004Z Hyperparameters

I will use this section to discuss the hyperparameters

ICM Monte Carlo

These parameters can seriously affect the behaviour of Monte Carlo. A recipe tree is provided to help selection.

• Acceptance Ratio

• temperature = 300 determines the acceptance ratio in Monte Carlo. Higher temperature increase acceptance ratio. It affect "heat" action below as "heat" doubles temperature. The temperature can be adjusted by a cosine schedule tempCycle = {10000.,600.,2.,0.} e.g. temperature amplitude (10000,600) cosine period is 2 times longer than MC calls, so it guarantee to fall to 600 at the end of the MC.

• Suggestion

• Not-difficult escape - temperature = 300;tempCycle = {310.,300.,2.,0.}
• Difficult escape - temperature = 600;tempCycle = {3000.,600.,2.,0.}

• Iteration

• mncallsMC = 1000 determines maximal number of function calls, including minimisation steps (capped by mncalls=100) and random steps (undetermined); mncallsMC is their sum thus would determine the number of random step performed.

• Note that the ICM Monte Carlo oscillates between minimization steps and random steps. The period of oscillation is determined by Actions below, but seldom by mncalls.
• Early exits possible, therefore maximum number.
• Suggestion

• <10 residues - mncallsMC = 100000
• >10 residues - mncallsMC = 5000000

• Discrete Conformer Stacks

• mnconf = 50 determines the maximum number of conformers allowable. After overflow, start replacing conformers with high energy

• Suggestion (Advisable not to change it)

• mnconf = mnvisits

• vicinity = 15.0 determines whether two conformers are considered within the same discrete stack conformation. e.g. a RMS difference = 3.0 could be consider no difference for discrete bins of 5.0; both conformers will be placed in the same stack. This parameter is linked to visitsAction.

• Suggestion (Advisable not to change it, unless a different comparison method e.g. angstrom rather than default degree is used.)

• vicinity = 15.0

• Scenario Controls

• Five types are available - "heat","stack-jump","random","cross","exit". They are actions to handle scenarios listed below (visitsAction, rejectAction, highEnergyAction)

• "heat" - Double temperature.
• "stackjump" - jump to adopt least visited conformation in the stack.
• "random" - randomize all free variables according to the mcJump parameter
• "exit" - exit the MC procedure
• "cross" - ???

• visitsAction = "heat" determines action when one discrete stack is overvisited i.e. mnvisits = 50 is reached. Note the stack is updated according to highEnergyAction if all/consecutive consequent visits results in higher energy. If "heat" does not help, it is valid to use "random"; both are heuristics.

• Suggestion

• <10 residues - mnvisits = 50
• >10 residues - mnvisits = 100
• Not-difficult escape - visitsAction = "heat"
• Difficult escape - visitsAction = "random"

• highEnergyAction = "stackjump" determines action taken when there is no change in stack for consecutive amount of accepted trials (mnhighEnergy = 50). The trials are accepted because they are downhill (even slightest), but the stack was not replaced as the accepted trials all have higher energy than the existing stack.

• Default action is "stackjump" i.e. jump to adopt the least visited conformer in stack in hope that the next random change will allow a better than current conformer such that the stack takes it in, but if the hope is dismissed, it will just waste mncallsMC (e.g. a wide area of high/low energy such that the random move won't escape the area).
• Suggestion

• Not-difficult escape - highEnergyAction = "stackjump"
• Difficult escape - highEnergyAction = "random"

• rejectAction = "heat" determines action taken when mnreject = 10 consecutive uphill is met. e.g. high energy or temperature too low. Advisable not to change it.

• Amplitude of Random Movements

• mcJump
• mcShake
• nLocalDeformVar = 10 determines number of phi psi torsion to be changed simultaneously. Note that ICM requires this number and the number of phi psi contained in selection to be >8.

• Computation Power

• nProc = 4 ICM seems to detect and use multiple processor in MC.