Project ID: plumID:19.061
Source: diffusion_meta.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#Restart the simulationRESTARTActivate restart. More details
#Define the guest molecule in the simulation guest: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=169-186 guest_com:the numerical indexes for the set of atoms in the groupCOMCalculate the center of mass for a group of atoms. More detailsATOMS=guestthe list of atoms which are involved the virtual atom's definition
#Define the cage centre of mass centre_com:COMCalculate the center of mass for a group of atoms. More detailsATOMS=1-168the list of atoms which are involved the virtual atom's definition
#Define the centres of the windows as the centre of the three phenyl H atoms in the window circle1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=22,78,134 circle2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=36,64,162 circle3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=8,106,148 circle4:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=50,92,120the group of atoms that you are calculating the Gyration Tensor for
#Define distances between the guest centre of mass and the centres of the windows of interest d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=guest_com,circle1 d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=guest_com,circle2the pair of atom that we are calculating the distance between
#Define distances that will need energetic walls - these are the distances to the other two windows and the overall distance from the cage centre of mass d3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=guest_com,circle3 d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=guest_com,circle4 dc:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=centre_com,guest_comthe pair of atom that we are calculating the distance between
lwalls:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d3,d4the arguments on which the bias is actingAT=0.25,0.25the positions of the wallKAPPA=4500,4500the force constant for the wallOFFSET=0,0the offset for the start of the wallEXP=2,2the powers for the wallsEPS=1,1 uwall:the values for s_i in the expression for a wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dcthe arguments on which the bias is actingAT=0.45the positions of the wallKAPPA=3500the force constant for the wallOFFSET=0the offset for the start of the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wall
#Deposit Gaussians, with the distances d1 and d2 as the collective variable meta:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=d1,d2the input for this action is the scalar output from one or more other actionsSIGMA=0.01,0.01the widths of the Gaussian hillsHEIGHT=1.2the heights of the Gaussian hillsBIASFACTOR=15use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=500the frequency for hill additionGRID_MIN=-2.0,-2.0the lower bounds for the gridGRID_MAX=6.0,6.0the upper bounds for the gridGRID_BIN=4000,4000the number of bins for the gridPrint quantities to a file. More detailsARG=d1,d2,d3,d4,meta.*,uwall.*,lwallsthe 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=2000the frequency with which the quantities of interest should be output