CV:NALSTP
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Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NALSTP
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Definition
The local base-pair step parameters for the A1:B1//A2:B2 base-pair step fully compatible with the 3DNA definition.
IMPORTANT: It is critical that the A1, A2, B1, and B2 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: NALSTP
Key | Type | Default | Description |
name | string | unique CV name | |
group_a | mask | atoms for the base A1 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 B1 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 | atoms for the base A2 ring | |
reference_c | 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_c | |
group_d | mask | atoms for the base B2 ring | |
reference_d | 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_d | |
parameter | string | type of parameter (one of): slide, shift, rise, tilt, roll, twist | |
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.