PLUMED-NEST

Project ID: plumID:19.078
Source: meta_reweigthing/6_D/plumed_reweight.dat
Originally used with PLUMED version: 2.5-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

# plumed input file for reweighting
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=4.0*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)+4.0*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)+4.0*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)+4.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+(5.0*x3+5.0)^2+(5.0*x4+5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3+5.0)^2+(5.0*x4+5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3-5.0)^2+(5.0*x4-5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2-0.591751709536137*x3-0.591751709536137*x4+4.40824829046386*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2-0.591751709536137*x3+4.40824829046386*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2+4.40824829046386*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1+4.40824829046386*x2-0.591751709536137*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0+4.40824829046386*x1-0.591751709536137*x2-0.591751709536137*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(0.408248290463863*x0+0.408248290463863*x1+0.408248290463863*x2+0.408248290463863*x3+0.408248290463863*x4+0.408248290463863*x5)^8.0)+1.0/((5.0*x3+5.0)^2.0+(5.0*x4+5.0)^2.0+(5.0*x5+5.0)^2.0+(-2.88675134594813*x0-1.05662432702594*x1+3.94337567297406*x2)^2.0+(-2.88675134594813*x0+3.94337567297406*x1-1.05662432702594*x2)^2.0+(0.577350269189626*x0+0.577350269189626*x1+0.577350269189626*x2)^8.0)+1.0/((5.0*x1-5.0)^2.0+(5.0*x2-5.0)^2.0+(0.577350269189626*x3+0.577350269189626*x4+0.577350269189626*x5)^8.0+(-2.88675134594813*x0-1.66666666666667*x3-1.66666666666667*x4+3.33333333333333*x5+2.88675134594813)^2.0+(-2.88675134594813*x0-1.66666666666667*x3+3.33333333333333*x4-1.66666666666667*x5+2.88675134594813)^2.0+(-2.88675134594813*x0+3.33333333333333*x3-1.66666666666667*x4-1.66666666666667*x5+2.88675134594813)^2.0))


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 filemt: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z PACEthe frequency for hill addition=1
SIGMAthe widths of the Gaussian hills=0.1,0.1,0.1,0.1,0.1,0.1 
HEIGHTthe heights of the Gaussian hills=4.0 BIASFACTORuse well tempered metadynamics and use this bias factor=3 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potentialrw: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details ARG the biases that must be taken into account when reweighting=mt.bias TEMPthe system temperature=1  
The REWEIGHT_BIAS action with label rw calculates the following quantities:
 Quantity   
 Description  
rw.value
the weight to use for this frame to negate the effect the biascc: COLLECT_FRAMESCollect atomic positions or argument values from the trajectory for later analysis More details ARGthe labels of the values whose time series you would like to collect for later analysis=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations when calculating averages=rw STRIDE the frequency with which data should be stored for analysis=10
The COLLECT_FRAMES action with label cc calculates the following quantities:
 Quantity   
 Description  
cc.data
the data that is being collected by this action
cc.logweights
the logarithms of the weights of the data pointsit: ITREThis action is not part of PLUMED and was included by using a LOAD command More details ARG=cc.logweights TEMP=1 MAXITER=10
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=it FILEthe name of the file on which to output these quantities=c_t FMTthe format that should be used to output real numbers=%8.4f