Project ID: plumID:23.029
Source: GELSOLIN/SLC_OFF/plumed.dat
Originally used with PLUMED version: 2.9
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
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MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=template_AA.pdba file in pdb format containing a reference structureSAXS...Calculates SAXS intensity. This action has hidden defaults. More detailsLABEL=saxsdataa label for the action so that its output can be referenced in the input to other actionsATOMS=1-11880The atoms to be included in the calculation, eONEBEADcalculate SAXS for a single bead modelTEMPLATE=template_AA.pdb #GPUA PDB file is required for ONEBEAD mappingSOLVDENS=0.334Density of the solvent to be used for the correction of atomistic form factorsSOLVATION_CORRECTION=0.00 #SOLVATION_STRIDE= #SASA_CUTOFF= #QVALUE RANGE 0.01-0.25 (stride: 0.0150014)Solvation layer electron density correction (ONEBEAD only)QVALUE1=0.0101007Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT1=0.9655268182607186Add an experimental value for each q valueQVALUE2=0.0251021Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT2=0.8074336052768617Add an experimental value for each q valueQVALUE3=0.0401035Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT3=0.5867844124283979Add an experimental value for each q valueQVALUE4=0.0551049Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT4=0.3778068043742405Add an experimental value for each q valueQVALUE5=0.0701063Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT5=0.2199053983683388Add an experimental value for each q valueQVALUE6=0.0851077Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT6=0.1176236764450616Add an experimental value for each q valueQVALUE7=0.1001091Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT7=0.0598961117861482Add an experimental value for each q valueQVALUE8=0.1151105Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT8=0.0320698663426488Add an experimental value for each q valueQVALUE9=0.1301119Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT9=0.0197961291442457Add an experimental value for each q valueQVALUE10=0.1451133Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT10=0.0131910258635653Add an experimental value for each q valueQVALUE11=0.1601147Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT11=0.0090075507724353Add an experimental value for each q valueQVALUE12=0.1751161Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT12=0.0070054764797778Add an experimental value for each q valueQVALUE13=0.1901175Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT13=0.0060413990626627Add an experimental value for each q valueQVALUE14=0.2051189Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT14=0.0049136955389689Add an experimental value for each q valueQVALUE15=0.2201203Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT15=0.0039878840479083Add an experimental value for each q valueQVALUE16=0.2351217Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT16=0.0037107186252386Add an experimental value for each q valueQVALUE17=0.2501231Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT17=0.0033106578718972Add an experimental value for each q valueOPTSIGMAMEAN=SEM_MAXSet to NONE/SEM to manually set sigma mean, or to estimate it on the flySIGMA_MAX_STEPS=500000Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is usedAVERAGING=500Stride for calculation of averaged weights and sigma_meanDOSCOREactivate metainferenceSIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateSCALEDATASet to TRUE if you want to sample a scaling factor common to all values and replicasSCALE0=1.0initial value of the scaling factorDSCALE=0.01maximum MC move of the scaling factorSCALE_PRIOR=GAUSSIANeither FLAT or GAUSSIANSIGMA0=0.5initial value of the uncertainty parameterSIGMA_MIN=0.0001minimum value of the uncertainty parameterSIGMA_MAX=0.5maximum value of the uncertainty parameterNOISETYPE=MGAUSS ... SAXSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
# METAINFERENCE saxsbias:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=(saxsdata\.scorethe input for this action is the scalar output from one or more other actionsSTRIDE=2 ens:the frequency with which the forces due to the bias should be calculatedENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More detailsARG=(saxsdata\.qthe input for this action is the scalar output from one or more other actions
# STATISTICS statcg:STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=(ensthe input for this action is the scalar output from one or more other actionsPARARG=(saxsdata\.expthe input for this action is the scalar output from one or more other actions without derivativesPrint quantities to a file. More detailsARG=(ensthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=../ENS.SAXSINTthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=(saxsdata\.score),(saxsdata\.scale),(saxsdata\.acceptSigma),(saxsdata\.sigmathe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=BAYES.SAXSthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=(saxsdata\.qthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=SAXSINTthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=statcgthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=ST.SAXSCGthe name of the file on which to output these quantities