PLUMED-NEST

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

#SETTINGS NREPLICAS=2
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=template.pdb

The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=1-355

a: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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
The CENTER action with label a calculates the following quantities:
 Quantity   
 Description  
a.value
the position of the center of massb: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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
The CENTER action with label b calculates the following quantities:
 Quantity   
 Description  
b.value
the position of the center of massa1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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
The CENTER action with label a1 calculates the following quantities:
 Quantity   
 Description  
a1.value
the position of the center of massa2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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
The CENTER action with label a2 calculates the following quantities:
 Quantity   
 Description  
a2.value
the position of the center of massb1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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
The CENTER action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.value
the position of the center of massb2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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
The CENTER action with label b2 calculates the following quantities:
 Quantity   
 Description  
b2.value
the position of the center of massd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,b NOPBC ignore the periodic boundary conditions when calculating distances
#relativ orientation
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomstor1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=a1,a2,b1,b2 NOPBC ignore the periodic boundary conditions when calculating distances

The TORSION action with label tor1 calculates the following quantities:
 Quantity   
 Description  
tor1.value
the TORSION involving these atomsrg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe 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


The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightsALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=linktor1
REFERENCEthe reference values for each of the torsional angles=0
ATOMS1the atoms involved for each of the torsions you wish to calculate=179,181,183,186
ATOMS2the atoms involved for each of the torsions you wish to calculate=181,183,186,188
ATOMS3the atoms involved for each of the torsions you wish to calculate=183,186,188,191
ATOMS4the atoms involved for each of the torsions you wish to calculate=186,188,191,192
ATOMS5the atoms involved for each of the torsions you wish to calculate=188,191,192,193
ATOMS6the atoms involved for each of the torsions you wish to calculate=191,192,193,195
... ALPHABETA

The ALPHABETA action with label linktor1 calculates the following quantities:
 Quantity   
 Description  
linktor1.value
the alpha beta CVSAXSCalculates SAXS intensity. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=test2
ATOMSThe 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

QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0178612
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0290150
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0401689
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0513227
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0624766
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0736304
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0847843
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0959381
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1070922
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.118246
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.129399
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.140553
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.151707
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.162861
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.174015
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.185169
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.196323
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.207476
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.218630
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.229784
QVALUE21Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.240938

EXPINT1Add an experimental value for each q value=1.11825
EXPINT2Add an experimental value for each q value=1.02402
EXPINT3Add an experimental value for each q value=0.901402
EXPINT4Add an experimental value for each q value=0.768395
EXPINT5Add an experimental value for each q value=0.637896
EXPINT6Add an experimental value for each q value=0.51898
EXPINT7Add an experimental value for each q value=0.417004
EXPINT8Add an experimental value for each q value=0.333873
EXPINT9Add an experimental value for each q value=0.268715
EXPINT10Add an experimental value for each q value=0.218862
EXPINT11Add an experimental value for each q value=0.18084
EXPINT12Add an experimental value for each q value=0.151206
EXPINT13Add an experimental value for each q value=0.127107
EXPINT14Add an experimental value for each q value=0.106525
EXPINT15Add an experimental value for each q value=0.0882832
EXPINT16Add an experimental value for each q value=0.0718846
EXPINT17Add an experimental value for each q value=0.0572756
EXPINT18Add an experimental value for each q value=0.0446096
EXPINT19Add an experimental value for each q value=0.0340539
EXPINT20Add an experimental value for each q value=0.0256793
EXPINT21Add an experimental value for each q value=0.0194114

... SAXS

The SAXS action with label test2 calculates the following quantities:
 Quantity   
 Description  
test2.score
the Metainference score
test2.sigma
uncertainty parameter
test2.sigmaMean
uncertainty in the mean estimate
test2.neff
effective number of replicas
test2.acceptSigma
MC acceptance for sigma values
test2.q
The # SAXS of qlsaxs: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(test2\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(test2\.exp-.*)

The STATS action with label lsaxs calculates the following quantities:
 Quantity   
 Description  
lsaxs.sqdevsum
the sum of the squared deviations between arguments and parameters
lsaxs.corr
the correlation between arguments and parameters
lsaxs.slope
the slope of a linear fit between arguments and parameters
lsaxs.intercept
the intercept of a linear fit between arguments and parametersPBMETADUsed to performed Parallel Bias metadynamics. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=bias
ARGthe labels of the scalars on which the bias will act=d1,tor1,rg,linktor1
HEIGHTthe height of the Gaussian hills, one for all biases=0.1
PACEthe frequency for hill addition, one for all biases=200
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=20
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
GRID_WFILESdump 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_WSTRIDEfrequency for dumping the grid=2000
#GRID_RFILES=GRID.0,GRID.1,GRID.2,GRID.3
SIGMAthe widths of the Gaussian hills=10000
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.005,0.005,0.005,0.005
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.2,0.2,0.2,0.2

GRID_MINthe lower bounds for the grid=0,-pi,0,0
GRID_MAXthe 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_FROMOnly update this action from this time=2000
... PBMETAD

The PBMETAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.bias
the instantaneous value of the bias potentialMETAINFERENCECalculates 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
AVERAGINGStride for calculation of averaged weights and sigma_mean=100
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MOUTLIERS
ARGthe labels of the scalars on which the bias will act=(test2\.q-.*),bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy PARARGreference 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_MINminimum value of the offset=-1 OFFSET_MAXmaximum value of the offset=1 DOFFSETmaximum MC move of the offset=0.002
SCALE0 initial value of the scaling factor=1.00 SCALE_MINminimum value of the scaling factor=0.9 SCALE_MAXmaximum value of the scaling factor=1.1 DSCALEmaximum 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 DSIGMAmaximum 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
LABELa 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
STRIDEthe frequency with which the forces due to the bias should be calculated=5
... METAINFERENCE


The METAINFERENCE action with label bq calculates the following quantities:
 Quantity   
 Description  
bq.bias
the instantaneous value of the bias potential
bq.sigma
uncertainty parameter
bq.sigmaMean
uncertainty in the mean estimate
bq.neff
effective number of replicas
bq.acceptSigma
MC acceptance for sigma values
bq.acceptScale
MC acceptance for scale value
bq.weight
weights of the weighted average
bq.biasDer
derivatives with respect to the bias
bq.scale
scale parameter
bq.offset
offset parameterensaxs: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(test2\.q-.*),bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
The ENSEMBLE action with label ensaxs calculates the following quantities:
 Quantity   
 Description  
ensaxs..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsstatsq: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(ensaxs\.test2\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(test2\.exp-.*)

The STATS action with label statsq calculates the following quantities:
 Quantity   
 Description  
statsq.sqdevsum
the sum of the squared deviations between arguments and parameters
statsq.corr
the correlation between arguments and parameters
statsq.slope
the slope of a linear fit between arguments and parameters
statsq.intercept
the intercept of a linear fit between arguments and parametersFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(test2\.q-.*),(test2\.exp-.*) FILEthe 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
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=RESTRAINTS ARGthe labels of the values that you would like to print to the file=bq.* STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=q.dat ARGthe labels of the values that you would like to print to the file=statsq.*,lsaxs.* STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=Analyse.dat ARGthe labels of the values that you would like to print to the file=d1,tor1,rg,linktor1 STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=BIAS ARGthe labels of the values that you would like to print to the file=bias.bias STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ENSAXS ARGthe labels of the values that you would like to print to the file=(ensaxs\.test2\.q-.*) STRIDE the frequency with which the quantities of interest should be output=100

enANA: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=d1,tor1,rg,linktor1,bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
The ENSEMBLE action with label enANA calculates the following quantities:
 Quantity   
 Description  
enANA..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsPRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ENANA ARGthe labels of the values that you would like to print to the file=enANA.* STRIDE the frequency with which the quantities of interest should be output=100