Instabillity in large proteins

marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies

Apache License 2.0

84 stars 37 forks source link

Instabillity in large proteins #557

Open fgrunewald opened 8 months ago

fgrunewald commented 8 months ago

Instead of removing these bonds we should replace them with #ifdef flexibles. At the moment proteins that are a little off in backbone positions are nearly impossible to run.

https://github.com/marrink-lab/vermouth-martinize/blob/1593bf140277c85193cf22c5e9ac05222fd590c7/vermouth/data/force_fields/martini3001/aminoacids.ff#L1000-L1010