CV:NASBO: Difference between revisions
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{{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''' | ||
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| | | | ||
| 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.'' | ||