Cerius<sup>2</sup> Builders - Amorphous Builder

Cerius² Builders

6 Amorphous Builder

The C²·Amorphous Builder module builds amorphous molecular structures, which can be represented in the molten state, in solution, or in the semicrystalline state. The amorphous structure can be built nonperiodically as an isolated single or multiple chain or as a 3D-periodic system to represent the bulk state. The structures are generated by varying the rotatable torsions using a random method or a rotational isomeric state (RIS) method. Features are available that make it easy to generate several structures, automatically relax them to relieve strain, and save their coordinates for analysis.

For information about See
Mixtures of polymers. The discussion of the Blends module in Cerius² Computational Instruments Property Prediction.
Diffraction from amorphous structures. The discussion of the Diffraction-Amorphous module in Cerius² Analytical Instruments.
The format of the ris files written by the amorphous builder. Files.

For information about	See
Mixtures of polymers.	The discussion of the Blends module in Cerius² Computational Instruments Property Prediction.
Diffraction from amorphous structures.	The discussion of the Diffraction-Amorphous module in Cerius² Analytical Instruments.
The format of the ris files written by the amorphous builder.	Files.

Accessing the tools

Controls belonging to the C²·Amorphous Builder module are contained on the AMORPHOUS BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the AMORPHOUS BUILDER card, click its name to bring it to the front of the deck of cards, which should now look like this:

How the amorphous builder works

The starting structure

The amorphous builder works on the current model. This can be a single- or multiple-chain structure that has been read in or built using the Polymer Builder, the 3D-Sketcher, or one of the other builders. You can make multiple copies of structures and place them in the model window (Cloning to create starting models). Solvents, plasticizers, or additives can also be included in the current model space.

Varying the torsions

The amorphous structure is grown by varying the angles of rotatable torsions. You can specify that certain types of torsions be considered not rotatable (Fixing torsions), for example, torsions involving single-bond sp²-sp² interactions, double bonds, or methyl groups.

Random and RIS build methods

Several algorithms can be used to generate the amorphous structure: a Monte Carlo method that assigns random values to all torsions and two rotational isomeric state (RIS) methods:

The random method results in a random distribution of torsion angles.
The RIS ratio method refines this by enabling you to explicitly specify a distribution of isomeric states (i.e., torsion angles, along with angle tolerances and a relative frequencies) for the torsion type.
The RIS energy method calculates the appropriate distribution of isomeric states (torsion angles) using the Boltzmann partition function, given the specified RIS temperature and relative energies of the various isomeric states.

A method is specified for each unique rotatable torsion, thus allowing a combination of methods to be used (Specifying torsion rotation methods).

Building 3D periodic systems

If the structure is to be built as a 3D-periodic system, the amorphous builder constructs a cube of the appropriate volume to contain the structure at a requested density. Whenever the chain leaves the cell while it is being built, its periodic image is generated on the opposite face of the cell and growth continues into the cell. By the end of the building process, the complete chain may effectively traverse many unit cells.

Bump checking

A bump-checking algorithm is used to control how close together nonbonded atoms are allowed to come when the amorphous structure is being built. The minimum nonbond distance allowed is equal to the sum of the two atoms' van der Waals radii multiplied by the van der Waals scale. The number entered is used for a hard-sphere van der Waals approximation.

van der Waals scale values can range from 0 to 0.89. If 0 is used, all bumps are disregarded and phantom chain growth is permitted. The maximum value is 0.89, which is the distance at which the Lennard-Jones 12-6 potential becomes strongly repulsive:

U (0.89 r0) = 0

Here U is the potential energy and r0 is the minimum-energy distance. van der Waals scale values close to 0.300 (the default) are recommended. As the van der Waals scale gets larger, the van der Waals energy of the system becomes more favorable. However, because the atoms are not allowed to come as close together, this makes it more difficult to construct an atomistic model. For many systems, values greater than 0.600 may prevent Cerius² from building a structure.

The smaller the value used for the van der Waals scale, the faster structures are generated, but subsequent energy minimization calculations take longer.

By default, hydrogen atoms are included when performing the van der Waals bump checking. You can specify otherwise, however (Bump checking).

Retry attempts

You can specify how many attempts should be made to find an acceptable angle for each rotatable torsion (Torsion placement attempts). If an acceptable value is not found after this many attempts, Cerius² backs up to the previous torsion, sets a new value for its angle, and then tries the problem bond again. Cerius² may have to back up several bonds before acceptable values are found. You can also specify how many times Cerius² should back up all the way to the beginning and start building again before it aborts building a conformation and goes on to the next one (Torsion placement attempts).

Relaxing the structures

The amorphous structures can be automatically relaxed by energy minimization after each one is built.

Building amorphous structures

This section contains information on:

: Building amorphous structures using the default settings
: Building amorphous structures using custom settings

Technical notes

Initiating the build process by clicking the RUN BUILD pushbutton in the Amorphous Builder control panel initiates the build process using the current model and the current settings in the amorphous builder control panels. If a torsion search has not already been performed, it is automatically done before running the build. (A torsion sort is also done if required.)

Structure-building continues until the specified number of samples have been generated. A statistically unique conformation is generated each time. If it is not possible to build a structure with the current parameter values, a message to that effect is displayed in the text window.

The model window is updated with the coordinates of the new structures after they are generated. If the structures are to be relaxed, plots showing the energies and rms force can be displayed.

The build process can be stopped at any time by clicking the INTERRUPT button in the Processing... dialog box.

Building amorphous structures using the default settings

The default settings

The amorphous builder defaults are set up so that you can easily build a single nonperiodic amorphous structure using the random method. The rotatable torsions are determined by excluding single-bond sp²-sp² interactions, double bonds, and methyl rotors; torsions that differ only in chirality or atom name are not considered unique. The VdW Scale is set to 0.30 for a quick build, and hydrogen atoms are included in the bump checking. The structure generated appears in the model window but is not relaxed or saved.

Starting the process

Place the starting structure in the current model space.

The starting structure can be loaded from a file or built using the polymer builder or one of the other builders. Multiple copies can easily be made by using the Amorphous Builder Clone control panel (Cloning to create starting models).

Accessing the tools

Open the Amorphous Builder control panel by selecting the Build menu item on the AMORPHOUS BUILDER card.

Building the structure

To start the build, click the RUN BUILD pushbutton.

Additional information

Please see the on-screen help for information about all the controls in this control panel. Using the polymer builder is discussed under Polymer Builder. Information on building and editing models is contained in Cerius² Modeling Environment, published separately by MSI.

Building amorphous structures using custom settings

Typical build process

Generally, you start building an amorphous structure by finding all the unique rotatable torsions for your structure and assigning a build method to each (the random method is generally the default). For torsions where data are available, you would probably want to use the RIS ratio or RIS energy method. For these methods, you must specify the angles, tolerances, and ratios or energies for each isomeric state. For the latter, you also need to specify the temperature.

You should specify values for the periodic density if you are building a 3D-periodic structure.

You also need to specify a van der Waals scale (for bump checking, see Bump checking) that is appropriate for your system and that takes performance issues into account.

Some trial builds may be required to determine optimal settings, and you may find that you need to modify the retry parameters to achieve a successful build.

You will probably want to generate several structures, relax them, and save them in a trajectory file for later analysis.

Starting the process

Place the starting structure in the current model space.

The starting structure can be loaded from a file or built using the polymer builder or one of the other builders. Multiple copies of a structure can easily be made using the Amorphous Builder Clone control panel (Cloning to create starting models).

Accessing the tools

Open the Amorphous Builder control panel by selecting the Build menu item on the AMORPHOUS BUILDER card.

Click the Output... pushbutton to open the Amorphous Builder Output control panel.

Click the Preferences... pushbutton to open the Amorphous Builder Preferences control panel.

Rotatable torsions

Define the rules used to determine which torsions are rotatable (see Defining rotatable torsions and torsion rules).

If you are not using the random method for all torsions, find the unique rotatable torsions and assign a build method and RIS variables to each (see Finding unique rotatable torsions and Specifying torsion rotation methods).

Bump checking

Enter a value for the VdW Scale (0 to 0.89) in the Amorphous Builder control panel. This value is used to determine how closely atoms can approach one another before they are considered to be too close (Bump checking).

Hydrogens are included in bump checking by default, resulting in a lower-energy structure. However, you may want to exclude hydrogens when building large structures, to speed up the build process.

To exclude hydrogen atoms from van der Waals bump checking, check the Ignore H's in VdW Bump Checking check box in the Amorphous Builder Preferences control panel.

Type of structure

Select Nonperiodic in the Amorphous Builder control panel to build a nonperiodic amorphous structure or 3D Periodic to construct a 3D-periodic system to represent the bulk state.

If you are building 3D-periodic structures, enter the desired unit cell density for the bulk state in g cm-3 in the Periodic Density entry box.

Number of structures

Enter the Number of Samples (in the Amorphous Builder control panel) to be generated. If you want more than one sample, you should save (in a trajectory file) the coordinates of each structure generated (Saving structures).

Torsion placement attempts

Sometimes steric hindrance prevents a given torsion from being placed, so Cerius² can go back in the build process to change previous torsions. Retry options are set to prevent Cerius² from getting stuck in an endless loop, so that it will abort a nonproductive build and move on to the next conformation.

Enter the Maximum Attempts Per Torsion allowed (in the Amorphous Builder Preferences control panel) before going back to the previous rotatable bond. This entry box specifies the number of attempts that can be made to find an acceptable value for each unique torsion. If an acceptable value is not found after this many attempts, Cerius² goes back to the previous rotatable bond, sets a new value for its torsion, and tries the problem bond again. (Maximum Attempts Per Torsion are allowed each time.)

Build restarts

Cerius² may have to go back several bonds, or even go all the way back to the beginning, before an acceptable value is found.

To abort building a conformation when more than some Maximum Restarts (from the beginning) are required:

Check the Abort After Maximum Restarts check box in the Amorphous Builder Preferences control panel.
In the Maximum Restarts entry box in the Amorphous Builder Preferences control panel, enter the number of restarts allowed before aborting. This specifies the number of times that Cerius² can back up all the way to the beginning when trying to build a structure.

If Cerius² needs to abort the build for the current conformation, a message to that effect is displayed in the text window. Cerius² then goes on to build the next conformation. (The total number of conformations generated will thus be fewer than the number of samples requested, above.)

Tip

You can increase the likelihood of generating a conformation by decreasing the value for the periodic density or van der Waals scale and/or by increasing the tolerance scale, maximum attempts per torsion, or maximum restarts and then starting a new build.

You can increase the likelihood of generating a conformation by decreasing the value for the periodic density or van der Waals scale and/or by increasing the tolerance scale, maximum attempts per torsion, or maximum restarts and then starting a new build.

Interrupt controls

Interrupts are allowed by default, so that you can stop the build at any time. However, this can be turned off, or the frequency of checking for interrupts can be decreased. This speeds up the build process somewhat.

To disable build interruptions, uncheck the Allow User Interrupts check box.

To allow the build process to be interrupted if necessary:

Check the Allow User Interrupts check box.
Enter a value for the Interrupt Check Interval. The default is each time 2.0% of the process has been completed.

Relaxing the structures

If you want to minimize the structures, check the Relax Structure check box in the Amorphous Builder Preferences control panel. The amorphous structure generated from each build appears in the model window and then is minimized.

Important

If you want nondefault minimization conditions, you need to go to the Minimizer module (see Cerius² Simulation Tools) to set up the minimization job before starting the build.

If you want nondefault minimization conditions, you need to go to the Minimizer module (see Cerius² Simulation Tools) to set up the minimization job before starting the build.

If you are writing the built structures to a trajectory file (below), the coordinates of the final structure are saved.

Updating the model display

To repeatedly update the model display as the build proceeds, check the Update Model check box in the Amorphous Builder Output control panel and enter a value for the Update Frequency (entering n means to update each time n% of the rotatable torsions are placed).

To update the display only at the end of the build, uncheck the box.

Saving structures

To save the generated amorphous structures in a trajectory file:

Check the Create POLYGRAF Trajectory File check box in the Amorphous Builder Output control panel.
Enter any desired comments in the Comments entry boxes.
Enter a filename prefix in the Filename entry box (the .trj extension is added automatically).

: If a file of the same name already exists, a dialog box opens. Click Overwrite File to overwrite the file or click Ignore Action and specify a different filename.

If you do not want to save the structures, uncheck the Create POLYGRAF Trajectory File check box.

Building the structure

To start the build, click the RUN BUILD pushbutton in the Amorphous Builder control panel.

Additional information

Please see the on-screen help for information about all the controls in these control panels. Using the polymer builder is discussed under Polymer Builder. Information on building and editing models is contained in Cerius² Modeling Environment, published separately by MSI.

Cloning to create starting models

The Amorphous Builder works on the current model. If you want to create multiple-chain models, you can use the Edit/Copy and Edit/Paste items on the menu bar in the main Visualizer control panel (see Cerius² Modeling Environment, published separately by MSI) to create such a model from single-chain structures. However, this method copies only one structure at a time.

The Amorphous Builder Clone control panel enables you to quickly make one or more copies of several different structures and place them in the same model space. The cloned structures are placed in a new model space.

Starting the process

Read in or build the structures from which you want to create clones. If you are using more than one structure and want different numbers of copies of each, put them in separate model spaces.

Accessing the tools

Open the Amorphous Builder Clone control panel by selecting the Clone menu item from the AMORPHOUS BUILDER card.

Specifying the copies

To specify the models you want to copy, click the Show Model Information action button at the bottom of the Amorphous Builder Clone control panel. The names of suitable models currently in Cerius²'s memory are listed in the Model Name list box.

Enter the number of copies you would like in the Copies entry box next to each model listed.

Making the copies

To make the copies, click the CLONE pushbutton.

Additional information

Please see the on-screen help for information about all the controls in this control panel. Please see Cerius² Modeling Environment for information about other ways of copying models from one space to another.

Specifying what torsions to rotate during building

This section contains information on:

: Defining rotatable torsions and torsion rules
: Finding unique rotatable torsions

Defining rotatable torsions and torsion rules

Technical notes

The amorphous structure is grown by selecting the angles for the rotatable torsions. Which torsions are defined as rotatable is crucial in determining how the structure is built. You can exclude certain types of torsions from those that are allowed to vary, for example, torsions involving single-bond sp²-sp² interactions, multiple bonds, or methyl rotors.

Torsions that differ only in chirality or atom name are not considered unique. The atom name option is provided so that you can make a particular torsion unique by assigning a different name to one of its atoms. This enables you to specify a different build method or RIS variables for that torsion.

Unique torsions need to be found and specified before starting the build (Building amorphous structures).

Accessing the tools

Open the Amorphous Builder Torsions control panel by selecting the Torsions menu item from the AMORPHOUS BUILDER card.

Click the Rules... pushbutton to open the Amorphous Torsion Rules control panel.

Setting torsion rules

To exclude torsions involving single-bond sp²-sp² interactions from the list of rotatable torsions, check the Ignore SP2-SP2 Single Bonds check box. It might be useful to include such torsions for biphenyl-like molecules (for the single bond joining the rings), but probably not where more planar structures are involved (for example, the N-C bond in amide-like compounds).

To exclude torsions involving double, triple, or resonant bonds from the list of rotatable torsions, check the Ignore Multiple Bonds check box.

To exclude torsions involving --CH₃ groups from the list of rotatable torsions, check the Ignore Methyl Rotors check box.

To specify that torsions that are the same except for chirality are not considered to be different torsion types, uncheck the Ignore Chirality check box.

To specify that torsions that are the same except for atom name(s) are not considered to be different torsion types, uncheck the Ignore Atom Names check box.

Sorting bond arrays after torsion search

To always have the bond arrays sorted after a torsion search, check the Always Sort Bond Arrays check box. (When this box is unchecked, sorts are automatically done if needed.)

Because the sort process takes time (nearly doubling the find time), this box should be checked only when anomalous behavior is observed during a build (for example, when parts of the molecule flash in the display--as can be seen if the Update Model check box on the Amorphous Builder Output control panel is checked). This indicates that Cerius² is not accounting for all possibilities in determining when a sort is needed, so a forced sort is required.

Additional information

Please see the on-screen help for information about all the controls in this control panel.

Finding unique rotatable torsions

Technical notes

You can find all the unique rotatable torsions for a structure with the Amorphous Builder Torsions control panel. When the search ends, all torsions that satisfy the current torsion rules are listed in the unique torsions table in that control panel. The atom names comprising each torsion type are listed, and torsion names are assigned sequentially (t1, t2, etc.).

If overlapping bond vectors are found during the search, the torsions are sorted. That is, they are reordered so that no overlap occurs. (Overlap prevents the build from proceeding properly.) However, you can force a sort following every torsion search (but this can nearly double the find time).

The torsion types listed in the unique torsions table also appear in the Amorphous Builder State Table control panel, which allows you to change the build method and RIS variable assignments (Specifying torsion rotation methods).

Accessing the tools

Open the Amorphous Builder Torsions control panel by selecting the Torsions menu item on the AMORPHOUS BUILDER card.

Click the Edit... pushbutton in the Amorphous Builder Torsions control panel to open the Amorphous Builder State Table control panel.

Finding the torsions

To find all the unique torsions types that meet the rules set in the Amorphous Torsion Rules control panel (Defining rotatable torsions and torsion rules), click the FIND pushbutton in the Amorphous Builder Torsions control panel.

All unique rotatable torsion types are found and listed in the unique torsions table (which lists the names of the atom types constituting each torsion) in the Amorphous Builder Torsions control panel.

Renaming torsions

If you want to rename torsion types, select a name from the Table Entry popup in the unique torsions table for the torsion to be renamed. You might, for example, want to use this feature if you want two different torsion types to be treated identically during building, if you created new torsion entries in the Amorphous Builder State Table control panel (Entering data in the state table), or if you created or edited some entries in that control panel.

If merely want to give a torsion type an easy-to-remember name, simply enter the new name in the appropriate Table Entries entry box in the Amorphous Builder State Table control panel (Editing the state table, specifying rotation methods).

Viewing the torsions

You can display torsion types on the model:

To display all torsions of a given type, set the Display Mode popup to ALL. To show just the first occurrence of the torsion type, set it to FIRST.
Click the Show action button associated with the desired torsion type. The four atoms and three bonds constituting the torsion(s) are highlighted.

Additional information

Please see the on-screen help for information about all the controls in this control panel.

Specifying torsion rotation methods

The build method, RIS variables, and couplings assigned to each unique rotatable torsion are specified in the Amorphous Builder State Table control panel (this section). Data can easily be entered, edited, and saved.

Following some introductory material (below), this section contains information on:

: Entering data in the state table
: Editing the state table, specifying rotation methods
: Saving state table data

Random and RIS build methods

As mentioned previously (Random and RIS build methods), the amorphous builder provides three building methods: a Monte Carlo method that assigns random values to torsions and two RIS methods.

A method is specified for each unique rotatable torsion type, which allows a combination of methods to be used in the model. For example, you might have data on the distribution of isomeric states for some, but not all, torsion types. You could assign the RIS ratio method to these torsions and use the random method for the others.

Fixing torsions

You can also specify that particular torsions be fixed (that is, not rotated). This is done by choosing IGNORED for the building method.

Tolerances

With the two RIS methods, you can specify a tolerance for the torsion angle for each of the isomeric states. The angle tolerance value affects performance: loose tolerances speed the process of generating a trial structure but may increase the number of computational cycles required to optimize the structure later. Conversely, tight tolerances slow the building process but result in a better (that is, lower-energy) structure that requires fewer optimization steps.

All the specified tolerances are multiplied by a tolerance scale factor (default = 1.0). This enables you to increase or decrease all tolerances at once without having to enter new values for each.

Coupling

Considerable evidence supports the interdependence of bond rotations for neighboring bonds in chain molecules (Flory et al. 1989). When using one of the RIS build methods, you can couple the angle selected for a torsion to the isomeric state chosen for the bond immediately preceding it.