Units of measurement appear to be undefined in most parts of Ensembler, which may not be an issue for many applications.
However, I ran into inconveniences with unspecified and maybe inconsistent units when I was working on my reweighting project. Here, the temperature factors into some of the reweighting methods. This became apparent, when I used the LangevinIntegrator and afterwards a MetropolisMonteCarloIntegrator as samplers. While a temperature of 298 for the MetropolisMonteCarlo sampler produced a sensible distribution in my desired range, the LangevinIntegrator takes this temperature as an invitation to go fully of the charts, i. e. produces the distribution of what seems to be a much higher temperature than what the MetropolisMonteCarloIntegrator sampler interprets. Afterwards I struggle to interpret that and simulation outputs are hard to compare. That also makes it more difficult, for example, to combine Ensembler with the pyEMMA package.
I was wondering whether there was a way for units to be kept consistent across the package and at least to be documented.
Units of measurement appear to be undefined in most parts of Ensembler, which may not be an issue for many applications.
However, I ran into inconveniences with unspecified and maybe inconsistent units when I was working on my reweighting project. Here, the temperature factors into some of the reweighting methods. This became apparent, when I used the LangevinIntegrator and afterwards a MetropolisMonteCarloIntegrator as samplers. While a temperature of 298 for the MetropolisMonteCarlo sampler produced a sensible distribution in my desired range, the LangevinIntegrator takes this temperature as an invitation to go fully of the charts, i. e. produces the distribution of what seems to be a much higher temperature than what the MetropolisMonteCarloIntegrator sampler interprets. Afterwards I struggle to interpret that and simulation outputs are hard to compare. That also makes it more difficult, for example, to combine Ensembler with the pyEMMA package.
I was wondering whether there was a way for units to be kept consistent across the package and at least to be documented.