CV:NASBO: Difference between revisions
Jump to navigation
Jump to search
(Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NASBO ---- {{CVS}} ===Definition=== The simple base pair opening for th...") |
No edit summary |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 4: | Line 4: | ||
{{CVS}} | {{CVS}} | ||
===Definition=== | ===Definition=== | ||
The simple base pair opening for the A:B base pair. This is an earlier implementation providing only opening, full set of simple base pair parameters is availble via [[CV: | The simple base pair opening for the A:B base pair. This is an earlier implementation providing only opening, full set of simple base pair parameters is availble via [[CV:NASBPP]]. | ||
'''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 | '''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=== | ||
Section name: ''' | Section name: '''NASBO''' | ||
{| | {| | ||
| style="width: 5em;" | '''Key''' | | style="width: 5em;" | '''Key''' | ||
| Line 42: | Line 42: | ||
| | | | ||
| 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''' | | 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''' | ||
|- | |||
| 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 17:27, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NASBO
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Definition
The simple base pair opening for the A:B base pair. This is an earlier implementation providing only opening, full set of simple base pair parameters is availble via CV:NASBPP.
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: NASBO
| 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 | |
| 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.