Initial configurations for Molecular Dynamics Simulations by packing optimization

Institute of Chemistry and Institute of Mathematics
University of Campinas
Institute of Mathematics and Statistics
University of São Paulo
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See also:
ComplexMixtures.jl MDLovoFit
CellListMap.jl LovoAlign
The TANGO project
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JM Home-Page
EGB Home-Page
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• From version 15.133 on, it is possible to assign different radii to different atoms.

• The "constrain rotation" option can now constrain the angle of rotation of all molecules of one type, so that they their centers are randomly placed in space, but the molecules have an overall common orientation. This can be used also to build lipid layers, for example, or maybe to build anisotropic liquids.

• Packmol now prints the molecules in the same order that they were setup in the input file.

• Constraints can be applied to a part of the molecules, in such a way that molecules can be oriented in space. This is done by using the atom selection.

• Thirteen different types of constraints allow you to build complex starting configurations. The molecules (or some atoms within them) can be placed inside or outside cubes, boxes, spheres, ellipsoids, cylinders, over or below planes or can be fixed in a specified position.

• The function is now evaluated with an algorithm that scales linearly with the number of atoms of the system: very large problems can be solved in reasonable time.

• The powerful optimization algorithm GENCAN is now used as the optimization subroutine providing greater speed and reliability (see The TANGO Project link).

• The use of memory was optimized and now the only critical parameter is the maximum number of atoms of the system.

• Much clearer code turns it possible for developers to change the package to fit their needs.

To-do list

Features that users want but we didn't have the time to implement.

• A graphical interface to VMD.

• Use periodic boundary conditions explicitly.

• Constrain the distance between molecules.

• Triclinical boxes and periodic conditions.