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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…
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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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I'm interested in, after running a simulation, generating the energies at a number of new energy functions given the configurations I sampled. openmmtools handles running lots of new alchemical stat…
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I am working on REMD . I set up the simulation using the worked out example proposed in link : [REMD Openmmtools](https://openmmtools.readthedocs.io/en/0.18.1/api/generated/openmmtools.multistate.Repl…
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I tested out dtram.py for long MD data at different thermodynamic states and it works very well. May I ask how to apply dtram.py to REMD data since the input simulation files have no way to tell the c…
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Hi, I'm interested in analysing the nc file generated by the openmmtools outside the openmmtools.
I noted that I could extract the potential array but I cannot extract the current lambda (e.g. `ster…
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Formulas for the meta-stable states just inside the vapor dome are provided in [IAPWS R7-97(2012)](http://www.iapws.org/relguide/IF97-Rev.html), the "_Revised Release on the IAPWS Industrial Formulati…