- Structure
-
- 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>
- 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.