CV:NASBPP

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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.