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
#SETTINGS NREPLICAS=2MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=template.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-355the atoms that make up a molecule that you wish to align
a:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=31,32,34,36,40,42,45,47,49,51,52,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,88,89,92,94,96,98,101,103,104,106,108,110,112,114,116,119,121,123,127,128,129,132,134,136,138,140,141,144,146,148,150,152,156,158,160,162,167,169,171,173,177,179the group of atoms that you are calculating the Gyration Tensor forNOPBCb:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=193,195,197,199,203,205,208,210,212,214,215,218,220,222,224,226,228,230,232,234,236,238,240,242,244,246,248,251,252,255,257,259,261,264,266,267,269,271,273,275,277,279,282,284,286,290,291,292,295,297,299,301,303,304,307,309,311,313,315,319,321,323,325,328,330,332,334,336,340,342the group of atoms that you are calculating the Gyration Tensor forNOPBCignore the periodic boundary conditions when calculating distances
#Centers in ubiquitin a1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=31,32,34,36,40,42,45,47,49,51,52,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,88,89,92,94,96,98,101,103,104the group of atoms that you are calculating the Gyration Tensor forNOPBCa2:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=106,108,110,112,114,116,119,121,123,127,128,129,132,134,136,138,140,141,144,146,148,150,152,156,158,160,162,167,169,171,173,177,179the group of atoms that you are calculating the Gyration Tensor forNOPBCb1:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=193,195,197,199,203,205,208,210,212,214,215,218,220,222,224,226,228,230,232,234,236,238,240,242,244,246,248,251,252,255,257,259,261,264,266,267the group of atoms that you are calculating the Gyration Tensor forNOPBCb2:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=269,271,273,275,277,279,282,284,286,290,291,292,295,297,299,301,303,304,307,309,311,313,315,319,321,323,325,328,330,332,334,336,340,342the group of atoms that you are calculating the Gyration Tensor forNOPBCignore the periodic boundary conditions when calculating distances
# distance both ubiquitin d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=a,bthe pair of atom that we are calculating the distance betweenNOPBC#relativ orientation tor1:ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=a1,a2,b1,b2the four atoms involved in the torsional angleNOPBCignore the periodic boundary conditions when calculating distances
rg:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsATOMS=1,3,4,6,10,14,18,22,26,30,31,32,34,36,40,42,45,47,49,51,52,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,88,89,92,94,96,98,101,103,104,106,108,110,112,114,116,119,121,123,127,128,129,132,134,136,138,140,141,144,146,148,150,152,156,158,160,162,165,167,169,171,173,177,179,181,183,186,188,191,192,193,195,197,199,203,205,208,210,212,214,215,218,220,222,224,226,228,230,232,234,236,238,240,242,244,246,248,251,252,255,257,259,261,264,266,267,269,271,273,275,277,279,282,284,286,290,291,292,295,297,299,301,303,304,307,309,311,313,315,319,321,323,325,328,330,332,334,336,340,342,344,346,349,351,354,355the group of atoms that you are calculating the Gyration Tensor forNOPBCignore the periodic boundary conditions when calculating distancesALPHABETA...Calculate the alpha beta CV More detailsLABEL=linktor1a label for the action so that its output can be referenced in the input to other actionsREFERENCE=0the reference values for each of the torsional anglesATOMS1=179,181,183,186the atoms involved for each of the torsions you wish to calculateATOMS2=181,183,186,188the atoms involved for each of the torsions you wish to calculateATOMS3=183,186,188,191the atoms involved for each of the torsions you wish to calculateATOMS4=186,188,191,192the atoms involved for each of the torsions you wish to calculateATOMS5=188,191,192,193the atoms involved for each of the torsions you wish to calculateATOMS6=191,192,193,195 ... ALPHABETAthe atoms involved for each of the torsions you wish to calculateSAXS...Calculates SAXS intensity. More detailsLABEL=test2a label for the action so that its output can be referenced in the input to other actionsATOMS=1-355The atoms to be included in the calculation, eNOPBCIgnore the periodic boundary conditions when calculating distancesMARTINICalculate SAXS for a Martini modelQVALUE1=0.0178612Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE2=0.0290150Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE3=0.0401689Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE4=0.0513227Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE5=0.0624766Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE6=0.0736304Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE7=0.0847843Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE8=0.0959381Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE9=0.1070922Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE10=0.118246Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE11=0.129399Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE12=0.140553Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE13=0.151707Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE14=0.162861Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE15=0.174015Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE16=0.185169Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE17=0.196323Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE18=0.207476Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE19=0.218630Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE20=0.229784Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE21=0.240938Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT1=1.11825Add an experimental value for each q valueEXPINT2=1.02402Add an experimental value for each q valueEXPINT3=0.901402Add an experimental value for each q valueEXPINT4=0.768395Add an experimental value for each q valueEXPINT5=0.637896Add an experimental value for each q valueEXPINT6=0.51898Add an experimental value for each q valueEXPINT7=0.417004Add an experimental value for each q valueEXPINT8=0.333873Add an experimental value for each q valueEXPINT9=0.268715Add an experimental value for each q valueEXPINT10=0.218862Add an experimental value for each q valueEXPINT11=0.18084Add an experimental value for each q valueEXPINT12=0.151206Add an experimental value for each q valueEXPINT13=0.127107Add an experimental value for each q valueEXPINT14=0.106525Add an experimental value for each q valueEXPINT15=0.0882832Add an experimental value for each q valueEXPINT16=0.0718846Add an experimental value for each q valueEXPINT17=0.0572756Add an experimental value for each q valueEXPINT18=0.0446096Add an experimental value for each q valueEXPINT19=0.0340539Add an experimental value for each q valueEXPINT20=0.0256793Add an experimental value for each q valueEXPINT21=0.0194114 ... SAXSAdd an experimental value for each q value
lsaxs:STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=(test2\.qthe input for this action is the scalar output from one or more other actionsPARARG=(test2\.expthe input for this action is the scalar output from one or more other actions without derivativesPBMETAD...Used to performed Parallel Bias metadynamics. More detailsLABEL=biasa label for the action so that its output can be referenced in the input to other actionsARG=d1,tor1,rg,linktor1the input for this action is the scalar output from one or more other actionsHEIGHT=0.1the height of the Gaussian hills, one for all biasesPACE=200the frequency for hill addition, one for all biasesBIASFACTOR=20use well tempered metadynamics with this bias factor, one for all biasesADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeGRID_WFILES=GRID.0,GRID.1,GRID.2,GRID.3dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILESGRID_WSTRIDE=2000 #GRID_RFILES=GRID.0,GRID.1,GRID.2,GRID.3frequency for dumping the gridSIGMA=10000the widths of the Gaussian hillsSIGMA_MIN=0.005,0.005,0.005,0.005the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.2,0.2,0.2,0.2the upper bounds for the sigmas (in CV units) when using adaptive hillsGRID_MIN=0,-pi,0,0the lower bounds for the gridGRID_MAX=7,pi,6,6the upper bounds for the gridWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRUPDATE_FROM=2000 ... PBMETADOnly update this action from this timeMETAINFERENCE...Calculates the Metainference energy for a set of experimental data. More detailsSCALEDATASet to TRUE if you want to sample a scaling factor common to all values and replicasAVERAGING=100Stride for calculation of averaged weights and sigma_meanNOISETYPE=MOUTLIERSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)ARG=(test2\.q-.*),bias.biasthe input for this action is the scalar output from one or more other actionsREWEIGHTsimple REWEIGHT using the latest ARG as energyPARARG=(test2\.expreference values for the experimental data, these can be provided as arguments without derivativesSCALE_PRIOR=FLATeither FLAT or GAUSSIANADDOFFSETSet to TRUE if you want to sample an offset common to all values and replicasOFFSET_PRIOR=FLATeither FLAT or GAUSSIANOFFSET0=0initial value of the offsetOFFSET_MIN=-1minimum value of the offsetOFFSET_MAX=1maximum value of the offsetDOFFSET=0.002maximum MC move of the offsetSCALE0=1.00initial value of the scaling factorSCALE_MIN=0.9minimum value of the scaling factorSCALE_MAX=1.1maximum value of the scaling factorDSCALE=0.00005maximum MC move of the scaling factorSIGMA0=0.001initial value of the uncertainty parameterSIGMA_MIN=0minimum value of the uncertainty parameterSIGMA_MAX=0.02maximum value of the uncertainty parameterDSIGMA=0.0001maximum MC move of the uncertainty parameterOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyLABEL=bqa label for the action so that its output can be referenced in the input to other actionsWRITE_STRIDE=10000write the status to a file every N steps, this can be used for restart/continuationSTRIDE=5 ... METAINFERENCEthe frequency with which the forces due to the bias should be calculated
ensaxs:ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More detailsARG=(test2\.q-.*),bias.biasthe input for this action is the scalar output from one or more other actionsREWEIGHTstatsq:simple REWEIGHT using the latest ARG as energySTATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=(ensaxs\.test2\.qthe input for this action is the scalar output from one or more other actionsPARARG=(test2\.expthe input for this action is the scalar output from one or more other actions without derivativesFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=(test2\.q-.*),(test2\.expthe input for this action is the scalar output from one or more other actionsFILE=CV.datthe name of the file on which to output these quantitiesSTRIDE=100the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsFILE=RESTRAINTSthe name of the file on which to output these quantitiesARG=bqthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsFILE=q.datthe name of the file on which to output these quantitiesARG=statsq.*,lsaxsthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsFILE=Analyse.datthe name of the file on which to output these quantitiesARG=d1,tor1,rg,linktor1the input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsFILE=BIASthe name of the file on which to output these quantitiesARG=bias.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsFILE=ENSAXSthe name of the file on which to output these quantitiesARG=(ensaxs\.test2\.qthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be output
enANA:ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More detailsARG=d1,tor1,rg,linktor1,bias.biasthe input for this action is the scalar output from one or more other actionsREWEIGHTsimple REWEIGHT using the latest ARG as energyPrint quantities to a file. More detailsFILE=ENANAthe name of the file on which to output these quantitiesARG=enANAthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be output