Instabillity in large proteins

[fgrunewald]

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.

vermouth-martinize/vermouth/data/force_fields/martini3001/aminoacids.ff

Lines 1000 to 1010 in 1593bf1

	[ link ]
	resname $protein_resnames
	[ constraints ]
	#meta {"group": "Backbone bonds"}
	BB +BB 1 0.310
	[ !bonds ]
	BB +BB
	[ patterns ]
	BB {"cgsecstruct": "H|1|2|3"} +BB
	BB +BB {"cgsecstruct": "H|1|2|3"}