PyDHAMed

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Bias potential matrix

50

Hi, I wanted to make sure that I understand the definition of the bias potential matrix correctly. Assuming an umbrella sampling experiment with 4 windows A, B, C, D and...

and-tos

To do: 1. Calculate rates trajectories where dynamics effectively evolve with the "true" dynamics (E.g., sets of short trajectories). 2. Calculate rates from biased dynamics (e.g., umbrella sampling)...

lukas-stelzl

- [ ] Implement uncertainty estimation - [ ] Benchmark for model system

lukas-stelzl

Add GLIC example

1

Add GLIC ion-permeation channel example Jupyter.

lukas-stelzl

- Transition counts and bias potentials of states not properly connect to the other states need to be excluded in a consistent fashion. - Will be important for DHAMed calculations...

lukas-stelzl

*Enable users to run binless WHAM in the same framework as DHAMed.

lukas-stelzl

Division by zero error

1

Dear Lukas I am trying to use PyDHAMed to compute a PMF for a small molecule crossing a membrane bilayer. I performed umbrella sampling in 1.5Å windows, spanning approx. 7nm...

WaDhondt

Generating Bias Matrix

1

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...

Cal-JWRW