Project ID: plumID:20.009
Source: Ub2/plumed-cv.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.9
tested onmaster
#SETTINGS NREPLICAS=2
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
STRUCTURE
a file in pdb format containing a reference structure
=template.pdb
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the atoms that make up a molecule that you wish to align
=1-355
a:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=31,32,34,36,40,42,45,47,49,51,52,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,88,89,92,94,96,98,101,103,104,106,108,110,112,114,116,119,121,123,127,128,129,132,134,136,138,140,141,144,146,148,150,152,156,158,160,162,167,169,171,173,177,179
NOPBC
ignore the periodic boundary conditions when calculating distances
b:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=193,195,197,199,203,205,208,210,212,214,215,218,220,222,224,226,228,230,232,234,236,238,240,242,244,246,248,251,252,255,257,259,261,264,266,267,269,271,273,275,277,279,282,284,286,290,291,292,295,297,299,301,303,304,307,309,311,313,315,319,321,323,325,328,330,332,334,336,340,342
NOPBC
ignore the periodic boundary conditions when calculating distances

#Centers in ubiquitin a1:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=31,32,34,36,40,42,45,47,49,51,52,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,88,89,92,94,96,98,101,103,104
NOPBC
ignore the periodic boundary conditions when calculating distances
a2:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=106,108,110,112,114,116,119,121,123,127,128,129,132,134,136,138,140,141,144,146,148,150,152,156,158,160,162,167,169,171,173,177,179
NOPBC
ignore the periodic boundary conditions when calculating distances
b1:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=193,195,197,199,203,205,208,210,212,214,215,218,220,222,224,226,228,230,232,234,236,238,240,242,244,246,248,251,252,255,257,259,261,264,266,267
NOPBC
ignore the periodic boundary conditions when calculating distances
b2:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=269,271,273,275,277,279,282,284,286,290,291,292,295,297,299,301,303,304,307,309,311,313,315,319,321,323,325,328,330,332,334,336,340,342
NOPBC
ignore the periodic boundary conditions when calculating distances

# distance both ubiquitin d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=a,b
NOPBC
ignore the periodic boundary conditions when calculating distances
#relativ orientation tor1:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=a1,a2,b1,b2
NOPBC
ignore the periodic boundary conditions when calculating distances

rg:
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,3,4,6,10,14,18,22,26,30,31,32,34,36,40,42,45,47,49,51,52,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,88,89,92,94,96,98,101,103,104,106,108,110,112,114,116,119,121,123,127,128,129,132,134,136,138,140,141,144,146,148,150,152,156,158,160,162,165,167,169,171,173,177,179,181,183,186,188,191,192,193,195,197,199,203,205,208,210,212,214,215,218,220,222,224,226,228,230,232,234,236,238,240,242,244,246,248,251,252,255,257,259,261,264,266,267,269,271,273,275,277,279,282,284,286,290,291,292,295,297,299,301,303,304,307,309,311,313,315,319,321,323,325,328,330,332,334,336,340,342,344,346,349,351,354,355
NOPBC
ignore the periodic boundary conditions when calculating distances

ALPHABETA
Calculate the alpha beta CV More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=linktor1
REFERENCE
the reference values for each of the torsional angles
=0
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=179,181,183,186
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=181,183,186,188
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=183,186,188,191
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=186,188,191,192
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=188,191,192,193
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=191,192,193,195 ... ALPHABETA
SAXS
Calculates SAXS intensity. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=test2
ATOMS
The atoms to be included in the calculation, e
=1-355
NOPBC
Ignore the periodic boundary conditions when calculating distances
MARTINI
Calculate SAXS for a Martini model
QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0178612
QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0290150
QVALUE3
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0401689
QVALUE4
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0513227
QVALUE5
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0624766
QVALUE6
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0736304
QVALUE7
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0847843
QVALUE8
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.0959381
QVALUE9
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.1070922
QVALUE10
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.118246
QVALUE11
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.129399
QVALUE12
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.140553
QVALUE13
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.151707
QVALUE14
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.162861
QVALUE15
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.174015
QVALUE16
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.185169
QVALUE17
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.196323
QVALUE18
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.207476
QVALUE19
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.218630
QVALUE20
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.229784
QVALUE21
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,
=0.240938
EXPINT1
Add an experimental value for each q value
=1.11825
EXPINT2
Add an experimental value for each q value
=1.02402
EXPINT3
Add an experimental value for each q value
=0.901402
EXPINT4
Add an experimental value for each q value
=0.768395
EXPINT5
Add an experimental value for each q value
=0.637896
EXPINT6
Add an experimental value for each q value
=0.51898
EXPINT7
Add an experimental value for each q value
=0.417004
EXPINT8
Add an experimental value for each q value
=0.333873
EXPINT9
Add an experimental value for each q value
=0.268715
EXPINT10
Add an experimental value for each q value
=0.218862
EXPINT11
Add an experimental value for each q value
=0.18084
EXPINT12
Add an experimental value for each q value
=0.151206
EXPINT13
Add an experimental value for each q value
=0.127107
EXPINT14
Add an experimental value for each q value
=0.106525
EXPINT15
Add an experimental value for each q value
=0.0882832
EXPINT16
Add an experimental value for each q value
=0.0718846
EXPINT17
Add an experimental value for each q value
=0.0572756
EXPINT18
Add an experimental value for each q value
=0.0446096
EXPINT19
Add an experimental value for each q value
=0.0340539
EXPINT20
Add an experimental value for each q value
=0.0256793
EXPINT21
Add an experimental value for each q value
=0.0194114 ... SAXS
lsaxs:
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
ARG
the input for this action is the scalar output from one or more other actions
=(test2\.q
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(test2\.exp
PBMETAD
Used to performed Parallel Bias metadynamics. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bias
ARG
the input for this action is the scalar output from one or more other actions
=d1,tor1,rg,linktor1
HEIGHT
the height of the Gaussian hills, one for all biases
=0.1
PACE
the frequency for hill addition, one for all biases
=200
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=20
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
GRID_WFILES
dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES
=GRID.0,GRID.1,GRID.2,GRID.3
GRID_WSTRIDE
frequency for dumping the grid
=2000 #GRID_RFILES=GRID.0,GRID.1,GRID.2,GRID.3
SIGMA
the widths of the Gaussian hills
=10000
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.005,0.005,0.005,0.005
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.2,0.2,0.2,0.2
GRID_MIN
the lower bounds for the grid
=0,-pi,0,0
GRID_MAX
the upper bounds for the grid
=7,pi,6,6
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
UPDATE_FROM
Only update this action from this time
=2000 ... PBMETAD
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
...
SCALEDATA
Set to TRUE if you want to sample a scaling factor common to all values and replicas
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=100
NOISETYPE
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MOUTLIERS
ARG
the input for this action is the scalar output from one or more other actions
=(test2\.q-.*),bias.bias
REWEIGHT
simple REWEIGHT using the latest ARG as energy
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(test2\.exp
SCALE_PRIOR
either FLAT or GAUSSIAN
=FLAT
ADDOFFSET
Set to TRUE if you want to sample an offset common to all values and replicas
OFFSET_PRIOR
either FLAT or GAUSSIAN
=FLAT
OFFSET0
initial value of the offset
=0
OFFSET_MIN
minimum value of the offset
=-1
OFFSET_MAX
maximum value of the offset
=1
DOFFSET
maximum MC move of the offset
=0.002
SCALE0
initial value of the scaling factor
=1.00
SCALE_MIN
minimum value of the scaling factor
=0.9
SCALE_MAX
maximum value of the scaling factor
=1.1
DSCALE
maximum MC move of the scaling factor
=0.00005
SIGMA0
initial value of the uncertainty parameter
=0.001
SIGMA_MIN
minimum value of the uncertainty parameter
=0
SIGMA_MAX
maximum value of the uncertainty parameter
=0.02
DSIGMA
maximum MC move of the uncertainty parameter
=0.0001
OPTSIGMAMEAN
Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bq
WRITE_STRIDE
write the status to a file every N steps, this can be used for restart/continuation
=10000
STRIDE
the frequency with which the forces due to the bias should be calculated
=5 ... METAINFERENCE
ensaxs:
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
ARG
the input for this action is the scalar output from one or more other actions
=(test2\.q-.*),bias.bias
REWEIGHT
simple REWEIGHT using the latest ARG as energy
statsq:
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
ARG
the input for this action is the scalar output from one or more other actions
=(ensaxs\.test2\.q
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(test2\.exp
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
STRIDE
the frequency with which all the open files should be flushed
=1000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=(test2\.q-.*),(test2\.exp
FILE
the name of the file on which to output these quantities
=CV.dat
STRIDE
the frequency with which the quantities of interest should be output
=100
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=RESTRAINTS
ARG
the input for this action is the scalar output from one or more other actions
=bq
STRIDE
the frequency with which the quantities of interest should be output
=100
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=q.dat
ARG
the input for this action is the scalar output from one or more other actions
=statsq.*,lsaxs
STRIDE
the frequency with which the quantities of interest should be output
=100
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=Analyse.dat
ARG
the input for this action is the scalar output from one or more other actions
=d1,tor1,rg,linktor1
STRIDE
the frequency with which the quantities of interest should be output
=100
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=BIAS
ARG
the input for this action is the scalar output from one or more other actions
=bias.bias
STRIDE
the frequency with which the quantities of interest should be output
=100
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=ENSAXS
ARG
the input for this action is the scalar output from one or more other actions
=(ensaxs\.test2\.q
STRIDE
the frequency with which the quantities of interest should be output
=100
enANA:
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
ARG
the input for this action is the scalar output from one or more other actions
=d1,tor1,rg,linktor1,bias.bias
REWEIGHT
simple REWEIGHT using the latest ARG as energy
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=ENANA
ARG
the input for this action is the scalar output from one or more other actions
=enANA
STRIDE
the frequency with which the quantities of interest should be output
=100