Macrocycle Threading: Difference between revisions
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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> | |||