- meld.system.patchers.rdc_alignment.add_rdc_alignment(spec, num_alignments, alignment_mass=1000.0, scale_factor=0.0001)
Add RDC alignments to the system
SystemSpec) – system specification to modify
int) – number of alignments to add
alignment_step_size – step size for alignment tensor update
float) – scale factor for the alignment tensor
- Return type
the modified system specification
The alignment tensor is encoded as five independent components, s1 through s5. The components can be combined to produce the aligmnet tensor as follows:
s1 - s2 s3 s4 s3 -s1 - s2 s5 s4 s5 2*s2
The values of the alignment tensor are typically on the order of 1e-4. Setting scale_factor=1e-4 serves to scale these values to be on the order of unity.
The mass of alignment tensor determines how quickly the alignment tensor responds to changes in the structure. A mass that is too small will result instability and crashes. A mass that is too large will lead to slow exploration as the alignment tensor will change very slowly. The default value of 1000.0 is a reasonable compromise that results in the alignment tensor changing over ~10-20 ps.