CV:NASBPP: Difference between revisions
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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:NASBPP]] | Navigation: [[Documentation]] / [[Collective Variables]] / [[Nucleic Acids]] / [[CV:NASBPP]] | ||
---- | ---- | ||
{{CVS}} | {{CVS}} | ||
===Definition=== | ===Definition=== | ||
The simple base pair parameters for the A:B base pair. | The simple base pair parameters for the A:B base pair fully compatible with the 3DNA definition. | ||
'''IMPORTANT:''' It is critical that the A and B bases are not separated during simulation due to imaging of DNA chains into the simulation box. Use ether topjoinmol from CATs or use correct value of iwrap in sander or pmemd. | '''IMPORTANT:''' It is critical that the A and B bases are not separated during simulation due to imaging of DNA chains into the simulation box. Use ether topjoinmol from CATs to merge both chains into a single molecule or use the correct value of iwrap in sander or pmemd. | ||
===Specification=== | ===Specification=== | ||
| Line 46: | Line 46: | ||
| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atom | | atom defining origin of y-axis | ||
|- | |- | ||
| '''group_d''' | | '''group_d''' | ||
| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atom | | atom defining end of y-axis | ||
|- | |- | ||
| '''parameter''' | | '''parameter''' | ||
| string | | string | ||
| | | | ||
| type of parameter: | | type of parameter (one of): shear, stretch, stagger, buckle, propeller, opening | ||
|- | |||
| skip_mass_test | |||
| logical | |||
| .false. | |||
| if .true. it does not control atom masses between the system and loaded reference structures | |||
|} | |} | ||
''Keys in bold are mandatory.'' | ''Keys in bold are mandatory.'' | ||
Latest revision as of 17:09, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NASBPP
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Definition
The simple base pair parameters for the A:B base pair fully compatible with the 3DNA definition.
IMPORTANT: It is critical that the A and B bases are not separated during simulation due to imaging of DNA chains into the simulation box. Use ether topjoinmol from CATs to merge both chains into a single molecule or use the correct value of iwrap in sander or pmemd.
Specification
Section name: NASBPP
| Key | Type | Default | Description |
| name | string | unique CV name | |
| group_a | mask | atoms for the base A ring | |
| reference_a | string | name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a | |
| group_b | mask | atoms for the base B ring | |
| reference_b | string | name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_b | |
| group_c | mask | atom defining origin of y-axis | |
| group_d | mask | atom defining end of y-axis | |
| parameter | string | type of parameter (one of): shear, stretch, stagger, buckle, propeller, opening | |
| skip_mass_test | logical | .false. | if .true. it does not control atom masses between the system and loaded reference structures |
Keys in bold are mandatory.