Action: WRAPAROUND
| Module | generic |
|---|---|
| Description | Usage |
| Rebuild periodic boundary conditions around chosen atoms. |   |
| This action outputs data to a file. You can read more about how PLUMED manages output files here |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| AROUND | atoms | reference atoms |
| ATOMS | atoms | wrapped atoms |
Further details and examples
Rebuild periodic boundary conditions around chosen atoms.
This action modifies the position of the atoms indicated by ATOMS by shifting them by lattice vectors so that they are as close as possible to the atoms indicated by AROUND. More precisely, for every atom i in the ATOMS list the following procedure is performed: - The atom j among those in the AROUND list is searched that is closest to atom i. - The atom i is replaced with its periodic image that is closest to atom j.
This action works similarly to WHOLEMOLECULES in that it replaces atoms coordinate. Notice that only atoms specified with ATOMS are replaced, and that, at variance with WHOLEMOLECULES, the order in which atoms are specified is irrelevant.
This is often convenient at a post processing stage (using the driver), but sometime it is required during the simulation if collective variables need atoms to be in a specific periodic image.
[!CAUTION] 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 computational cost of this action grows with the product of the size of the two lists (ATOMS and AROUND), so this action can become very expensive. If you are using it to analyze a trajectory this is usually not a big problem. If you use it to analyze a simulation on the fly, e.g. with DUMPATOMS to store a properly wrapped trajectory, consider using the STRIDE keyword here (with great care).
Examples
This command instructs plumed to move all the ions to their periodic image that is as close as possible to the rna group.
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rna: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-100 ions: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=101-110 # first make the rna molecule whole WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=rna WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=ions AROUNDreference atoms=rna DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump.xyz ATOMSthe atom indices whose positions you would like to print out=rna,ions
In case you want to do it during a simulation and you only care about wrapping the ions in
the dump.xyz file, you can use the following input:
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# add some restraint that do not require molecules to be whole: a: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,10,11 RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=a ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=5 # then do the things that are required for dumping the trajectory # notice that they are all done every 100 steps, so as not to # unnecessarily overload the calculation
rna: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-100 ions: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=101-110 # first make the rna molecule whole WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=rna STRIDE the frequency with which molecules are reassembled=100 WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=ions AROUNDreference atoms=rna STRIDE the frequency with which molecules are reassembled=100 DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump.xyz ATOMSthe atom indices whose positions you would like to print out=rna,ions STRIDE the frequency with which the atoms should be output=100
Notice that if the biased variable requires a molecule to be whole, you might have to put the WHOLEMOLECULES command before computing that variable and leave the default STRIDE=1.
This command instructs plumed to center all atoms around the center of mass of a solute molecule.
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solute: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-100 all: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-1000 # center of the solute: # notice that since plumed 2.2 this also works if the # solute molecule is broken com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=solute # notice that we wrap around a single atom. this should be fast WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=all AROUNDreference atoms=com DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump.xyz ATOMSthe atom indices whose positions you would like to print out=all
Notice that whereas WHOLEMOLECULES is designed to make molecules whole, WRAPAROUND can easily break molecules. In the last example, if solvent (atoms 101-1000) is made e.g. of water, then water molecules could be broken by WRAPAROUND (hydrogen could end up in an image and oxygen in another one). One solution is to use WHOLEMOLECULES on all the water molecules after WRAPAROUND. This is tedious. A better solution is to use the GROUPBY option which is going to consider the atoms listed in ATOMS as a list of groups each of size GROUPBY. The first atom of the group will be brought close to the AROUND atoms. The following atoms of the group will be just brought close to the first atom of the group. Assuming that oxygen is the first atom of each water molecules, in the following examples all the water oxygen atoms will be brought close to the solute, and all the hydrogen atoms will be kept close to their related oxygen.
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solute: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-100 water: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=101-1000 com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=solute # notice that we wrap around a single atom. this should be fast WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=solute AROUNDreference atoms=com # notice that we wrap around a single atom. this should be fast WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=water AROUNDreference atoms=com GROUPBY group atoms so as not to break molecules=3 DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump.xyz ATOMSthe atom indices whose positions you would like to print out=solute,water
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| AROUND | input | none | reference atoms |
| ATOMS | input | none | wrapped atoms |
| STRIDE | compulsory | 1 | the frequency with which molecules are reassembled |
| GROUPBY | compulsory | 1 | group atoms so as not to break molecules |
| PAIR | optional | false | Pair atoms in AROUND and ATOMS groups |