10_Glossary

Glossary

Term	Explanation
ab_util.py	In order to extract coordinates the ab_util.py script in the ambuild directory (/opt/ambuild/ambuild/ab_util.py) can be used.
ab_util.py -b	The util script also accepts a "-b" argument, which tells the script to write out separate files for each block in the cell.
ab_util.py -f	The util script also accepts a "-f" argument, which tells the script to write out files for each fragment separately.
addBondType	Specifies a bonding rule between two endGroups.
atomMargin	The additional distance to be added onto the van der Waals radii of two atoms to determine if they are close enough to clash.
bondAngleMargin	The tolerance (in degrees) from the ideal of 180 that defines an acceptable bond.
bondMargin	Two atoms are considered close enough to bond if they are within the bond length defined for the two atoms +/- the bondMargin.
bondType	The bondType as was specified when using the addBondType argument.
boxDim	This is a list of three numbers specifying the size of the cell A, B and C dimensions (given in angstroms, from 0 to A, B and C).
capAtom	This is the index of the atom in the .car file that is to be the capAtom.
cellEndGroups	A list of the endGroup types in the cell that the new blocks will be bonded to.
center	True or False argument asking whether to place the first block in the centre of the cell or not (if possible).
clashCheck	True or False check for clashes between the bond and any atoms that fall within a cylinder of radius clashDist.
clashDist	A float specifying the perpendicular distance from the bond axis that determines if an atom is clashing with the bond.
count	The maximum number of permissible bonds for a single fragment.
delAtom	This optional column specifies an atom that will be removed when the endGroup forms a bond.
deleteBlocksIndices	Removes blocks from the simulation cell.
deleteBlocksTypes	This deletes numBlocks of the specified fragment type.
dihedral	This optional column specifies the atom that defines the dihedral angle around the bond between two endGroups.
doDihedral	This asks whether or not to include the dihedral terms (True or False).
dolmproper	This asks whether or not to include the improper terms (True or False).
doLog	This argument (expressed as True or False) specifies if a log file will be created.
dump	A True or False command asking whether or not to save the current state of the cell at various intervals.
dumpPeriod	How often to save the current state of the cell.
endGroup	This is the index of the atom in the .car file that is to be the endGroup.
filename	The path to the .car file. There will need to be a corresponding .csv file that defines the endGroups etc.
filePath	The filePath argument gives the location of the .car file containing the cell dimensions and the coordinaties of molecules.
fragmentType	A name that will be used to identify the fragment. This cannot contain the ":" and "-" characters, or be named "fragment" or "fragmentFactory"
growBlocks	Growing a building block involves adding a fragment to an existing block in the cell. This is done with a growBlocks command.
growPolymer	The simplest and most automatic way to create a structure. This builds a linear polymer.
indices	A list of the indices of the blocks to be deleted.
integrator	The integrator option can be either "nvt", or "npt", where "nvt" runs by default.
joinBlocks	The joinBlocks command is used to join existing blocks in the cell together.
length	The number of subunits that will be created.
libraryAddFragment	Creates a cell library containing all the building blocks that will be used in the simulation.
libraryEndGroups	A list of the endGroup types from the library that will be used to form the bonds.
maxTries	The maximum number of attempts to make when performing a particular function.
mdCycles	This is the number of HOOMD-blue MD cycles to run.
monomers	The list of Ambuild fragmentTypes that will be joined to create a subunit.
multiple	If True, this will remove blocks that contain more than one fragment, if False, this will only remove single-fragment blocks.
nblocks	The number of building blocks of that fragmentType to add to the cell.
numBlocks	This optional variable specifies the number of blocks to remove.
optCycles	This is the number of HOOMD-blue optimisation cycles to run.
optimiseGeometry	Optimises the geometry of the simulation cell.
P	The pressure coefficient used in the simulation.
point	A list of three floats defining a point around which the centroids of the blocks will be seeded (requires the radius argument).
quiet	This asks whether the normal HOOMD-blue runtime output should be printed to the screen (False) or not (True).
radius	A single float specifying the radius of a sphere within which the centroids of the building blocks will be seeded.
random	Whether to build up the polymer deterministically or stochastically. Expressed as True or False.
ratio	A list of integers specifying the number of each type in the subunit. This list should be as long as the list of monomers.
rCut	This is the van der Waals cut-off distance used (angstroms).
rigidBody	This asks whether to do a rigid-body (True) or all-atom (False) optimisation.
runMD	Runs a molecular dynamics simulation on the cell contents.
runMDAndOptimise	This runs a very short optimisation loop, then an MD simulation, before running a full geometry optimisation to convergence.
save	This saves all of the deleted blocks so they can be re-added with the restoreBlocks command.
seed	The seed command is used to seed the system with molecular building blocks.
selfBond	This is a True or False check that asks whether or not a block should be allowed to bond to itself, with default True.
Solvent	This optional variable can be used to specify that this fragmentType is solvent and so won’t be clash-checked in Zip steps.
T	The temperature coefficient used in the simulation (this doesn’t directly relate to a temperature in kelvin).
toGrow	Specifies the number of blocks to add.
toJoin	The number of blocks to join.
Type	This is a string (starting with a letter) that names the endGroup. This is used to specify bonding rules as an example.
zipBlocks	The zipBlocks command joins existing building blocks in the cell by changing the bondMargin and bondAngleMargin parameters.
zone	A list of six floats in the form of (x1, x2, y1, y2, z1, z2) specifying a box within the cell within which the centroids of the blocks will be seeded.