The solute and solvent are defined in ComplexMixtures as lists (vectors) of the indexes of the atoms of the system. The solute and solvent information is stored in the
Selection structure. For example, if the solute is a molecule formed by the first 5 atoms of the system, it would be defined as:
indexes = [ 1, 2, 3, 4, 5 ] solute = Selection(indexes,nmols=1)
We need to inform the
Selection function about the number of atoms of each molecule (using
natomspermol=3, for example), or the number of molecules (using
nmols=1000, for example), such that the atoms belonging to each molecule can be determined without ambiguity.
The atom names can be also provided such that some of the output files contain more information on the atomic contributions. In this case the syntax is:
indexes = [ 1, 2, 3, 4, 5 ] names = [ "H1", "H2", "H3", "H4", "C" ] solute = Selection(indexes,names,nmols=1)
The indexing in ComplexMixtures is 1-based. That means that the first atom of your structure file is in position 1 of the coordinates. Please be careful if using any selection tool to be sure that your selection is correct.
PDBTools is a package we developed to read and write PDB files, which provides a simple selection tool. It is installed as a dependency of ComplexMixtures. Given a PDB file of the simulated system, the solute can be defined as, for example,
using PDBTools atoms = PDBTools.readPDB("system.pdb") protein = PDBTools.select(atoms,"protein") solute = Selection(protein,nmols=1)
If the solvent is, for instance, water, the indexes of the water molecules can be obtained with:
water = PDBTools.select(atoms,"water") solvent = Selection(water,natomspermol=3)
or, alternatively, a more compact syntax can be used, for example:
water = PDBTools.select("system.pdb","resname TIP3P") solvent = Selection(water,natomspermol=3)
or even providing just the names of the input file and selection, which will run PDBTools in background:
solvent = Selection("sytem.pdb","water",water,natomspermol=3)
The selection syntax of
PDBTools is somewhat limited. Verify if the selections correspond to the the desired sets of atoms every time.
VMD is a very popular and powerful package for visualization of simulations. It contains a very versatile library to read topologies and trajectory files, and a powerful selection syntax. We provide here a wrapper to VMD which allows using its capabilities.
For example, the solute can be defined with:
indexes, names = VMDselect("./system.gro","protein",vmd="/usr/bin/vmd") solute = Selection(indexes,names,nmols=1)
The main advantage here is that all the file types that VMD supports are supported. But VMD needs to be installed and is run in background, and it takes a few seconds.
VMD uses 0-based indexing and
VMDselect adjusts that. However, if a selection is performed by index, as with
index 1, VMD will select the second atom, and the output will be
. Selections by type, name, segment, residue name, etc, won't be a problem.