Hello,
I am trying to run Replica Exchange Umbrella Sampling along a reaction coordinate for a molecule. I have run both Umbrella sampling and REMD simulations separately before, but never together. My idea is to create replicas at different points on the reaction coordinate (i.e. chosen angle at 180,175,170..... etc) and run H-REMD (remd=3) with added harmonic restraints (like in umbrella sampling).
Is this the correct workflow?If not can anyone suggest me a tutorial or a paper that describes a clear workflow?
Also I normally use a WHAM to create the PMF of the umbrella sampling. But I don't think I can use it directly here. I would really appreciate it, if someone can give me an idea or suggest a tutorial about the post-processing and analysis of this kind of a simulation. Any response is highly appreciated. Thanks!
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Received on Thu Aug 29 2024 - 12:30:02 PDT
