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Hi,
I would like to run REMD simulations using the `ReplicaExchangeSampler` from this library. I have quite a few replicas for which I would like to run simulations in parallel to reduce the overal…
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### Discussed in https://github.com/OpenModelica/OpenModelica/discussions/9320
Originally posted by **bilderbuchi** August 23, 2022
I recently found some puzzling behaviour when initialising a…
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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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*HIP-RA-X review from @kfbeckers via email on 2024-02-01:*
I reviewed the HIP-RA-X code on https://github.com/NREL/GEOPHIRES-X/blob/main/src/hip_ra_x/hip_ra_x.py and here are my comments and sugge…
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@andrrizzi
Could you take a look at the diagrammatic representation of YANK:
https://docs.google.com/drawings/d/1ds1eRqqCM9T_gEklX1a1f3I1ojx6RIk4JsgBNlDT4Bg/edit?usp=sharing
Feel free to add…
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Chapter 20, page 547: There is a string of problems here, centered around the concept of «thermal energy». This is in some ways related to issue #35.
~~In a previous chapter, «thermal energy» was d…
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For Ag-Cu binary phase diagram, there are only liquid phase and FCC solid solution phase. For Ag-Cu FCC solid solution phase(FCC_A1), "sublattice_model": [["AG", "CU"], ["VA"], "sublattice_site_ratios…
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This thread is to track the exact variables we want to isolate as we convert the restraints to the new [CustomCVForce](http://docs.openmm.org/development/api-python/generated/simtk.openmm.openmm.Custo…
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I am trying to use Fe2O3 in some of my thermodynamic calculations using 'thermo.chemical', but was unable to call it from the chemical database. I have used both methods shown below:
```
from thermo…
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Hi,
When i tried to the yank-example file. I got the following error.
2023-03-17 15:28:45,037: Running _compute_replica_energies serially.
Traceback (most recent call last):
File "/home/medici…