openmm-cookbook

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Coordinating OpenMM 8 tutorials

15

I am opening this thread to coordinate contributions to new tutorials for use in the OpenMM 8 paper. I'll keep this list updated with the discussion below: - [ ]...

jchodera

Add example illustrating use of collective variables

1

This suggestion comes from [twitter](https://twitter.com/roponpallab/status/1492912027676852231): 

jchodera

The notebook reads... restraint.addGlobalParameter('k', 100.0*kilojoules_per_mole/nanometer) should that be nm**2 instead? Thanks.

tonigi

We are looking for a tool to adjust side-chain collisions, without changing the position of main-chain atoms. This is needed to elaborate transition states among different conformations, therefore they need...

MonZop

Hello, hoping that it's not too late. I would like to suggest two tasks: -Setting up implicit solvent calculations with newer forcefields (i.e., ff14SB) - How to setup a replica...

DSKC44