Action: WHOLEMOLECULES

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

Further details and examples

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

This command performs an operation that is similar what was done by the ALIGN_ATOMS keyword from plumed1. This operation is needed as some MD dynamics code (e.g. GROMACS) can break molecules during the calculation. Whenever we are able we try to ensure that molecules are reconstructed automatically. You thus do not need to use this action when you are using actions such as COM, CENTER, GYRATION and so on as the reconstruction of molecules is done automatically in these actions. It is, however, important to understand molecule reconstruction as there are many cases (e.g. when you are calculating the end-to-end distance of a polymer) where not using the WHOLEMOLCULES command can cause the artifacts discussed in the attached reference.

If you think that you need to use this command a good idea is to use the DUMPATOMS directive to output the atomic positions. This will allow you to see the effect that including/not including WHOLEMOLECULES has on the calculation.

[!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.

Notice that the behavior of WHOLEMOLECULES is affected by the last MOLINFO action that is present in the input file before the WHOLEMOLECULES command. Specifically, if the MOLINFO action does not have a WHOLE flag, then the behavior is the following:

• The first atom of the list is left in place
• Each atom of the list is shifted by a lattice vectors so that it becomes as close as possible to the previous one, iteratively.

In this way, if an entity consists of a list of atoms such that consecutive atoms in the list are always closer than half a box side the entity will become whole. This can be usually achieved selecting consecutive atoms (1-100), but it is also possible to skip some atoms, provided consecutive chosen atoms are close enough.

If, by contrast, the MOLINFO action does have a WHOLE flag, then a minimum spanning tree is built based on the atoms passed to WHOLEMOLECULES using the coordinates in the PDB passed to MOLINFO as a reference, and this tree is used to reconstruct PBCs. This approach is more robust when dealing with complexes of multiple molecules.

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.

Click on the labels of the actions for more information on what each action computes

# to see the effect, one could dump the atoms as they were before molecule reconstruction:
# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
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=1-20
The WHOLEMOLECULES action with label  calculates somethingDUMPATOMSDump 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=1-20

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

Click on the labels of the actions for more information on what each action computes

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=1-20 ENTITY1the atoms that make up a molecule that you wish to align=30-40
The WHOLEMOLECULES action with label  calculates somethingDUMPATOMSDump 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=1-20,30-40

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

Click on the labels of the actions for more information on what each action computes

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=
regtest/basic/rt32/helix.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt32/helix.pdb
    
ATOM      1 HH31 ACE     1      -9.105  -2.402  21.804  0.00  0.00            
ATOM      2  CH3 ACE     1      -8.930  -3.352  22.308  0.00  0.00            
ATOM      3 HH32 ACE     1      -9.504  -3.501  23.223  0.00  0.00            
ATOM      4 HH33 ACE     1      -9.067  -4.173  21.604  0.00  0.00            
ATOM      5  C   ACE     1      -7.450  -3.303  22.659  0.00  0.00            
...
ATOM    129  CH3 NME    14      -1.690  -7.089  20.487  0.00  0.00            
ATOM    130 HH31 NME    14      -1.873  -6.629  21.459  0.00  0.00            
ATOM    131 HH32 NME    14      -1.152  -6.284  19.986  0.00  0.00            
ATOM    132 HH33 NME    14      -1.135  -8.020  20.602  0.00  0.00            
END
  
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details RESIDUESthis command specifies that the backbone atoms in a set of residues all must be aligned=all MOLTYPEthe type of molecule that is under study=protein

References

More information about how this action can be used is available in the following articles: - G. Bussi, G. A. Tribello, "Analyzing and Biasing Simulations with PLUMED" in Biomolecular Simulations (Springer New York, 2019; http://dx.doi.org/10.1007/978-1-4939-9608-7_21), pp. 529–578

Syntax

The following table describes the keywords and options that can be used with this action