This action is used to rebuild molecules that can become split by the periodic boundary conditions.

It is similar to the ALIGN_ATOMS keyword of plumed1, and is needed since some MD dynamics code (e.g. GROMACS) can break molecules during the calculation.

Running some CVs without this command can cause there to be discontinuities changes in the CV value and artifacts in the calculations. This command can be applied more than once. To see what effect is has use a variable without pbc or use the DUMPATOMS directive to output the atomic positions.

Attention: This directive modifies the stored position at the precise moment it is executed. This means that only collective variables which are below it in the input script will see the corrected positions. As a general rule, put it at the top of the input file. Also, unless you know exactly what you are doing, leave the default stride (1), so that this action is performed at every MD step.

The atoms involved can be specified using

ENTITY

the atoms that make up a molecule that you wish to align. To specify multiple molecules use a list of ENTITY keywords: ENTITY1, ENTITY2,... You can use multiple instances of this keyword i.e. ENTITY1, ENTITY2, ENTITY3...

Or alternatively by using

RESIDUES

this command specifies a set of residues which all must be aligned. It must be used in tandem with the MOLINFO action and the RES_ATOMS keyword. If you wish to use all the residues from all the chains in your system you can do so by specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues you are interested in as a list of numbers

Compulsory keywords

STRIDE

( default=1 ) the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!

RES_ATOMS

this command tells plumed what atoms should be aligned in each of the residues that are being aligned

Examples

This command instructs plumed to reconstruct the molecule containing atoms 1-20 at every step of the calculation and dump them on a file.

# to see the effect, one could dump the atoms as they were before molecule reconstruction:
# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
WHOLEMOLECULES STRIDE=1 ENTITY0=1-20
DUMPATOMS FILE=dump.xyz ATOMS=1-20

(see also DUMPATOMS)

This command instructs plumed to reconstruct two molecules containing atoms 1-20 and 30-40

WHOLEMOLECULES STRIDE=1 ENTITY0=1-20 ENTITY1=30-40
DUMPATOMS FILE=dump.xyz ATOMS=1-20,30-40

(see also DUMPATOMS)

This command instructs plumed to reconstruct the chain of backbone atoms in a protein

MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES STRIDE=1 RESIDUES=ALL RES_ATOMS=N,CA,CB,C,O

(See also MOLINFO)