biomolecules