Project ID: plumID:23.021
Source: plumed_metad/system3/metad_syst3.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
 |
 |
ring:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=515-614 c1:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1-60 #fullerene cx c2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=123-182 #fullerene sx c3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=343-402 #fullerene dx d1:the group of atoms that you are calculating the Gyration Tensor forDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=ring,c2 d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=ring,c3 d:the pair of atom that we are calculating the distance betweenCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=d1,d2the input to this functionFUNC=y-xthe function you wish to evaluatePERIODIC=NO #restrain stoppers to keep distance from center a:if the output of your function is periodic then you should specify the periodicity of the functionFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.822783,3.843150,-3.996667 b:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=-2.826600,3.851033,3.999600 r1:coordinates of the virtual atomDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c2,a r2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c3,b w:the pair of atom that we are calculating the distance betweenUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=1,1the positions of the wallARG=r1,r2the arguments on which the bias is actingKAPPA=200,200the force constant for the wallMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=dthe input for this action is the scalar output from one or more other actionsHEIGHT=1the heights of the Gaussian hillsPACE=500the frequency for hill additionSIGMA=0.1the widths of the Gaussian hillsGRID_MIN=-6the lower bounds for the gridGRID_MAX=6the upper bounds for the gridGRID_BIN=200the number of bins for the gridBIASFACTOR=25use well tempered metadynamics and use this bias factorFILE=HILLSa file in which the list of added hills is storedCALC_RCT... METAD potential:calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]MATHEVALAn alias to the ef CUSTOM function. More detailsARG=metad.bias,w.biasthe input to this functionFUNC=x+ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPrint quantities to a file. More detailsARG=d,metad.*,potential,w.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=1000the frequency with which the quantities of interest should be output