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Index
Subsections
Declaring and using collective variables
Each collective variable is defined as a combination of
individual quantities called components
(see Figure 6). To obtain a colvar
,
its components
are summed according to:
![$\displaystyle \xi(\mathbf{r}) = \sum_{i} c_{i} [q_{i}(\mathbf{r})]^{n_{i}}$](img173.png) |
(12) |
where each component appears with a unique coefficient
and
(positive integer) exponent
. Note: in most
applications, only one component per colvar needs to be defined:
accordingly,
and
are equal to 1 by default.
In the configuration file, a collective variable is initiated
by the keyword colvar,
followed by its configuration options, usually between curly braces:
colvar {...}. Each variable must
have one or more components, defined by blocks specifying a
functional form, atoms whose coordinates are used to evaluate
this functional form, and optional parameters as needed. Each
component block is initiated within the colvar block by the
keyword corresponding to a given functional form. For instance, the
block distance {...} adds a component whose value is
the distance between to atom groups.
The types of components used determine the properties of a
colvar, and which biases or analysis methods can be applied
to it. For instance, the colvar returns a scalar value if it
includes components of one or more of the following types:
distance, distanceZ, distanceXY,
angle, dihedral, coordnum, hBond,
rmsd, orientationAngle, gyration, and
alphaHelix. The colvar returns instead a
three-dimensional vector
if distanceVec is
used, a three-dimensional vector with a
constraint if distanceDir is used, and a unitary quaternion
(used to parameterize a rotation) if orientation is are used.
Currently, binning of colvar values on a grid can only be performed
for scalar components. In addition, some properties like the system
force, can be calculated only for some of these components. The
detail documentation all component types is provided in 9.2.1.
Note: restrictions only apply to the type of an individual
colvar. In fact, all of the implemented methods can be applied to
any number of collective variables.
Irrespective of which components it is built of, each colvar
can be provided the following parameters:
- name
(colvar) Name of this colvar
Acceptable Values: string
Default Value: ``colvar'' + numeric id
Description: The name is an unique case-sensitive string which allows the
colvar module to identify this colvar unambiguously; it
is also used in the trajectory file to label to the columns
corresponding to this colvar.
- width
(colvar) Typical fluctuation amplitude (or grid spacing)
Acceptable Values: positive decimal
Default Value: 1.0
Description: This number is a user-provided estimate of the typical
fluctuation amplitude for this collective variable, or conversely,
the typical width of a local free energy basin. Typically, twice
the standard deviation of this variable during a
short simulation run can be used. Biasing methods use this
parameter for different purposes: harmonic restraints
(9.3.3) use it to rescale the value
of this colvar, ABF (9.3.1) interprets it as
the grid spacing in the direction of this variable,
and metadynamics (9.3.2)
uses it as the width of newly added gaussians. This number is
expressed in the same physical unit as the colvar value.
- lowerBoundary
(colvar) Lower boundary of the colvar
Acceptable Values: positive decimal
Description: Defines the lowest possible value of this colvar that should be
sampled in the simulation. It can either be a true physical
boundary (under which the variable is not defined by
construction), or an artificially imposed repulsive wall if
lowerWallConstant is also defined. Together with
upperBoundary and width, it defines a grid of
values for the colvar. This number can only be defined for
a scalar colvar.
- upperBoundary
(colvar) Upper boundary of the colvar
Acceptable Values: positive decimal
Description: Similarly to lowerBoundary, defines the highest
possible or allowed value.
- lowerWallConstant
(colvar) Lower boundary force constant
(kcal/mol)
Acceptable Values: positive decimal
Description: If lowerBoundary is defined, enables a lower bounding restraint
on the colvar in the form of a ``half-harmonic'' potential centered on
lowerBoundary.
The energy scale of the constant is kcal/mol, while the spatial scale is
that of the colvar.
- upperWallConstant
(colvar) Upper boundary force constant
(kcal/mol)
Acceptable Values: positive decimal
Description: If upperBoundary is defined, enables an upper bounding restraint
on the colvar. The unit is the same as lowerWallConstant.
- outputValue
(colvar) Output a trajectory for this colvar
Acceptable Values: boolean
Default Value: on
Description: If colvarsTrajFrequency is defined, the value of this
colvar are written to the trajectory file every
colvarsTrajFrequency steps in the column labeled
``
name
''.
- outputVelocity
(colvar) Output a velocity trajectory for this colvar
Acceptable Values: boolean
Default Value: off
Description: If colvarsTrajFrequency is defined, the finite-difference
calculated velocity of this colvar are written to the
trajectory file under the label ``v_
name
''.
- outputSystemForce
(colvar) Output a system force trajectory for this
colvar
Acceptable Values: boolean
Default Value: off
Description: If colvarsTrajFrequency is defined, and all components
support its calculation, the total system force on this
colvar (i.e. the projection of all interatomic forces
except constraint forces on this colvar -- see
equation (23) in
section 9.3.1) are written to the trajectory
file under the label ``fs_
name
''. The
physical unit for this force is kcal/mol divided by the colvar
unit.
- outputAppliedForce
(colvar) Output an applied force trajectory for this colvar
Acceptable Values: boolean
Default Value: off
Description: If colvarsTrajFrequency is defined, the total force applied on
this colvar by biases within the colvar module are
written to the trajectory under the label
``fa_
name
''. The physical unit for this
force is kcal/mol divided by the colvar unit.
- extendedLagrangian
(colvar) Add an extra degree of freedom
Acceptable Values: boolean
Default Value: off
Description: Adds a fictitious particle with mass fictitiousMass,
coupled to the colvar by a harmonic potential with force constant
extendedForceConstant. Biasing forces on the colvar
are applied to this extra particle, rather than to the atoms
directly. This implements the extended Lagrangian formalism used
in some metadynamics simulations [27].
- extendedForceConstant
(colvar) Ext. Lagrangian force constant
(kcal/mol)
Acceptable Values: positive decimal
Default Value: 1.0
Description: Defines the force constant for the extendedLagrangian
mode. The physical unit is the same as
lowerWallConstant.
- fictitiousMass
(colvar) Fictitious mass of the colvar (amu)
Acceptable Values: positive decimal
Default Value: 1.0
Description: Sets the fictitious inertial mass of this colvar.
Collective variable components
Each colvar has one or more components, each of them
defined by a functional form, the atom positions from which it is
calculated, and any additional parameters of the functional form.
This section lists the types of components and their parameters. Each
component makes use of one or more atom groups, whose syntax of
definition is by their name followed by a definition block, e.g.
myatoms {...}; the options in the definition
block are described in (9.2.3).
The distance {...} block defines a distance component,
between two atom groups, group1 and group2.
- group1
(distance) First group of atoms
Acceptable Values: Block group1 {...}
Description: First group of atoms.
- group2
(distance) Second group of atoms
Acceptable Values: Block group2 {...}
Description: Second group of atoms.
- oneSiteSystemForce
(distance) Measure system force on group 1 only?
Acceptable Values: boolean
Default Value: no
Description: If this is set to yes, the system force is measured along a
vector field (see equation (23) in
section 9.3.1) that only involves atoms of group1.
This option is only useful for ABF, or custom biases that compute
system forces. See section 9.3.1 for details.
The value returned is a positive number (in Å), limited
between 0 and the largest possible interatomic distance
within the chosen boundary conditions (in PBC, the minimum image
convention is used).
The distanceZ {...} block defines a distance projection
component, which can be seen as measuring the distance between two groups
projected onto an axis, or the position of a group along such an axis. The axis
can be defined using either one reference group and a constant vector, or
dynamically based on two reference groups.
- main
(distanceZ, distanceXY) Main group of atoms
Acceptable Values: Block main {...}
Description: Group of atoms whose position
is measured.
- ref
(distanceZ, distanceXY) Reference group of atoms
Acceptable Values: Block ref {...}
Description: Reference group of atoms. The position of its center of mass is noted
below.
- ref2
(distanceZ, distanceXY) Secondary reference group
Acceptable Values: Block ref2 {...}
Default Value: none
Description: Optional group of reference atoms, whose position
can be used
to define a dynamic projection axis:
. In this case,
the origin is
, and the value of the component
is
.
- axis
(distanceZ, distanceXY) Projection axis (Å)
Acceptable Values: (x, y, z) triplet
Default Value: (0.0, 0.0, 1.0)
Description: The three components of this vector define (when normalized)
a projection axis
for the distance vector
joining the
centers of groups ref and main. The value of the component is then
.
The vector should be written as three components
separated by commas and enclosed in parentheses.
- oneSiteSystemForce
(distanceZ, distanceXY) Measure system force on group main only?
Acceptable Values: boolean
Default Value: no
Description: If this is set to yes, the system force is measured along a
vector field (see equation (23) in
section 9.3.1) that only involves atoms of main.
This option is only useful for ABF, or custom biases that compute
system forces. See section 9.3.1 for details.
This component returns a number (in Å) whose range is
determined by the chosen boundary conditions: if the
axis is used in
PBC, its value is limited between
and
, where
is the box length in the
direction.
The distanceXY {...} block defines a distance projected
on a plane, and accepts the same options as distanceZ, i.e.
main, ref, either ref2 or axis, and
oneSiteSystemForce. It returns the
norm of the projection of the distance vector between main and
ref onto the plane orthogonal to the axis. The axis is
defined using the axis parameter or as the vector joining
ref and ref2 (see distanceZ above).
The distanceVec {...} block
defines a distance vector component, which accepts the same options as
distance, group1 and group2. It returns a
3-dimensional vector
. The
range of values of
,
and
(in Å)
is determined by the chosen boundary conditions.
The distanceDir {...} block
defines a distance unit vector component, which accepts the same
options as distance, group1 and group2. It
returns a 3-dimensional unit vector
,
.
,
and
lie
within the
interval.
The angle {...} block defines an angle, which accepts the
options group1, group2 and group3 to define
the three groups. It returns an angle (in degrees) within the
interval
.
The dihedral {...} block defines a torsional angle, which
accepts the options group1, group2, group3
and group4 to define the four groups. It returns an angle
(in degrees) within the interval
. The colvar module
calculates all the distances between two angles taking into account
periodicity. For instance, reference values for restraints or range
boundaries can be defined by using any real number of choice.
- oneSiteSystemForce
(dihedral) Measure system force on group 1 only?
Acceptable Values: boolean
Default Value: no
Description: If this is set to yes, the system force is measured along a
vector field (see equation (23) in
section 9.3.1) that only involves atoms of group1.
See section 9.3.1 for an example.
The coordnum {...} block defines
a coordination number (or number of contacts), which calculates the
function
, where
is the
``cutoff'' distance, and
and
are exponents that can control
its long range behavior and stiffness [27]. This
function is summed over all pairs of atoms in group1 and
group2:
 |
(13) |
This colvar component accepts the same options as distance,
group1 and group2. In addition to them, it
recognizes the following options:
- cutoff
(coordnum) Reference distance (Å)
Acceptable Values: positive decimal
Default Value: 4.0
Description: This number defines the switching distance to define an
interatomic contact: for
, the switching function
is close to 1, at
it
has a value of
(
with the default
and
), and at
it goes to zero approximately like
. Hence,
for a proper behavior,
must be larger than
.
- expNumer
(coordnum) Numerator exponent
Acceptable Values: positive even integer
Default Value: 6
Description: This number defines the
exponent for the switching function.
- expDenom
(coordnum) Denominator exponent
Acceptable Values: positive even integer
Default Value: 12
Description: This number defines the
exponent for the switching function.
- cutoff3
(coordnum) Reference distance vector (Å)
Acceptable Values: ``(x, y, z)'' triplet of positive decimals
Default Value: (4.0, 4.0, 4.0)
Description: The three components of this vector define three different cutoffs
for each direction. This option is mutually exclusive with
cutoff.
- group2CenterOnly
(coordnum) Use only group2's center of
mass
Acceptable Values: boolean
Default Value: off
Description: If this option is on, only contacts between the atoms in
group1 and the center of mass of group2 are
calculated. By default, the sum extends over all pairs of
atoms in group1 and group2.
This component returns a dimensionless number, which ranges from
approximately 0 (all interatomic distances much larger than the
cutoff) to
(all distances
within the cutoff), or
if
group2CenterOnly is used. As a recommendation, at least
one group1 and group2 should be of limited size
(unless group2CenterOnly is used), because the size of
the loop over all pairs grows with the product of the sizes of
and
.
The hBond {...} block defines a hydrogen
bond, implemented as a coordination number (eq. 13)
between the donor and the acceptor atoms. Therefore, it accepts the
same options cutoff (with a different default value of
3.3 Å), expNumer (with a default value of 6) and
expDenom (with a default value of 8). Unlike
coordnum, it requires two atom numbers, acceptor and
donor, to be defined. It returns an adimensional number,
with values between 0 (acceptor and donor far outside the cutoff
distance) and 1 (acceptor and donor much closer than the cutoff).
The block
rmsd {...} defines the root mean square replacement
(RMSD) of a group of atoms with respect to a reference structure. For
each set of coordinates
, the colvar component rmsd calculates the
optimal rotation
that best superimposes the coordinates
onto a
set of reference coordinates
.
Both the current and the reference coordinates are centered on their
centers of geometry,
and
. The root mean square
displacement is then defined as:
 |
(14) |
The optimal rotation
is calculated within the formalism developed in
reference [15], which guarantees a continuous
dependence of
with respect to
. The options for rmsd
are:
- atoms
(rmsd) Atom group
Acceptable Values: atoms {...} block
Description: Defines the group of atoms of which the RMSD should be calculated.
- refPositions
(rmsd) Reference coordinates
Acceptable Values: space-separated list of (x, y, x) triplets
Description: This option (mutually exclusive with refPositionsFile
sets the reference coordinates to be compared with. The list
should be as long as the atom group atoms. This option
is independent from that with the same keyword within the
atoms {...} block.
- refPositionsFile
(rmsd) Reference coordinates file
Acceptable Values: UNIX filename
Description: This option (mutually exclusive with refPositions sets
the PDB file name for the reference coordinates to be compared
with. The format of the PDB file is the same as that provided by
refPositionsFile within the atoms {...}
block, but is independent from that with the same keyword within
the atoms {...} block.
- refPositionsCol
(rmsd) PDB column to use
Acceptable Values: X, Y, Z, O or B
Default Value: O
Description: If refPositionsFile is defined, and the file contains
all the atoms in the topology, this option sets which PDB field is
used to select the reference coordinates for atoms.
Otherwise, this field is ignored.
- refPositionsColValue
(rmsd) Value in the PDB column
Acceptable Values: positive decimal
Description: If defined, this value identifies in the PDB column
refPositionsCol of the file refPositionsFile
which atom positions are to be read. Otherwise, all positions
with a non-zero value will be read.
This component returns a positive real number (in Å).
The block orientation {...}
returns the same optimal rotation used in the rmsd component
to superimpose the coordinates
onto a set of
reference coordinates
. It accepts
all the options of rmsd: atoms,
refPositions, refPositionsFile and
refPositionsCol, and returns a four dimensional vector
, with
; this
quaternion expresses the optimal rotation
according to the
formalism in reference [15]. The quaternion
can also be written as
, where
is the angle and
the normalized axis of rotation; for example, a rotation
of 90
around the
axis should be expressed as
``(0.707, 0.0, 0.0, 0.707)''. The script
quaternion2rmatrix.tcl provides Tcl functions for converting
to and from a
rotation matrix in a format suitable for
usage in VMD.
Hint: to restrain the rotation of a macromolecule in solution
(e.g. when one of the cell dimensions is much longer than the others),
it is possible to define a colvar with an
orientation component, and restrain it throuh the
harmonic bias around the ``zero'' rotation, (1.0,
0.0, 0.0, 0.0).
The block
orientationAngle {...} accepts the same options of
rmsd and orientation (atoms,
refPositions, refPositionsFile and
refPositionsCol), but it returns instead the angle of
rotation
between the current and the reference positions.
This angle is expressed in degrees within the range
[-180
:180
].
The
block gyration {...} defines the parameters for
calculating the radius of gyration of a group of atomic positions
with
respect to their center of geometry,
:
 |
(15) |
This component must contain one atoms {...} block to
define the atom group, and returns a positive number, expressed in
Å.
The block alpha {...} defines the
parameters to calculate the helical content of a segment of protein
residues. The
-helical content across the
residues
to
is calculated by the formula:
 |
|
|
(16) |
 |
|
|
|
where the score function for the
angle is defined as:
 |
(17) |
and the score function for the
hydrogen bond is defined through a hBond
colvar component on the same atoms. The options recognized within the
alpha {...} block are:
This component returns positive values, always comprised between 0
(lowest
-helical score) and 1 (highest
-helical
score).
Any set of components can be combined within a colvar,
provided that they return
the same type of values (scalar, unit vector, vector, or quaternion).
By default, the colvar is the sum of its components.
Linear or polynomial combinations (following equation (12))
can be obtained by setting the following
parameters, which are common to all components:
Defining atom groups
Each component depends on one or more atom groups, which can be
defined by different methods in the configuration file. Each atom
group block is initiated by the name of the group itself within the
component block, followed by the instructions to the colvar module on
how to select the atoms involved. Here is an example configuration,
for an atom group called myatoms, which makes use of the most
common keywords:
# atom group definition
myatoms {
# add atoms 1, 2 and 3 to this group (note: numbers start from 1)
atomNumbers {
1 2 3
}
# add all the C-alphas within residues 11 to 20 of segment "PROT"
atomNameResidueRange CA 11-20
psfSegID PROT
# add all the atoms with occupancy 2 in the file atoms_occ1.pdb
atomsFile atoms_occ1.pdb
atomsCol O
atomsColValue 2.0
}
For any atom group, the available options are:
- atomNumbers
(atom group) List of atom numbers
Acceptable Values: space-separated list of positive integers
Description: This option adds to the group all the atoms whose numbers are in
the list. Atom numbering starts from 1.
- atomNumbersRange
(atom group) Atoms within a number range
Acceptable Values:
Starting number
-
Ending number
Description: This option adds to the group all the atoms whose numbers are
within the range specified. It can be used multiple times for the
same group. Atom numbering starts from 1. May be repeated.
- atomNameResidueRange
(atom group) Named atoms within a range of residue numbers
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 range provided. May be repated.
- psfSegID
(atom group) PSF segment identifier
Acceptable Values: string (max 4 characters)
Description: This option sets the PSF segment identifier for all instances of
atomNameResidueRange within this atom group. This option
need not be provided when non-PSF topologies are used by NAMD.
- atomsFile
(atom group) PDB file name for atom selection
Acceptable Values: string
Description: This option selects atoms from the PDB file provided and adds them
to the group according to the value in the column
atomsCol. Note: the PDB file provide must match
the number of atoms in the topology.
- atomsCol
(atom group) PDB column to use for the selection
Acceptable Values: X, Y, Z, O or B
Default Value: O
Description: This option specifies which column in atomsFile is used
to determine the atoms to be included in the group.
- atomsColValue
(atom group) Value in the PDB column
Acceptable Values: positive decimal
Description: If defined, this value identifies in atomsCol of
atomsFile which atoms are to be read; otherwise, all
atoms with a non-zero value will be read.
- dummyAtom
(atom group) Dummy atom position (Å)
Acceptable Values: (x, y, z) triplet
Description: If no actual atoms are defined for the group, this option may be
used to make this group return a fixed position in space. This is
useful e.g. to make colvar components that normally calculate
functions of the group's center of mass work with an absolute
reference position. If this option is specified for the group,
disableForces is turned on, the (x, y, z)
position provided is returned as its center of mass, and zero
velocities and system forces are reported.
- centerReference
(atom group) Ignore the translations of this group
Acceptable Values: boolean
Default Value: off
Description: If this option is on, the center of mass of this group is
centered on a reference frame, determined either by
refPositions or refPositionsFile. This
transformation occurs before any colvar component has
access to the coordinates of the group: hence, only the recentered
coordinates are available to the colvars.
- rotateReference
(atom group) Ignore the rotations of this group
Acceptable Values: boolean
Default Value: off
Description: If this option is on, this group is rotated around its
center of mass to optimally reproduce the coordinates given by
refPositions or refPositionsFile. This is done
before recentering the group, if centerReference is also
defined. The algorithm used is the same employed in the
orientation colvar component [15]. Forces
applied to this group from within the colvar module are rotated
back to the reference frame of the simulation prior being
communicated to the MD integrator. Note: care must be
taken when a torque is applied on the group, which could bring the
simulation out of control; to avoid such problems,
disableForces could be used for this group.
- refPositions
(atom group) Reference positions for the group (Å)
Acceptable Values: space-separated list of (x, y, z) triplets
Description: If either centerReference or rotateReference
is on, these coordinates are used to determine the
center of mass translation and the optimal rotation between them
and the current coordinates of the group. In the latter case, the
list must be of the same length as this atom group.
- refPositionsFile
(atom group) Reference positions for the group
Acceptable Values: UNIX filename
Description: If either centerReference or rotateReference is
on, the coordinates from this file are used to determine
the center of mass's translation and the optimal rotation between
them and the current coordinates of the group. This file can
either i) contain as many atoms as the group (in which case
all of the ATOM records are read) or ii) a larger
number of atoms (in which case atoms will be selected according to
refPositionsCol). A typical usage may be to reuse
atomsFile. Unlike atomsFile, however, it need
not match the number of atoms in the topology.
- refPositionsCol
(atom group) Reference positions for the group
Acceptable Values: X, Y, Z, O or B
Default Value: O
Description: Analogous to atomsCol.
- refPositionsColValue
(atom group) Value in the PDB column
Acceptable Values: positive decimal
Description: Analogous to atomsColValue.
- refPositionsGroup
(atom group) Group to be used
Acceptable Values: Block refPositionsGroup { ... }
Default Value: This group itself
Description: If either centerReference or rotateReference is
defined, this keyword allows to define an additional atom group,
which is used instead of this one to calculate the translation or
the rotation to the reference positions.
- disableForces
(atom group) Disable application of colvar forces on this group
Acceptable Values: boolean
Default Value: off
Description: If this option is on, all the forces applied from the
colvars to the atoms in this group are ignored. However, the
applied forces on each colvar are still written to the
trajectory file, if requested. In some cases
it may be desirable to use this option in order not to perturb the
motion of selected groups of atoms. However, it is not advisable
to perform a potential of mean force (PMF) calculation with this
flag, because the biasing forces would not be applied uniformly.
Also, when disabling the forces on one of several groups defining
a colvar, a non-zero net force (or torque) is applied to the
entire system, leading to an undesired center of mass motion
(resp. rotation).
To minimize the length of the NAMD standard output, messages from the
previous options are not echoed by default. They can be enabled by
using the boolean keyword verboseOutput.
Nearly all the
calculations of colvar components are based on user-specified atom
groups. These guidelines could be useful when choosing the atom
groups to define a collective variable:
- When using periodic boundary conditions, NAMD maintains the
coordinates of all the atoms within a molecule contiguous to each
other (i.e. there are no ``jumps'' due to the periodic boundary
conditions). The colvar module relies on this when calculating a
group's center of mass, but this condition may fail when the group
spans different molecules. In this case, writing the NAMD output
files wrapAll or wrapWater could produce wrong
results when a simulation run is continued from a previous one.
There are however cases in which wrapAll or
wrapWater can be safely applied:
- i)
- the group has only one atom;
- ii)
- it has all its atoms within the same molecule;
- iii)
- it is used by a colvar component which does
not access its center of mass (coordnum,
hBond, alpha);
- iv)
- it is used by a colvar component that ignores the
ill-defined Cartesian components of its center of mass (such as
the
and
components of a membrane's center of mass by
distanceZ).
In the general case, the user should determine, according to which
type of calculation is being performed, whether wrapAll or
wrapWater can be enabled.
- The colvars calculation is is not parallelized over the
computational nodes. Therefore, the extra load on the first node,
where the colvars module is executed, should be maintained lower
than that of any other node. In most cases this condition is very
well satisfied, but there may be some specific configurations for
which such extra load may affect the parallel performance of NAMD.
As a general guideline, an atom group should include for a large
fraction of the whole system only when necessary.
Statistical analysis of individual collective variables
When the global keyword analysis is defined in the
configuration file, calculations of statistical properties for
individual colvars can be performed. At the moment, several types of
time correlation functions, running averages and running standard
deviations are available.
- corrFunc
(colvar) Calculate a time correlation function?
Acceptable Values: boolean
Default Value: off
Description: Whether or not a time correlaction function should be calculated
for this colvar.
- corrFuncWithColvar
(colvar) Colvar name for the correlation function
Acceptable Values: string
Description: By default, the auto-correlation function (ACF) of this colvar,
, is calculated. When this option is specified, the
correlation function is calculated instead with another colvar,
, which must be of the same type (scalar, vector, or
quaternion) of
.
- corrFuncType
(colvar) Type of the correlation function
Acceptable Values: velocity, coordinate or
coordinate_p2
Default Value: velocity
Description: With coordinate or velocity, the correlation
function
=
is calculated between
the variables
and
, or their velocities.
is the scalar product when calculated
between scalar or vector values, whereas for quaternions it is the
cosine between the two corresponding rotation axes. With
coordinate_p2, the second order Legendre polynomial,
, is used instead of the cosine.
- corrFuncNormalize
(colvar) Normalize the time correlation function?
Acceptable Values: boolean
Default Value: on
Description: If enabled, the value of the correlation function at
= 0
is normalized to 1; otherwise, it equals to
.
- corrFuncLength
(colvar) Length of the time correlation function
Acceptable Values: positive integer
Default Value: 1000
Description: Length (in number of points) of the time correlation function.
- corrFuncStride
(colvar) Stride of the time correlation function
Acceptable Values: positive integer
Default Value: 1
Description: Number of steps between two values of the time correlation function.
- corrFuncOffset
(colvar) Offset of the time correlation function
Acceptable Values: positive integer
Default Value: 0
Description: The starting time (in number of steps) of the time correlation
function (default:
= 0). Note: the value at
= 0 is always
used for the normalization.
- corrFuncOutputFile
(colvar) Output file for the time correlation function
Acceptable Values: UNIX filename
Default Value:
name
.corrfunc.dat
Description: The time correlation function is saved in this file.
- runAve
(colvar) Calculate the running average and standard deviation
Acceptable Values: boolean
Default Value: off
Description: Whether or not the running average and standard deviation should
be calculated for this colvar.
- runAveLength
(colvar) Length of the running average window
Acceptable Values: positive integer
Default Value: 1000
Description: Length (in number of points) of the running average window.
- runAveStride
(colvar) Stride of the running average window values
Acceptable Values: positive integer
Default Value: 1
Description: Number of steps between two values within the running average window.
- runAveOutputFile
(colvar) Output file for the running average and standard deviation
Acceptable Values: UNIX filename
Default Value:
name
.runave.dat
Description: The running average and standard deviation are saved in this file.
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Up: Collective Variable-based Calculations1
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