Project ID: plumID:22.029
Source: metad.dat
Originally used with PLUMED version: 2.5
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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# RESTART append output files of several restartsWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-85the atoms that make up a molecule that you wish to align
#groups ang_noh:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsNDX_FILE=index_meta2.ndxthe name of index file (gromacs syntax)NDX_GROUP=ang_noh waters_noh:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsNDX_FILE=index_meta2.ndxthe name of index file (gromacs syntax)NDX_GROUP=ang_noh donors:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsNDX_FILE=index_meta2.ndxthe name of index file (gromacs syntax)NDX_GROUP=donors acceptors:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsNDX_FILE=index_meta2.ndxthe name of index file (gromacs syntax)NDX_GROUP=acceptors #gyration radiusthe name of the group to be imported (gromacs syntax) - first group found is used by defaultGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=1-85the group of atoms that you are calculating the Gyration Tensor forLABEL=rga label for the action so that its output can be referenced in the input to other actions
#walls uw:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rgthe arguments on which the bias is actingKAPPA=10000the force constant for the wallAT=0.85 lw:the positions of the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rgthe arguments on which the bias is actingKAPPA=10000the force constant for the wallAT=0.5the positions of the wall
# Coordination number c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=ang_nohFirst list of atomsGROUPB=waters_nohSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.35 hbs:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=donorsFirst list of atomsGROUPB=acceptorsSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.25The r_0 parameter of the switching function
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=rg,hbsthe input for this action is the scalar output from one or more other actionsGRID_MIN=0,0the lower bounds for the gridGRID_MAX=1,56the upper bounds for the gridSIGMA=0.1,0.1the widths of the Gaussian hillsHEIGHT=1.2the heights of the Gaussian hillsPACE=500the frequency for hill additionBIASFACTOR=15use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=metada label for the action so that its output can be referenced in the input to other actionsCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]Print quantities to a file. More detailsARG=rgthe input for this action is the scalar output from one or more other actionsFILE=rg.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=metadthe input for this action is the scalar output from one or more other actionsFILE=metad_data.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=cthe input for this action is the scalar output from one or more other actionsFILE=all_coordination_45.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=hbsthe input for this action is the scalar output from one or more other actionsFILE=all_coordination_25.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=rg,hbs,metad.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=lw.*,uwthe input for this action is the scalar output from one or more other actionsFILE=restraint.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=500the frequency with which all the open files should be flushed