Rigid cluster decomposition (FIRST) parameters (defaults are recommended)

Energy cutoff for hydrogen bonds (in kcal/mol):
0.0 = all hydrogen bond constraints are considered, results in the most rigid network.
-10.0 = results in the most flexible network.

Between 0 and -10; values in the range between -0.2 to -2.0 are most meaningful.

Method for placing hydrophic constraints:
0: no hydrophobic constraints are included in the network.
1: the most hydrophobic constraints are included.
3: the least hydrophobic constraints are included.

Either 0, 1, 2 or 3.

Cutoff for including hydrophobic constraints (in Angstrom):
The larger the value is, the more hydrophobic constraints are included.
Between 0 and 0.5.


Normal mode (RCNMA) parameters (defaults are recommended)

Method to use:
RCNMA (Rigid cluster normal mode analysis) or ENM (Elastic network model, i.e., not considering any coarse-graining).

Distance cutoff for interactions between C-alpha atoms (in Angstrom):
Between 4 and 20.


Simulation (NMSim) parameters (defaults are recommended)

Number of trajectories:
Number of independent trajectories to generate.
Between 1 and 10 for large scale motions. 1 for others.

Number of simulation cycles (by recalculating normal modes):
Number of simulation cycles for calling RCNMA and NMSim subsequently.
Between 1 and 1000.

Number of NMSim cycles (using the same set of normal modes):
Between 1 and 10.

Frequency of writing out conformations:
Must NOT be greater than No. of NMSim cycles.
Between 1 and No. of NMSim cycles.

Randscaling (side-chain distortions):
Scaling factor for random component in side-chain directions.
Between 0 and 1.

Normal mode range (excluding zero frequency modes):
Normal mode range used for linear combination.
Between 1 and 50.

ROG-guided simulation type:
LC = Use linear combination of modes.
SB = Use the single best mode at each cycle.

ROG mode:
1 = guides the simulation towards the lowest ROG
2 = guides the simulation towards the highest ROG

Step size (in Angstrom):
Structure distortion along the normal mode directions in an NMSim cycle
Between 0 and 2.