lucastepper / memtools Goto Github PK

Python 3 tool suite for the computation of memory kernels from time series

Please read (and cite) the following reference, where the details of the algorithm are explained.

J. O. Daldrop, J. Kappler, F. N. Brünig, and R. R. Netz, Butane dihedral angle dynamics in water is dominated by internal friction, Proc. Natl. Acad. Sci. U. S. A. 115, 5169 (2018). DOI: 10.1073/pnas.1722327115u

Run

pip install .

to install, and see example/example.ipynb to get started. Also have a look at the documentation and at the main class Igle, which is defined in memtools/igle.py.

Here, we have adapted the memtools repository slightly for out upcomming paper:

C. Ayaz, L. Tepper, F. N. Brünig, J. Kappler, J. O. Daldrop, R. R. Netz Non-Markovian Modeling of Protein Folding PNAS, in press

We introduced a new extraction method, see example notebook.