Project ID: plumID:21.021
Source: FFH_scripts/plumed_FFH.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 betweenCOMPONENTSd2:calculate the x, y and z components of the distance separately and store them as labelDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,3the 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.z,d2.x,d2.y,d2.zthe input to this functionVAR=x0,x1,x2,x3,x4,x5the 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=10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4-1.0)^2-4.0*(x5-1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4-1.0)^2-4.0*(x5+1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4+1.0)^2-4.0*(x5-1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3+1.0)^2-4.0*(x4-1.0)^2-4.0*(x5+1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2+1.0)^2-4.0*(x3-1.0)^2-4.0*(x4+1.0)^2-4.0*(x5-1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1+1.0)^2-4.0*(x2-1.0)^2-4.0*(x3+1.0)^2-4.0*(x4-1.0)^2-4.0*(x5+1.0)^2)+10.0*exp(-4.0*(x0+1.0)^2-4.0*(x1-1.0)^2-4.0*(x2+1.0)^2-4.0*(x3-1.0)^2-4.0*(x4+1.0)^2-4.0*(x5-1.0)^2)+10.0/(1.0/(25.0*(x0+1)^2+25.0*(x1-1)^2+25.0*(x2+1)^2+25.0*(x3-1)^2+25.0*(x4+1)^2+25.0*(x5-1)^2+1)+1.0/(25.0*(x0-1)^2+25.0*(x1+1)^2+25.0*(x2-1)^2+25.0*(x3+1)^2+25.0*(x4-1)^2+25.0*(x5+1)^2+1)+1.0/(25.0*(x0-1)^2+25.0*(x1-1)^2+25.0*(x2+1)^2+25.0*(x3-1)^2+25.0*(x4+1)^2+25.0*(x5-1)^2+1)+1.0/(25.0*(x0-1)^2+25.0*(x1-1)^2+25.0*(x2-1)^2+25.0*(x3+1)^2+25.0*(x4-1)^2+25.0*(x5+1)^2+1)+1.0/(25.0*(x0-1)^2+25.0*(x1-1)^2+25.0*(x2-1)^2+25.0*(x3-1)^2+25.0*(x4+1)^2+25.0*(x5-1)^2+1)+1.0/(25.0*(x0-1)^2+25.0*(x1-1)^2+25.0*(x2-1)^2+25.0*(x3-1)^2+25.0*(x4-1)^2+25.0*(x5+1)^2+1)+1.0/(25.0*(x0-1)^2+25.0*(x1-1)^2+25.0*(x2-1)^2+25.0*(x3-1)^2+25.0*(x4-1)^2+25.0*(x5-1)^2+1)+1.0/(16.0*(-0.559016994374948*x0+0.25*x1-0.25*x2+0.25*x3+x4+0.25*x5+0.559016994374948)^2.0+16.0*(-0.559016994374948*x0+0.25*x1+x2+0.25*x3-0.25*x4+0.25*x5+0.559016994374948)^2.0+16.0*(0.559016994374948*x0-0.25*x1+0.25*x2-0.25*x3+0.25*x4+x5-0.559016994374948)^2.0+16.0*(0.559016994374948*x0-0.25*x1+0.25*x2+x3+0.25*x4-0.25*x5-0.559016994374948)^2.0+16.0*(0.559016994374948*x0+x1+0.25*x2-0.25*x3+0.25*x4-0.25*x5-0.559016994374948)^2.0+1.0)+1.0/(12.9006803429558*(-0.568313630059616*x0-0.392078407514904*x1+0.392078407514904*x2-0.392078407514904*x3+0.392078407514904*x4+x5)^2.0+12.9006803429558*(-0.568313630059616*x0-0.392078407514904*x1+0.392078407514904*x2+x3+0.392078407514904*x4-0.392078407514904*x5)^2.0+12.9006803429558*(-0.568313630059616*x0+x1+0.392078407514904*x2-0.392078407514904*x3+0.392078407514904*x4-0.392078407514904*x5)^2.0+12.9006803429558*(0.568313630059616*x0+0.392078407514904*x1-0.392078407514904*x2+0.392078407514904*x3+x4+0.392078407514904*x5)^2.0+12.9006803429558*(0.568313630059616*x0+0.392078407514904*x1+x2+0.392078407514904*x3-0.392078407514904*x4+0.392078407514904*x5)^2.0+1.0)+1.0/(25.0*(x1-1)^2.0+14.0625*(-0.666666666666667*x0+0.333333333333333*x2-0.333333333333333*x3+0.333333333333333*x4+x5+0.666666666666667)^2.0+14.0625*(-0.666666666666667*x0+0.333333333333333*x2+x3+0.333333333333333*x4-0.333333333333333*x5+0.666666666666667)^2.0+14.0625*(0.666666666666667*x0-0.333333333333333*x2+0.333333333333333*x3+x4+0.333333333333333*x5-0.666666666666667)^2.0+14.0625*(0.666666666666667*x0+x2+0.333333333333333*x3-0.333333333333333*x4+0.333333333333333*x5-0.666666666666667)^2.0+1.0)+1.0/(25.0*(x1-1)^2.0+25.0*(x3-1)^2.0+25.0*(x5-1)^2.0+15.5502116982037*(0.732050807568877*x0-x2+0.267949192431122*x4)^2.0+15.5502116982037*(0.732050807568877*x0+0.267949192431122*x2-x4)^2.0+1.0)+1.0/(25.0*(x1-1)^2.0+25.0*(x2-1)^2.0+11.1111111111111*(-0.866025403784439*x0+0.5*x3+x4+0.5*x5+0.866025403784439)^2.0+11.1111111111111*(0.866025403784439*x0-0.5*x3+0.5*x4+x5-0.866025403784439)^2.0+11.1111111111111*(0.866025403784439*x0+x3+0.5*x4-0.5*x5-0.866025403784439)^2.0+1.0)+1.0/(25.0*(x1-1)^2.0+25.0*(x2-1)^2.0+25.0*(x3-1)^2.0+12.5*(-x0+0.707106781186548*x4+0.707106781186547*x5+1)^2.0+12.5*(x0+0.707106781186547*x4+0.707106781186548*x5-1)^2.0+1.0)+1.0/(25.0*(x0-1)^2.0+25.0*(x1-1)^2.0+25.0*(x2-1)^2.0+25.0*(x3-1)^2.0+25.0*(x4-1)^2.0+1 bb:the function you wish to evaluateBIASVALUETakes 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
atlas:ATLAS... ARG=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z REFERENCE=cluster.dat PACE=500 SIGMA=0.2 BIASFACTOR=10 HEIGHT=2.0 GRID_MAX=5.0 GRID_BIN=500 TEMP=1 TRUNCATE_GRIDS REGULARISE=1E-8 ADAPTIVE_WALL=1.0 STATIC_WALL=0.0 ...This action is not part of PLUMED and was included by using a LOAD command More detailsPrint quantities to a file. More detailsARG=atlas,atlas_wtfactthe input for this action is the scalar output from one or more other actionsFILE=atlas.global_biasthe 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=atlas_adaptive_wallthe input for this action is the scalar output from one or more other actionsFILE=atlas.wallthe 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.x,d1.y,d1.z,d2.x,d2.y,d2.zthe 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 output