SIMONAPreprocessor
POEM++ Expert settings
Structure
D_POEM_ExpStruct.png


  • Set all dihedral angles to pi:
    makes the molecule be completely extended.
    XML-sample:
    1 <SetDihedralAbsolute weight="1.0">
    2  <dihedral_id>0</dihedral_id>
    3  <value>-3.14159265359</value>
    4 </SetDihedralAbsolute>
  • Use C_alpha model:
    Use only $ C_{\alpha}$-atoms for amino-acids.
  • Generate coarse grained model:
    Use barycenters for calculations.
  • Add simulation box:
    Define a box in which your simulation should take place.
Cloner
D_POEM_ExpClone.png


Duplicate the input molecule
  • Random generate:
    Select maximum translation [A], maximum rotation [rad] and amount of your duplicates here. Click generate to add them to the list below.
  • Load from file
    You might want to load the information described above from a file. File syntax is: "%f %f %f %f %f %f %f".1-3: translation, 4-6: rot. axis, 7: rot. angle
Offset
D_POEM_ExpOff.png
IMMoleculeBuilder::offset_structures is called. The option is still work in progress but usable, but you need to change parameters in the python code. Chains from a two-subunit protein are offset to allow redocking.
Constraints
D_POEM_ExpConstr.png
These functions are not yet implemented.
End output
D_POEM_ExpOut.png


In this section you can request additional output information about the used forcefields. Choose a forcefield from the drop-down-menu and click add. By clicking Del you can remove single ones and by using Clear the complete list will be cleared.
EBS
D_POEM_ExpEBS.png


Entropy Biased Sampling
You have to select:
  • start temperature, T_start [K]
  • end temperature, T_end [K]
  • number of forcefields, # forcefields
  • Total steps
  • interaction range at the beginning, First range
  • interaction range at the end, Last range
Algorithm
D_POEM_ExpAlg.png


  • Metropolis Monte Carlo:
    "Normal" thermodynamic simulation
  • Generalized Multiple-Try Metropolis
  • Multi-Evulotionary Algorithm
  • Accept all criterion:
    Every step will be accepted



Go to next section Preprocessor output, return to previous page Output or return return to Details mainpage.