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Hello,
My understanding is that multimodal distributions are a common use case for parallel tempering. I'm assuming that this is true for this particular algorithm in Pigeons.jl. If so, it might be…
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# Description
I found that if I try to extend a finished parallel tempering simulation from the netcdf file, this error would be thrown:
```python
Traceback (most recent call last):
File "test_…
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Need to write some more extensive documentation.
- [x] General background
- [x] How tools fit together `assemble`, `call` etc.
- [ ] Use of more advanced features such as parallel tempering
- [x…
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**Submitting author:** @nikola-sur (Nikola Surjanovic)
**Repository:** https://github.com/Julia-Tempering/Pigeons-Paper
**Branch with paper.md** (empty if default branch):
**Version:**
**Editor:** @…
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Hello Everyone.
I tried setting up Temperature REMD simulations using two scripts. The first one is using ReplicaExchangeSampler
```
# Set up the temperature range for replicas
n_replicas = 20
mi…
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Things to consider:
- [ ] Do minibatch for burn-in?
- [ ] Implement minibatch option
- [ ] implement tempering option
- [ ] HMC (may be slow, but mixing will be faster)
- for Z, I'll need
…
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See https://dissem.in/p/107445189/distribution-of-sodium-cations-in-faujasite-type-zeolite-a-canonical-parallel-tempering-simulation-study which is missing a link to the HAL version of the same paper …
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DREAM has different final distributions than Parallel Tempering and MCMC. PT and MCMC match the result from Harmon et al 2017, but that's unsurprising given that the paper used an earlier version of …
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After reading the examples for calculating the PMF based on data by parallel-templering and umbrella-sampling simulations, i found that there is a discrepancy in calculating u_kln(reduced potential e…
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https://pubs.acs.org/doi/full/10.1021/ct0502864
kntkb updated
2 years ago