We have found a troubling beaviour when running PT-WTE simulations: despite using identical system configurations, force fields, and biasing parameters, the exchange probabilities between replicas differ dramatically between the two GROMACS versions:
Exchange Probabilities (Biasing Phase)
-
GROMACS 2023:
Average exchange probability: 0.070 ± 0.010
Range: 0.05 - 0.09
All 30 inter-replica exchanges show consistently low acceptance rates
-
GROMACS 2024.3:
Average exchange probability: 0.314 ± 0.044
Range: 0.22 - 0.38
All 30 inter-replica exchanges show consistently high acceptance rates
Overall increase: ~4.5x increase in average exchange probability when using GROMACS 2024.3
This plot shows the exchange probabilities between 31 replicas:
The energy distributions are also different between the two gromacs versions, but surprisingly gromacs 2023 produces larger fluctuations than 2024:
All the files needed to reproduce the simulations are available in this Zenodo repository: https://doi.org/10.5281/zenodo.19203432.
The outputs of the 2023 and 2024 versions are also there, together with a jupyter notebook with more analysis and plots.
We believe that this issue is related to this one.
We have found a troubling beaviour when running PT-WTE simulations: despite using identical system configurations, force fields, and biasing parameters, the exchange probabilities between replicas differ dramatically between the two GROMACS versions:
Exchange Probabilities (Biasing Phase)
GROMACS 2023:
Average exchange probability: 0.070 ± 0.010
Range: 0.05 - 0.09
All 30 inter-replica exchanges show consistently low acceptance rates
GROMACS 2024.3:
Average exchange probability: 0.314 ± 0.044
Range: 0.22 - 0.38
All 30 inter-replica exchanges show consistently high acceptance rates
Overall increase: ~4.5x increase in average exchange probability when using GROMACS 2024.3
This plot shows the exchange probabilities between 31 replicas:
The energy distributions are also different between the two gromacs versions, but surprisingly gromacs 2023 produces larger fluctuations than 2024:
All the files needed to reproduce the simulations are available in this Zenodo repository: https://doi.org/10.5281/zenodo.19203432.
The outputs of the 2023 and 2024 versions are also there, together with a jupyter notebook with more analysis and plots.
We believe that this issue is related to this one.