Project ID: plumID:21.021
Source: meta_inputs/meta_3d/plumed.dat
Originally used with PLUMED version: 2.7-mod
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 detailsNATURALd1:use natural unitsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as label
ff:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=d1.x,d1.y,d1.zthe input to this functionVAR=x0,x1,x2the names to give each of the arguments in the functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionFUNC=30.0*exp(-4.0*(x0-1)^2-4.0*(x1-1)^2-4.0*(x2+1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2-4.0*(x2+1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1-1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2-4.0*(x2+1)^2)+30.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0+5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((10.0*x0-10.0)^2+(0.5*x1-0.5*x2)^8+(7.0710678*x1+7.0710678*x2)^2)+1.0/((0.5*x0-0.5*x2)^8+(7.0710678*x0+7.0710678*x2)^2+(10.0*x1-10.0)^2)+1.0/((-7.0710678*x0-7.0710678*x1)^2+(0.288675134189626*x0-0.288675134189626*x1-0.408248289205788*x2)^8+(5.0*x0-5.0*x1+7.0710678*x2)^2)+1.0/(1.0*x2^8+(10.0*x0+10.0)^2+(10.0*x1+10.0)^2)+1.0/(1.0*x0^8+(10.0*x1+10.0)^2+(10.0*x2+10.0)^2)+1.0/(1.0*x0^8+(10.0*x1+10.0)^2+(10.0*x2-10.0)^2the function you wish to evaluate
bb:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=ffthe input for this action is the scalar output from one or more other actions
mt:METAD...Used to performed metadynamics on one or more collective variables. More detailsARG=d1.x,d1.y,d1.zthe input for this action is the scalar output from one or more other actionsPACE=500the frequency for hill additionGRID_MIN=-1.75,-1.75,-1.75the lower bounds for the gridGRID_MAX=1.75,1.75,1.75the upper bounds for the gridGRID_BIN=300,300,300the number of bins for the gridHEIGHT=2.0the heights of the Gaussian hillsSIGMA=0.05,0.05,0.05the widths of the Gaussian hillsBIASFACTOR=10use well tempered metadynamics and use this bias factorTEMP=1.0the system temperature - this is only needed if you are doing well-tempered metadynamicsCALC_RCT#REWEIGHTING_NGRID=100,100,100 ...calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]Print quantities to a file. More detailsARG=mt.bias,mt.rct,mt.rbiasthe input for this action is the scalar output from one or more other actionsFILE=rr.bias_500the 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=mt.bias,mt.rct,mt.rbiasthe input for this action is the scalar output from one or more other actionsFILE=rr.bias_50the name of the file on which to output these quantitiesSTRIDE=50the frequency with which the quantities of interest should be outputDUMPATOMSDump selected atoms on a file. More detailsSTRIDE=500the frequency with which the atoms should be outputFILE=traj.xyzfile on which to output coordinates; extension is automatically detectedATOMS=1,2the atom indices whose positions you would like to print out