Hello,
I was wondering if you could recommend any libraries for MD simulations of proteins with ligands in Python. They may also be accessible via bash.
They need to be available for free in any form and have completely open-sourced code.
Thanks
i am writing such a code from scratch, but it is not public (yet):
https://www.researchgate.net/project/MOLECULAR-DYNAMICS-SIMULATOR
Implemented: classical MD simulation, linear interaction energy (LIE), linear response approximation (LRA), and uncharging free energy perturbation (FEP). Non-periodic system only (sphere). No cutoff for nonbonded interactions.
Speed on my laptop: 2.5 to 5 times slower than equivalent code written in Fortran, with some room for improvement.
Dear Julian M. Kleber
MDAnalysis is what you are looking for.
It is an object-oriented Python library, and it also is open source.
Mehran Shahpari MDAnalysis is for analyzing the MD results, not for doing molecular dynamic simulations.
OpenMM should be a candidate instead
Dear Quyen V. Vu
MD in MDAnalysis stands for Molecular Dynamic!!
How come it is not able to do molecular dynamic simulations???
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