Simulated Annealing (SA), as well as similar procedures like grid search, Monte Carlo, parallel tempering, genetic algorithm, etc., involves the generation of a random sequence of trial structures starting from an appropriate 3D model. The parameters defing the model are modified until a good match between the calculated and the observed pattern is found. The information about chemical knowledge of molecules is actively used to reduce the number of parameters to be changed: bond distances and angles are usually known and kept fixed. Global parameters defining the orientation and the postion of each fragment are varied during the procedure, together with internal parameters like torsion angles.
The dynamical occupancy correction for atoms lying on special positions and atoms sharing the same position in the crystal structure may be taken into account.
In the following images, the Simulated Annealing dialog, the Sir2014 window during the run and the solution menu are reported.
To start click on
To look at solutions use
To run Sir2014 for structure solution by Simulated Annealing you need to create an input file (*.sir) using a text editor or using the program interface. File, New.
In the tab 'Solve' select 'Simulated Annealing' in the frame Solving strategy and import the starting model. The following picture is an example of the interface for the crystal structure determination of the structure cnba using Simulated Annealing.
"%sannel" is a command to access to the simulated annealing graphical interface."%fragment struct.mol" is the command to import the starting structural model for simulated annealing in MDL Molfile format (*.mol). This command can be repeted several times to import more than one fragment. Some other file type can be import in the same way: MOPAC file (*.mop), Tripos Sybyl file (*.mol2,*.ml2), C.I.F. file (*.cif), Protein Data Bank file (*.pdb), Sir fragment or Free Fractional Format (*.frac), XYZ format (*.xyz). Refer to openbabel wiki or http://www.ch.ic.ac.uk/chemime for information about common molecular file formats. Refer to http://en.wikipedia.org/wiki/Molecule_editor and http://www.ccp14.ac.uk/solution/2d_3d_model_builders/index.html for an exhaustive list of programs for building 3D starting models. Suggested free available programs for building 3D models are ACD/ChemSketch (windows), Avogadro (all platforms), Marvin (all platforms), ghemical (linux).
NIST Chemisty webbook and Drugbank are useful links to look up fragments.
Instead of command "%sannel", you can access directly to the graphical interface from menu "Solve" > "Simulated Annealing".
The dialog of Simulated Anneling in Sir2014 is composed by 4 pages (tabs).
The first page 'SA conditions' contains the general settings of the Simulated Annealing algorithm:
Cost function: 2 cost functions can be selected: R structure factor (default cost function), R intensities.
Resolution: define the maximum resolution used by Simulated Annealing procedure.
Random seed: select the value determining the sequence of random numbers used from the algorithm. When it is set to 0 the random seed will be calculated by the system clock.
Nr. of runs: select the number of Simulated Annealing (SA) runs. At the beginning of each run a new value of random seed is calculated.
Solutions: browse the best solutions saved at the end of each run.
The second page 'External DOF' contains information about the external degrees of freedom (DOF)
Select fragment: select the fragment and visualize the corresponding structure information.
Atoms: list of the atoms in the selected fragment
Parameter for fragment: list of the external DOFs for the selected fragment. Check the parameters to refine, enter the lower and upper bounds of the parameters.
The third page 'Internal DOF' contains information about the internal DOFs
Internal DOFs: list of the torsions associated to each refinable internal DOF. Check the parameters to refine, enter the lower and upper bounds of parameters.
Dynamical Occupancy Correction: automatic detection of atoms in special position and atoms that share the same position. If this option is not active all refined atoms are considered in general position (default).
The 'Atomic parameters' button give access to the following dialog
X Y Z: check the buttons on column 'X Y Z' to refine the position of atoms, in this case the fragment is not rigid but the position of atoms are shifted respect to the barycentre. Click on label 'X Y Z' to select all checks in the column.
B[iso]: check the buttons on column 'Thermal parameters' to refine the thermal parameters of atoms (B). Click on label 'Thermal parameter' to select all checks in the column. If the thermal parameters are non indicated in the imported fragment file, the program assigns the default values of B=3.0 for non-hydrogen atoms and B=6.0 for hydrogen atoms. These default values can be changed editing the new values in the column.
Maximum shift on position: enter the value of the maximum shift of the atoms position. 0.020 is the suggested value. Increasing this value the space explored by the algorithm becomes wider and the probability of falling in a local minimum increases.
The fourth page 'Anti-bump' contains information about the anti-bump restraints.
When simulated annealing is running the progress of structure solution is monitored and the user can examine the graph of the minimum values of cost function (CF) vs. the number of moves. The crystal packing is plotted in the JAV viewer.
The output file contains information on:
1) the starting structure
2) the volume per atom
2) the connectivity
3) the internal and external DOFs
4) the refined parameters by SA
5) the information about each SA run
6) the summary of all the SA runs
7) the selected structure
At the end of each run the structure coordinates are saved in CIF file with name created by project name with suffix _best1,_best2, ... (e.g. cnba_best1.cif is the best solution, cnba_best2.cif is the second best solution, ...). The order number in the name represents the position in the list of structures ordered according to the cost function.
If Simulated Annealing fails:
Usually you don't need to know the directives unless you are interested to run Simulated Annealing without interaction with the graphic interface. The list of directives is available here.
For suggestions and bugs contact corrado.cuocci@ic.cnr.it
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