CV:NASSTPOLD

Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NASSTPOLD

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Definition

The simple base-pair step parameters for the A1:B1//A2:B2 base-pair step employing the OLD implementation. This implementation is NOT fully compatible with 3DNA because it uses the computational scheme borrowed from CV:NASBPP (dihedral angles), while CV:NASSTP uses the CEHS scheme. Values are similar, but larger deviations were observed for Tilt and Twist.

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: NASSTPOLD

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		atom defining the origin of the y-axis of the A1:B1 base pair
group_d	mask		atom defining the end of the y-axis of the A1:B1 base pair
group_e	mask		atoms for the base A2 ring
reference_e	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_e
group_f	mask		atoms for the base B2 ring
reference_f	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_f
group_g	mask		atom defining the origin of the y-axis of the A2:B2 base pair
group_h	mask		atom defining the end of the y-axis of the A2:B2 base pair
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.