meld.system.patchers.rdc_alignment.add_rdc_alignment

meld.system.patchers.rdc_alignment.add_rdc_alignment(spec, num_alignments, alignment_mass=1000.0, scale_factor=0.0001)[source]

Add RDC alignments to the system

Parameters

  • spec (SystemSpec) – system specification to modify

  • num_alignments (int) – number of alignments to add

  • alignment_step_size – step size for alignment tensor update

  • scale_factor (float) – scale factor for the alignment tensor

Return type

SystemSpec

Returns

the modified system specification

Note

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

Note

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.

Note

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.