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choderalab / feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
MIT License
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Implement ATM protocol #15

Open ijpulidos opened 7 months ago

ijpulidos commented 7 months ago

An implementation of a protocol that uses ATM is desired now that the new Openmm 8.1 release includes the ATMForce class for this specific purpose.

From @jchodera

Recent de Fabritiis ATM paper: https://doi.org/10.1021/acs.jcim.3c00178 I think they used a simplified version of restraints, but there are probably lots of other choices that work fine to align the molecules if needed. They also restrained the protein Ca atoms…