Project ID: plumID:20.009
Source: Ub3/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=1-489the atoms that make up a molecule that you wish to align
#ubi1 a:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75,77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150the group of atoms that you are calculating the Gyration Tensor forNOPBCa1:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75the 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=77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150the group of atoms that you are calculating the Gyration Tensor forNOPBC#ubi2 b:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313the 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=164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238the 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=,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313the group of atoms that you are calculating the Gyration Tensor forNOPBC#ubi3 c:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401,403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476the group of atoms that you are calculating the Gyration Tensor forNOPBCc1:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401the group of atoms that you are calculating the Gyration Tensor forNOPBCc2:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476the group of atoms that you are calculating the Gyration Tensor forNOPBCignore the periodic boundary conditions when calculating distances
# distance between ubiquitins d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=a,bthe pair of atom that we are calculating the distance betweenNOPBCd2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=a,cthe pair of atom that we are calculating the distance betweenNOPBCd3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=b,cthe 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 angleNOPBCtor2:ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=a1,a2,c1,c2the four atoms involved in the torsional angleNOPBCtor3:ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=b1,b2,c1,c2the four atoms involved in the torsional angleNOPBCignore the periodic boundary conditions when calculating distances
#global radius rg:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsATOMS=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75,77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150,152,154,157,159,162,163,164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313,315,317,320,322,325,326,327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401,403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476,478,480,483,485,488,489the group of atoms that you are calculating the Gyration Tensor forNOPBCignore the periodic boundary conditions when calculating distances
#linker angleALPHABETA...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=150,152,154,157the atoms involved for each of the torsions you wish to calculateATOMS2=152,154,157,159the atoms involved for each of the torsions you wish to calculateATOMS3=154,157,159,162the atoms involved for each of the torsions you wish to calculateATOMS4=157,159,162,163the atoms involved for each of the torsions you wish to calculateATOMS5=159,162,163,164the atoms involved for each of the torsions you wish to calculateATOMS6=162,163,164,166 ... ALPHABETAthe atoms involved for each of the torsions you wish to calculateALPHABETA...Calculate the alpha beta CV More detailsLABEL=linktor2a 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=313,315,317,320the atoms involved for each of the torsions you wish to calculateATOMS2=315,317,320,322the atoms involved for each of the torsions you wish to calculateATOMS3=317,320,322,325the atoms involved for each of the torsions you wish to calculateATOMS4=320,322,325,326the atoms involved for each of the torsions you wish to calculateATOMS5=322,325,326,327the atoms involved for each of the torsions you wish to calculateATOMS6=325,326,327,329 ... 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=1-489The 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=0.029015Selected 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=0.107092Selected 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=0.21863Selected 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=4.68143Add an experimental value for each q valueEXPINT2=4.11699Add an experimental value for each q valueEXPINT3=3.45783Add an experimental value for each q valueEXPINT4=2.76077Add an experimental value for each q valueEXPINT5=2.15094Add an experimental value for each q valueEXPINT6=1.67643Add an experimental value for each q valueEXPINT7=1.32305Add an experimental value for each q valueEXPINT8=1.06339Add an experimental value for each q valueEXPINT9=0.870742Add an experimental value for each q valueEXPINT10=0.721004Add an experimental value for each q valueEXPINT11=0.597613Add an experimental value for each q valueEXPINT12=0.493722Add an experimental value for each q valueEXPINT13=0.407671Add an experimental value for each q valueEXPINT14=0.337263Add an experimental value for each q valueEXPINT15=0.27869Add an experimental value for each q valueEXPINT16=0.228546Add an experimental value for each q valueEXPINT17=0.184443Add an experimental value for each q valueEXPINT18=0.144056Add an experimental value for each q valueEXPINT19=0.106039Add an experimental value for each q valueEXPINT20=0.0725692Add an experimental value for each q valueEXPINT21=0.0480033 ... 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,d2,d3,tor1,tor2,tor3,rg,linktor1,linktor2the 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=30use 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.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8dump 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.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8frequency for dumping the gridSIGMA=10000the widths of the Gaussian hillsSIGMA_MIN=0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2the upper bounds for the sigmas (in CV units) when using adaptive hillsGRID_MIN=0,0,0,-pi,-pi,-pi,0,0,0the lower bounds for the gridGRID_MAX=7,14,7,pi,pi,pi,7,6,6the upper bounds for the gridWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRUPDATE_FROM=10000 ... 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=-10minimum value of the offsetOFFSET_MAX=10maximum value of the offsetDOFFSET=0.005maximum MC move of the offsetSCALE0=1.00initial value of the scaling factorSCALE_MIN=0.8minimum value of the scaling factorSCALE_MAX=1.2maximum value of the scaling factorDSCALE=0.001maximum MC move of the scaling factorSIGMA0=0.01initial value of the uncertainty parameterSIGMA_MIN=0minimum value of the uncertainty parameterSIGMA_MAX=0.05maximum value 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\.exp enANA:the input for this action is the scalar output from one or more other actions without derivativesENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More detailsARG=d1,d2,d3,tor1,tor2,tor3,rg,linktor1,linktor2,bias.biasthe input for this action is the scalar output from one or more other actionsREWEIGHTsimple REWEIGHT using the latest ARG as energyFLUSHThis 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,d2,d3,tor1,tor2,tor3,rg,linktor1,linktor2the 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 outputPrint 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