Macrocycle Threading: Difference between revisions
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PMFLib offers two collective variables, [[CV:WORMPOS|WORMPOS]] and [[CV:WORMANG|WORMANG]], for the description of the mutual position of a macrocycle (host) and an axle (guest) in a complex. Their mathematical definition is rather intricate. Therefore, we will here provide only their setup and geometrical meaning. | PMFLib offers two collective variables, [[CV:WORMPOS|WORMPOS]] and [[CV:WORMANG|WORMANG]], for the description of the mutual position of a macrocycle (host) and an axle (guest) in a complex. Their mathematical definition is rather intricate. Therefore, we will here provide only their setup and geometrical meaning. | ||
[[File:Worm.png|center|600px]] | |||
The collective variable [[CV:WORMPOS|WORMPOS]] aims to determine the parametric position of the guest towards the host. The position is defined by the intersection between the guest worm-like representation and the plane representing the host. The guest can be discretized by control points corresponding to centers of masses (COMs) of selected guest fragments. The plane is obtained by the root-mean-square fit to selected atoms of the host. Since the guest can be naturally bent, there might be more intersections. Thus, the intersection is searched only within a selector zone represented by a sphere centered on the host COM. The parameters of the selector zone (seldist and steepness parameters) ensure that only the intersection occurring in the host cavity is considered. | The collective variable [[CV:WORMPOS|WORMPOS]] aims to determine the parametric position of the guest towards the host. The position is defined by the intersection between the guest worm-like representation and the plane representing the host. The guest can be discretized by control points corresponding to centers of masses (COMs) of selected guest fragments. The plane is obtained by the root-mean-square fit to selected atoms of the host. Since the guest can be naturally bent, there might be more intersections. Thus, the intersection is searched only within a selector zone represented by a sphere centered on the host COM. The parameters of the selector zone (seldist and steepness parameters) ensure that only the intersection occurring in the host cavity is considered. | ||
The supplementary collective variable [[CV:WORMANG|WORMANG]] is defined as an angle between the normal vector of the plane and a worm segment within the selector zone. | The supplementary collective variable [[CV:WORMANG|WORMANG]] is defined as an angle between the normal vector of the plane and a worm segment within the selector zone. | ||
===References=== | |||
* Kulkarni, S. G.; Jelinkova, K.; Necas, M.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Kulhanek, P.; Vicha, R. A Photochemical/Thermal Switch Based on 4,4 ’-Bis(Benzimidazolio)Stilbene: Synthesis and Supramolecular Properties. ''ChemPhysChem'' '''2020''', ''21 (18)'', 2084–2095. https://doi.org/10.1002/cphc.202000472. | |||
===Examples=== | |||
<pre> | |||
[WORMPOS] | |||
name tau | |||
nsegs 6 | |||
totlen 19.339 | |||
alpha_a 0.0000 | |||
alpha_b 0.1993 | |||
alpha_c 0.3983 | |||
alpha_d 0.6019 | |||
alpha_e 0.8009 | |||
alpha_f 1.0000 | |||
group_a :1-7 & (!@H=) | |||
x_direction :1@O4 | |||
y_direction :3@O4 | |||
seldist 1.968 | |||
steepness 2.334 | |||
segment_a :8@C4,C5,C6,C7,C8,C9 | |||
segment_b :8@C11 | |||
segment_c :8@C14,C16,C17 | |||
segment_d :8@C20,C21,C23 | |||
segment_e :8@C26 | |||
segment_f :8@C29,C30,C31,C32,C33,C34 | |||
[WORMANG] | |||
name chi | |||
nsegs 6 | |||
group_a :1-7 & (!@H=) | |||
x_direction :1@O4 | |||
y_direction :3@O4 | |||
seldist 1.968 | |||
steepness 2.334 | |||
wmode com | |||
segment_a :8@C4,C5,C6,C7,C8,C9 | |||
segment_b :8@C11 | |||
segment_c :8@C14,C16,C17 | |||
segment_d :8@C20,C21,C23 | |||
segment_e :8@C26 | |||
segment_f :8@C29,C30,C31,C32,C33,C34 | |||
</pre> | |||
Latest revision as of 13:39, 21 June 2021
Navigation: Documentation / Collective Variables / Macrocycle Threading
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Macrocycle Threading
PMFLib offers two collective variables, WORMPOS and WORMANG, for the description of the mutual position of a macrocycle (host) and an axle (guest) in a complex. Their mathematical definition is rather intricate. Therefore, we will here provide only their setup and geometrical meaning.
The collective variable WORMPOS aims to determine the parametric position of the guest towards the host. The position is defined by the intersection between the guest worm-like representation and the plane representing the host. The guest can be discretized by control points corresponding to centers of masses (COMs) of selected guest fragments. The plane is obtained by the root-mean-square fit to selected atoms of the host. Since the guest can be naturally bent, there might be more intersections. Thus, the intersection is searched only within a selector zone represented by a sphere centered on the host COM. The parameters of the selector zone (seldist and steepness parameters) ensure that only the intersection occurring in the host cavity is considered.
The supplementary collective variable WORMANG is defined as an angle between the normal vector of the plane and a worm segment within the selector zone.
References
- Kulkarni, S. G.; Jelinkova, K.; Necas, M.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Kulhanek, P.; Vicha, R. A Photochemical/Thermal Switch Based on 4,4 ’-Bis(Benzimidazolio)Stilbene: Synthesis and Supramolecular Properties. ChemPhysChem 2020, 21 (18), 2084–2095. https://doi.org/10.1002/cphc.202000472.
Examples
[WORMPOS] name tau nsegs 6 totlen 19.339 alpha_a 0.0000 alpha_b 0.1993 alpha_c 0.3983 alpha_d 0.6019 alpha_e 0.8009 alpha_f 1.0000 group_a :1-7 & (!@H=) x_direction :1@O4 y_direction :3@O4 seldist 1.968 steepness 2.334 segment_a :8@C4,C5,C6,C7,C8,C9 segment_b :8@C11 segment_c :8@C14,C16,C17 segment_d :8@C20,C21,C23 segment_e :8@C26 segment_f :8@C29,C30,C31,C32,C33,C34 [WORMANG] name chi nsegs 6 group_a :1-7 & (!@H=) x_direction :1@O4 y_direction :3@O4 seldist 1.968 steepness 2.334 wmode com segment_a :8@C4,C5,C6,C7,C8,C9 segment_b :8@C11 segment_c :8@C14,C16,C17 segment_d :8@C20,C21,C23 segment_e :8@C26 segment_f :8@C29,C30,C31,C32,C33,C34