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choderalab / yank-examples

Examples for use of YANK - getyank.org
MIT License
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softcore_beta and parameters in examples #34

Closed andrrizzi closed 8 years ago

andrrizzi commented 8 years ago

I've noticed that many example don't specify in the options softcore_beta: 0.0, should we add it in all of them? Does it make sense to change the default value of that parameter in AbsoluteAlchemicalFactory to be 0.0 instead of 1.0?

Also in many example the gaff or ff14sb forcefields are specified both in the molecule and in the system, but this is not necessary.

jchodera commented 8 years ago

I've noticed that many example don't specify in the options softcore_beta: 0.0, should we add it in all of them? Does it make sense to change the default value of that parameter in AbsoluteAlchemicalFactory to be 0.0 instead of 1.0?

Good idea---let's change the default in alchemy to disable alchemical softcore for charges (beta = 0.0) and remove that from the examples.

Also in many example the gaff or ff14sb forcefields are specified both in the molecule and in the system, but this is not necessary.

Let's fix that too!

jchodera commented 8 years ago

Let me know if you want me to make the change to alchemy.