Project ID: plumID:23.040
Source: plumed_metad/plumed_pyro.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=0.001 #Amstroeng, hartree, fsthe units of timeWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-76the atoms that make up a molecule that you wish to alignENTITY1=77-152the atoms that make up a molecule that you wish to alignENTITY2=153-228the atoms that make up a molecule that you wish to alignENTITY3=229-304the atoms that make up a molecule that you wish to alignENTITY4=305-380the atoms that make up a molecule that you wish to alignENTITY5=381-456the atoms that make up a molecule that you wish to align
# Group definition cal1: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 detailsATOMS=1-76 cal2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=77-152 cal3:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=153-228 cal4:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=229-304 cal5:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=305-380 cal6:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=381-456the numerical indexes for the set of atoms in the group
com1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=cal1 com2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=cal2 com3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=cal3 com4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=cal4 com5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=cal5 com6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=cal6the list of atoms which are involved the virtual atom's definition
d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com2 d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com3 d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com4 d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com5 d5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com6 d6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com2,com3 d7:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com2,com4 d8:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com2,com5 d9:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com2,com6 d10:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com3,com4 d11:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com3,com5 d12:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com3,com6 d13:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com4,com5 d14:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com4,com6 d15:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com5,com6the pair of atom that we are calculating the distance betweenDISTANCES...Calculate the distances between multiple piars of atoms More detailsLABEL=mul_dista label for the action so that its output can be referenced in the input to other actionsATOMS1=com1,com2the pairs of atoms that you would like to calculate the angles forATOMS2=com1,com3the pairs of atoms that you would like to calculate the angles forATOMS3=com1,com4the pairs of atoms that you would like to calculate the angles forATOMS4=com1,com5the pairs of atoms that you would like to calculate the angles forATOMS5=com1,com6the pairs of atoms that you would like to calculate the angles forATOMS6=com2,com3the pairs of atoms that you would like to calculate the angles forATOMS7=com2,com4the pairs of atoms that you would like to calculate the angles forATOMS8=com2,com5the pairs of atoms that you would like to calculate the angles forATOMS9=com2,com6the pairs of atoms that you would like to calculate the angles forATOMS10=com3,com4the pairs of atoms that you would like to calculate the angles forATOMS11=com3,com5the pairs of atoms that you would like to calculate the angles forATOMS12=com3,com6the pairs of atoms that you would like to calculate the angles forATOMS13=com4,com5the pairs of atoms that you would like to calculate the angles forATOMS14=com4,com6the pairs of atoms that you would like to calculate the angles forATOMS15=com5,com6the pairs of atoms that you would like to calculate the angles forBETWEEN1={GAUSSIAN LOWER=9. UPPER=12.5}calculate the number of values that are within a certain rangeBETWEEN2={GAUSSIAN LOWER=13. UPPER=17} ... DISTANCEScalculate the number of values that are within a certain range
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=mul_dist.between-1,mul_dist.between-2the input for this action is the scalar output from one or more other actionsGRID_MIN=0,0the lower bounds for the gridGRID_MAX=20,20the upper bounds for the gridSIGMA=0.1,0.1the widths of the Gaussian hillsHEIGHT=1.5the heights of the Gaussian hillsBIASFACTOR=30use 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_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]PACE=500 # 1ps ... METADthe frequency for hill additionPrint quantities to a file. More detailsARG=mul_dist.between-1,mul_dist.between-2,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=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15the 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 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