PLUMED-NEST

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

Click on the labels of the actions for more information on what each action computes

UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label  calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atoms
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 COMPONENTS calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.x
the x-component of the vector connecting the two atoms
d2.y
the y-component of the vector connecting the two atoms
d2.z
the z-component of the vector connecting the two atoms
d2.value
the DISTANCE between this pair of atomsff: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z VARthe names to give each of the arguments in the function=x0,x1,x2,x3,x4,x5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=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))
The MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
an arbitrary functionbb: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=ff

The BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Description  
bb.bias
the instantaneous value of the bias potential
bb._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileatlas: ATLASThis action is not part of PLUMED and was included by using a LOAD command More details ...
 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 
... 

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=atlas,atlas_wtfact FILEthe name of the file on which to output these quantities=atlas.global_bias STRIDE the frequency with which the quantities of interest should be output=500 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=atlas_adaptive_wall FILEthe name of the file on which to output these quantities=atlas.wall STRIDE the frequency with which the quantities of interest should be output=500 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=500