Nucleic Acids: Difference between revisions
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| style="width: 5em;" | '''Type''' | | style="width: 5em;" | '''Type''' | ||
| '''Description''' | | '''Description''' | ||
|- | |||
| [[CV:NALBPP|NALBPP]] | |||
| local base-pair parameters | |||
|- | |- | ||
| [[CV:NASBPP|NASBPP]] | | [[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]] | | [[CV:NASBO|NASBO]] | ||
| simple base pair opening | | simple base-pair opening | ||
|- | |- | ||
| [[CV:NAPBO|NAPBO]] | | [[CV:NAPBO|NAPBO]] | ||
| primitive base pair opening | | primitive base-pair opening | ||
|- | |- | ||
| [[CV:NABEND|NABEND]] | | [[CV:NABEND|NABEND]] | ||
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|} | |} | ||
== | == Base-Pair Parameters == | ||
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]] | [[File:SF3.png|center|600px]] | ||
== Base-Pair Step Parameters == | |||