From: Victor Zhao (yzhao01_at_g.harvard.edu)
Date: Mon Jan 25 2021 - 15:50:03 CST
I have been running replica exchange simulations (REST2). So far, I have focused on observables calculated on a per-frame basis and averaged to obtain ensemble values. But I am wondering, is it useful to calculate RMSF in a replica exchange simulation? Presumably you would do it over the replica index of interest (i.e. replica 0). But the trajectory at each replica setting includes exchanges between replicas. And yet I’ve read papers where RMSF is still calculated in replica exchange simulations.
Often, RMSF calculations presented in papers don’t appear to make a larger point beyond that different parts of the protein differ in flexibility, so I think RMSF calculations in a replica exchange simulation could serve the same purpose. But when it comes to the issue of comparing RMSF between different replica exchange simulations, wouldn’t different exchange acceptance rates prevent comparison between simulations? That is, suppose one simulation has a 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate of 0.25. In this case, the average time between exchanges would be different, which could affect RMSF. I am wondering what the experts on this list think.
PhD Candidate, Chemistry
Shakhnovich Lab, Harvard University
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