POEM++ Expert settings

Structure

• Set all dihedral angles to pi:
  makes the molecule be completely extended.
  XML-sample:

  <SetDihedralAbsolute weight="1.0">
    <dihedral_id>0</dihedral_id>
    <value>-3.14159265359</value>
  </SetDihedralAbsolute> 

• Use C_alpha model:
  Use only -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

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

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

These functions are not yet implemented.

End output

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

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

• 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.