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This is meant as an umbrella issue for documenting the steps required to depreciate `VarInfo` in favour of `SimpleVarInfo`-equivalwent.
Some known items:
- [x] Lineralisation for `SimpleVarInf…
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Hello!
I was playing around with the parallelization of MLP-MDs in mlp-train.
I have used the mlptrain/sampling/tests/test_umbrella.py as a template for my tests. I have notinced that each window in…
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After reading the examples for calculating the PMF based on data by parallel-templering and umbrella-sampling simulations, i found that there is a discrepancy in calculating u_kln(reduced potential e…
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Hi,
I'm running through the full set of DA_paper examples from a successfully built mlptrain-ace environment. Here are my results so far:
- training/implicit worked marvelously. The calculation …
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In the umbrella_sampling.py when I try to run the following:
`fes.generate_fes(u_kn, chi_n, fes_type="histogram", histogram_parameters=histogram_parameters)
`
on my data, I get this error:
`Ke…
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I have alreadly applied `pymbar` to umbrella sampling data successfully. Now I'd like to compute the effective mass of CV at the transition state. A function `compute_expectations` under `MBAR` can g…
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Hey!
I divided my membrane into 60 bins and after I run umbrella sampling simulations using Gromacs, I have 60 different umbrella{i}_pullf.xvg and umbrella{i}_pullx.xvg (i= 0 to 50) files. Do I ne…
ghost updated
3 years ago
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I have performed an Umbrella Sampling analysis on a membrane system in gromacs. My collective variable is the distance of a small molecule from the center of a membrane. Using the pullf file generated…
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I have been doing several tests with ABF&ANN + Particle separation as CV, with different number of walkers distributed in different regions of the expected PMF landscape (I have previously got the PMF…