Nucleic Acids: Difference between revisions

Nucleic Acids (view source)

Revision as of 11:49, 21 June 2021

587 bytes added , 21 June 2021

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Kulhanek

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@@ Line 8: / Line 8: @@
 | style="width: 5em;" | '''Type'''
 | '''Description'''
+|-
+| [[CV:NALBPP|NALBPP]]
+| local base-pair parameters
 |-
 | [[CV:NASBPP|NASBPP]]
-| simple base pair parameters
+| simple base-pair parameters
+|-
+| [[CV:NASBPPOLD|NASBPPOLD]]
+| simple base-pair parameters (OLD implementation)*
+|-
+| [[CV:NALSTP|NALSTP]]
+| local base-pair step parameters
+|-
+| [[CV:NASSTP|NASSTP]]
+| simple base-pair step parameters
+|-
+| [[CV:NASSTPOLD|NASSTPOLD]]
+| simple base-pair step parameters (OLD implementation)*
 |-
 | [[CV:NASBO|NASBO]]
-| simple base pair opening
+| simple base-pair opening
 |-
 | [[CV:NAPBO|NAPBO]]
-| primitive base pair opening
+| primitive base-pair opening
 |-
 | [[CV:NABEND|NABEND]]
@@ Line 22: / Line 37: @@
 |}
-== Simple Base Pair Parameters ==
+== Base-Pair Parameters ==
-All simple base pair parameters (''i.e.'', shear, stretch, stagger, buckle, propeller, opening) fully compatible with [https://x3dna.org/ 3DNA] are available via the [[CV:NASBPP|NASBPP]] collective variable. The collective variable [[CV:NASBPP|NASBO]] implements only the opening parameter and thus it should be a little bit computationally faster.
+PMFLib offers two variants of the base-pair parameters: local and simple. 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]], while the local version is provided [[CV:NASBPP|NASBPP]]. Both implementations are fully compatible with [https://x3dna.org/ 3DNA]. The collective variable [[CV:NASBO|NASBO]] implements simple Opening only and thus it should be a little bit computationally faster.
 [[File:SF3.png|center|600px]]
+== Base-Pair Step Parameters ==