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Hello.
I am trying to run some Temperature replica exchange simulations for small molecules. The relevant part of my script is as follows.
```
# Set up the temperature range for replicas
n_replica…
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Hi,
I would like to do a Hamiltonian REMD with custom defined states, with each state specified by a torchForce object with a different global parameter. But I am having trouble creating a Compound…
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![image](https://github.com/StructuralGenomicsConsortium/CNP16-iminoquinone-SarsRdRp-mechanstic-study/assets/147162201/e6026512-a8e3-4727-8db1-d1c955dba7aa)
In this project, we think we've seen an …
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@andrrizzi : Any idea what is going on here?
Let's check how many torsion terms there are:
```python
>>> from openmmtools import testsystems, states
>>> from simtk import unit, openmm
>>> tests…
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Tan Van Vu, Keiji Saito
> The thermodynamic and kinetic uncertainty relations indicate trade-offs between the relative fluctuation of observables and thermodynamic quantities such as dissipation an…
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I am attempting to run Replica Exchange for a system and would ideally like to access the context during the course of the simulation run in order to extract the forces. However I cannot seem to grab …
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Hello,
I have been using the minimize function in ReplicaExchangeSampler to minimize a set of replicas in different alchemical states like this:
_lsd_move = openmmtools.mcmc.LangevinSplittingDyn…
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@dominicrufa and I were trying to run repex on the endstates of a capped amino acid transformation (ALA->THR) (using the new [RepartitionedHybridTopologyFactory in perses](https://github.com/choderal…
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I got an error message when testing the example in paralleltempering.py ([https://github.com/choderalab/openmmtools/blob/main/openmmtools/multistate/paralleltempering.py](url))
The error message is a…
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I tried to run the example ParallelTemperingSampler script from a previously generated OpenMM checkpoint file.
Unfortunately, I end up with following error:
"Exception: All sampler states must have…