CV:NAPBO: Difference between revisions

CV:NAPBO (view source)

333 bytes removed , 12 February 2019

no edit summary

276

edits

Revision as of 17:15, 12 February 2019 (view source) Kulhanek (talk \| contribs) (Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NAPBO ---- {{CVS}} ===Definition=== Primitive definition of base pair o...")		Latest revision as of 17:17, 12 February 2019 (view source) Kulhanek (talk \| contribs) No edit summary
Line 6:		Line 6:
	Primitive definition of base pair opening for the A:B base pair defined as a dihedral angle between three vectors: base A vector (C and D points), helical axis vector (A and B points), and base B vector (E and F points). This CV should provide the same value as [[CV:DIH2]] but with the different order of atom groups.		Primitive definition of base pair opening for the A:B base pair defined as a dihedral angle between three vectors: base A vector (C and D points), helical axis vector (A and B points), and base B vector (E and F points). This CV should provide the same value as [[CV:DIH2]] but with the different order of atom groups.

	'''~~PBC note~~:''' ~~The minimum-image convention~~ is applied to vectors \|AB\|, \|CD\|, and \|EF\| only if the [[General setup\|fenable_pbc]] option is activated. The convention is not used to calculate the center of mass. It is therefore required that atoms within a group are either covalently bound or are part of complex that will not ~~be separated or reimaged during a simulation~~.		'''NOTE:''' This CV is not well tested.