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Could be nice to have a graphic for comparing free energies, like this:
![image](https://user-images.githubusercontent.com/18635705/60629788-2ec08d80-9dc5-11e9-8d48-e621d9674354.png)
One thing tha…
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[Kollman, Peter A., Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, et al. “Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Me…
cramg updated
3 years ago
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In the case of starting vba with the correct parameters, I expect it to evaluate the model twice to compute two free energies, which will be close enough for the algorithm to stop.
In our current i…
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I am writing to seek your guidance regarding an issue I am facing with my Fermipy analysis. I use the gta.lightcurve command to obtain the 10-day binned gamma-ray light curve. A broken power law mo…
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I'm trying to debug an odd issue in the newest [Folding@home Sprint 5 dashboard](https://fah-public-data-covid19-moonshot-sprints.s3.us-east-2.amazonaws.com/dashboards/sprint-5/sprint-5-x12073-monomer…
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Following from discussion in #528 .
@jchodera proposes to add to analyze the decomposition into restraining, charging, and nonbonded free energies. This may require saving into the `nc` file the alch…
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I've been using YANK (0.23.4) to simulate a protein-ligand system (6069 atoms and water box and around 100 replicas for both the complex and solvent phase), on a system with two GTX 1080Ti GPUs, and s…
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Hello.
After downloading the dataset from the website https://figshare.com/articles/dataset/MPF_2021_2_8/19470599 and merging the two .p files, you are on the right track to prepare the data for mode…
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We would like to analyze a subset of the simulation (e.g. 1000 iterations out of 20000 iterations) in order to have the calculated free energies and the convergence plots.
Is there a way to automat…
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Here is the run I am trying to replicate. Below, are the inputs: the two sample sequences, and using DNA parameters.
![image](https://github.com/ViennaRNA/ViennaRNA/assets/124276755/d49417a6-734c-4…