Selecting atoms

To define collective variables, atoms are usually selected as groups. Each group is defined using an identifier that is unique in the context of the specific colvar component (e.g. for a distance component, the two groups are group1 and group2). The identifier is followed by a brace-delimited block containing selection keywords and other parameters, including an optional name:

• name $<$ Unique name for the atom group $>$
  Context: atom group
  Acceptable Values: string
  Description: This parameter defines a unique name for this atom group, which can be referred to in the definition of other atom groups (including in other colvars) by invoking atomsOfGroup as a selection keyword.

Atom selection keywords

Selection keywords may be used individually or in combination with each other, and each can be repeated any number of times. Selection is incremental: each keyword adds the corresponding atoms to the selection, so that different sets of atoms can be combined. However, atoms included by multiple keywords are only counted once. Below is an example configuration for an atom group called ``atoms''. Note: this is an unusually varied combination of selection keywords, demonstrating how they can be combined together: most simulations only use one of them.

atoms {

  # add atoms 1 and 3 to this group (note: the first atom in the system is 1)
  atomNumbers {
    1 3
  }

  # add atoms starting from 20 up to and including 50
  atomNumbersRange 20-50

  # add all the atoms with occupancy 2 in the file atoms.pdb
  atomsFile atoms.pdb
  atomsCol O
  atomsColValue 2.0

  # add all the C-alphas within residues 11 to 20 of segments "PR1" and "PR2"
  psfSegID PR1 PR2
  atomNameResidueRange CA 11-20
  atomNameResidueRange CA 11-20

  # add index group (requires a .ndx file to be provided globally)
  indexGroup Water
}

The resulting selection includes atoms 1 and 3, those between 20 and 50, the $\mathrm{C}_{\alpha}$ atoms between residues 11 and 20 of the two segments PR1 and PR2, and those in the index group called ``Water''. The indices of this group are read from the file provided by the global keyword indexFile (see 9.2.4).

The complete list of selection keywords available in NAMD is:

• atomNumbers $<$ List of atom numbers $>$
  Context: atom group
  Acceptable Values: space-separated list of positive integers
  Description: This option adds to the group all the atoms whose numbers are in the list. The number of the first atom in the system is 1: to convert from a VMD selection, use ``atomselect get serial''.

• indexGroup $<$ Name of index group to be used (GROMACS format) $>$
  Context: atom group
  Acceptable Values: string
  Description: If the name of an index file has been provided by indexFile, this option allows to select one index group from that file: the atoms from that index group will be used to define the current group.

• atomsOfGroup $<$ Name of group defined previously $>$
  Context: atom group
  Acceptable Values: string
  Description: Refers to a group defined previously using its user-defined name. This adds all atoms of that named group to the current group.

• atomNumbersRange $<$ Atoms within a number range $>$
  Context: atom group
  Acceptable Values: $<$ Starting number$>$ -$<$ Ending number$>$
  Description: This option includes in the group all atoms whose numbers are within the range specified. The number of the first atom in the system is 1.

• atomNameResidueRange $<$ Named atoms within a range of residue numbers $>$
  Context: atom group
  Acceptable Values: $<$ Atom name$>$ $<$ Starting residue$>$ -$<$ Ending residue$>$
  Description: This option adds to the group all the atoms with the provided name, within residues in the given range.

• psfSegID $<$ PSF segment identifier $>$
  Context: atom group
  Acceptable Values: space-separated list of strings (max 4 characters)
  Description: This option sets the PSF segment identifier for atomNameResidueRange. Multiple values may be provided, which correspond to multiple instances of atomNameResidueRange, in order of their occurrence. This option is only necessary if a PSF topology file is used.

• atomsFile $<$ PDB file name for atom selection $>$
  Context: atom group
  Acceptable Values: UNIX filename
  Description: This option selects atoms from the PDB file provided and adds them to the group according to numerical flags in the column atomsCol. Note: the sequence of atoms in the PDB file provided must match that in the system's topology.

• atomsCol $<$ PDB column to use for atom selection flags $>$
  Context: atom group
  Acceptable Values: O, B, X, Y, or Z
  Description: This option specifies which PDB column in atomsFile is used to determine which atoms are to be included in the group.

• atomsColValue $<$ Atom selection flag in the PDB column $>$
  Context: atom group
  Acceptable Values: positive decimal
  Description: If defined, this value in atomsCol identifies atoms in atomsFile that are included in the group. If undefined, all atoms with a non-zero value in atomsCol are included.

• dummyAtom $<$ Dummy atom position (Å) $>$
  Context: atom group
  Acceptable Values: (x, y, z) triplet
  Description: Instead of selecting any atom, this option makes the group a virtual particle at a fixed position in space. This is useful e.g. to replace a group's center of geometry with a user-defined position.

Moving frame of reference.

The following options define an automatic calculation of an optimal translation (centerReference) or optimal rotation (rotateReference), that superimposes the positions of this group to a provided set of reference coordinates. This can allow, for example, to effectively remove from certain colvars the effects of molecular tumbling and of diffusion. Given the set of atomic positions $\mathbf{x}_{i}$ , the colvar $\xi$ can be defined on a set of roto-translated positions $\mathbf{x}_{i}' = R(\mathbf{x}_{i} - \mathbf{x}^{\mathrm{C}}) + \mathbf{x}^{\mathrm{ref}}$ . $\mathbf{x}^{\mathrm{C}}$ is the geometric center of the $\mathbf{x}_{i}$ , $R$ is the optimal rotation matrix to the reference positions and $\mathbf{x}^{\mathrm{ref}}$ is the geometric center of the reference positions.

Components that are defined based on pairwise distances are naturally invariant under global roto-translations. Other components are instead affected by global rotations or translations: however, they can be made invariant if they are expressed in the frame of reference of a chosen group of atoms, using the centerReference and rotateReference options. Finally, a few components are defined by convention using a roto-translated frame (e.g. the minimal RMSD): for these components, centerReference and rotateReference are enabled by default. In typical applications, the default settings result in the expected behavior.

Warning on rotating frames of reference and periodic boundary conditions.

rotateReference affects coordinates that depend on minimum-image distances in periodic boundary conditions (PBC). After rotation of the coordinates, the periodic cell vectors become irrelevant: the rotated system is effectively non-periodic. A safe way to handle this is to ensure that the relevant inter-group distance vectors remain smaller than the half-size of the periodic cell. If this is not desirable, one should avoid the rotating frame of reference, and apply orientational restraints to the reference group instead, in order to keep the orientation of the reference group consistent with the orientation of the periodic cell.

Warning on rotating frames of reference and ABF.

Note that centerReference and rotateReference may affect the Jacobian derivative of colvar components in a way that is not taken into account by default. Be careful when using these options in ABF simulations or when using total force values.

• centerReference $<$ Implicitly remove translations for this group $>$
  Context: atom group
  Acceptable Values: boolean
  Default Value: off
  Description: If this option is on, the center of geometry of the group will be aligned with that of the reference positions provided by either refPositions or refPositionsFile. Colvar components will only have access to the aligned positions. Note: unless otherwise specified, rmsd and eigenvector set this option to on by default.

• rotateReference $<$ Implicitly remove rotations for this group $>$
  Context: atom group
  Acceptable Values: boolean
  Default Value: off
  Description: If this option is on, the coordinates of this group will be optimally superimposed to the reference positions provided by either refPositions or refPositionsFile. The rotation will be performed around the center of geometry if centerReference is on, or around the origin otherwise. The algorithm used is the same employed by the orientation colvar component [26]. Forces applied to the atoms of this group will also be implicitly rotated back to the original frame. Note: unless otherwise specified, rmsd and eigenvector set this option to on by default.

• refPositions $<$ Reference positions for fitting (Å) $>$
  Context: atom group
  Acceptable Values: space-separated list of (x, y, z) triplets
  Description: This option provides a list of reference coordinates for centerReference and/or rotateReference, and is mutually exclusive with refPositionsFile. If only centerReference is on, the list may contain a single (x, y, z) triplet; if also rotateReference is on, the list should be as long as the atom group, and its order must match the order in which atoms were defined.

• refPositionsFile $<$ File containing the reference positions for fitting $>$
  Context: atom group
  Acceptable Values: UNIX filename
  Description: This option provides a list of reference coordinates for centerReference and/or rotateReference, and is mutually exclusive with refPositions. The acceptable file format is XYZ, which is read in double precision, or PDB; the latter is discouraged if the precision of the reference coordinates is a concern. Atomic positions are read differently depending on the following scenarios: (i) the file contains exactly as many records as the atoms in the group: all positions are read in sequence; (ii) (most common case) the file contains coordinates for the entire system: only the positions corresponding to the numeric indices of the atom group are read; (iii) if the file is a PDB file and refPositionsCol is specified, positions are read according to the value of the column refPositionsCol (which may be the same as atomsCol). In each case, atoms are read from the file in order of increasing number.

• refPositionsCol $<$ PDB column containing atom flags $>$
  Context: atom group
  Acceptable Values: O, B, X, Y, or Z
  Description: Like atomsCol for atomsFile, indicates which column to use to identify the atoms in refPositionsFile (if this is a PDB file).

• refPositionsColValue $<$ Atom selection flag in the PDB column $>$
  Context: atom group
  Acceptable Values: positive decimal
  Description: Analogous to atomsColValue, but applied to refPositionsCol.

• fittingGroup $<$ Use an alternate set of atoms to define the roto-translation $>$
  Context: atom group
  Acceptable Values: Block fittingGroup { ... }
  Default Value: This group itself
  Description: If either centerReference or rotateReference is defined, this keyword defines an alternate atom group to calculate the optimal roto-translation. Use this option to define a continuous rotation if the structure of the group involved changes significantly (a typical symptom would be the message ``Warning: discontinuous rotation!'').

  The following example illustrates the syntax of fittingGroup: a group called ``atoms'' is defined, including 8 C$_{\alpha}$ atoms of a protein of 100 residues. An optimal roto-translation is calculated automatically by fitting the C$_{\alpha}$ trace of the rest of the protein onto the coordinates provided by a PDB file.

  # Example: defining a group "atoms", with its coordinates expressed
  # on a roto-translated frame of reference defined by a second group
  atoms {
  
    psfSegID PROT
    atomNameResidueRange CA 41-48
  
    centerReference yes
    rotateReference yes
    fittingGroup {
      # define the frame by fitting the rest of the protein
      psfSegID PROT PROT
      atomNameResidueRange CA 1-40
      atomNameResidueRange CA 49-100
    }
    refPositionsFile all.pdb # can be the entire system
  }
  

The following two options have default values appropriate for the vast majority of applications, and are only provided to support rare, special cases.

• enableFitGradients $<$ Include the roto-translational contribution to colvar gradients $>$
  Context: atom group
  Acceptable Values: boolean
  Default Value: on
  Description: When either centerReference or rotateReference is on, the gradients of some colvars include terms proportional to $\partial{}R/\partial\mathbf{x}_{i}$ (rotational gradients) and $\partial\mathbf{x}^{\mathrm{C}}/\partial\mathbf{x}_{i}$ (translational gradients). By default, these terms are calculated and included in the total gradients; if this option is set to off, they are neglected. In the case of a minimum RMSD component, this flag is automatically disabled because the contributions of those derivatives to the gradients cancel out.

• enableForces $<$ Apply forces from this colvar to this group $>$
  Context: atom group
  Acceptable Values: boolean
  Default Value: on
  Description: If this option is off, no forces are applied the atoms in the group. Other forces are not affected (i.e. those from the MD engine, from other colvars, and other external forces). For dummy atoms, this option is off by default.

Treatment of periodic boundary conditions.

In simulations with periodic boundary conditions, NAMD maintains the coordinates of all the atoms within a molecule contiguous to each other (i.e. there are no spurious ``jumps'' in the molecular bonds). The Colvars module relies on this when calculating a group's center of geometry, but this condition may fail if the group spans different molecules. In that case, writing the NAMD output and restart files using wrapAll or wrapWater could produce wrong results when a simulation run is continued from a previous one. The user should then determine, according to which type of colvars are being calculated, whether wrapAll or wrapWater can be enabled.

In general, internal coordinate wrapping by NAMD does not affect the calculation of colvars if each atom group satisfies one or more of the following:

i)

it is composed by only one atom;

ii)

it is used by a colvar component which does not make use of its center of geometry, but only of pairwise distances (distanceInv, coordNum, hBond, alpha, dihedralPC);

iii)

it is used by a colvar component that ignores the ill-defined Cartesian components of its center of mass (such as the $x$ and $y$ components of a membrane's center of mass modeled with distanceZ);

iv)

it has all of its atoms within the same molecular fragment.

Performance of a Colvars calculation based on group size.

In simulations performed with message-passing programs (such as NAMD or LAMMPS), the calculation of energy and forces is distributed (i.e., parallelized) across multiple nodes, as well as over the processor cores of each node. When Colvars is enabled, certain atomic coordinates are collected on a single node, where the calculation of collective variables and of their biases is executed. This means that for simulations over large numbers of nodes, a Colvars calculation may produce a significant overhead, coming from the costs of transmitting atomic coordinates to one node and of processing them. The latency-tolerant design and dynamic load balancing of NAMD may alleviate both factors, but a noticeable performance impact may be observed.

Performance can be improved in multiple ways:

• The calculation of variables, components and biases can be distributed over the processor cores of the node where the Colvars module is executed. Currently, an equal weight is assigned to each colvar, or to each component of those colvars that include more than one component. The performance of simulations that use many colvars or components is improved automatically. For simulations that use a single large colvar, it may be advisable to partition it in multiple components, which will be then distributed across the available cores. In NAMD, this feature is enabled in all binaries compiled using SMP builds of Charm++ with the CkLoop extension. If printed, the message ``SMP parallelism is available.'' indicates the availability of the option. If available, the option is turned on by default, but may be disabled using the keyword smp (see 9.2.4) if required for debugging.

• NAMD also offers a parallelized calculation of the centers of mass of groups of atoms. This option is on by default for all components that are simple functions of centers of mass, and is controlled by the keyword scalable (see 9.3.2). When supported, the message ``Will enable scalable calculation for group ...'' is printed for each group.

• As a general rule, the size of atom groups should be kept relatively small (up to a few thousands of atoms, depending on the size of the entire system in comparison). To gain an estimate of the computational cost of a large colvar, one can use a test calculation of the same colvar in VMD (hint: use the time Tcl command to measure the cost of running cv update).