Nucleic Acids: Difference between revisions
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== Base-Pair Parameters == | == Base-Pair Parameters == | ||
PMFLib offers two variants of the base-pair parameters | PMFLib offers two variants of the base-pair parameters, local and simple, which both are fully compatible with [https://x3dna.org/ 3DNA]. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters, ''i.e.'', Shear, Stretch, Stagger, Buckle, Propeller, Opening. | ||
The simple version is provided by [[CV:NASBPP|NASBPP]]. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles. | The simple version is provided by [[CV:NASBPP|NASBPP]]. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles. | ||
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The local version is provided by [[CV:NALBPP|NALBPP]]. It uses a y-axis derived from the superimposed reference frames of two nucleobases and all parameters are calculated using the CEHS scheme. | The local version is provided by [[CV:NALBPP|NALBPP]]. It uses a y-axis derived from the superimposed reference frames of two nucleobases and all parameters are calculated using the CEHS scheme. | ||
The collective variable [[CV:NASBO|NASBO]] implements simple Opening only and thus it should be a little bit computationally faster than [[CV:NASBPP|NASBPP]]. | |||
[[File:SF3.png|center|600px]] | [[File:SF3.png|center|600px]] | ||
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== Base-Pair Step Parameters == | == Base-Pair Step Parameters == | ||
PMFLib offers two variants of the base-pair step parameters | PMFLib offers two variants of the base-pair step parameters, local and simple, which both are fully compatible with [https://x3dna.org/ 3DNA]. They differ in the definition of the y-axes, ''i.e.'', Shift, Slide, Rise, Tilt, Roll, Twist. | ||
The simple version is provided by [[CV:NASSTP|NASSTP]]. It uses explicitly defined y-axes of two base pairs and all parameters are calculated using the CEHS scheme. | The simple version is provided by [[CV:NASSTP|NASSTP]]. It uses explicitly defined y-axes of two base pairs and all parameters are calculated using the CEHS scheme. | ||