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