PLUMED-NEST

Project ID: plumID:20.017
Source: v-shape-potential/v-shape.plumed.dat
Originally used with PLUMED version: 2.7
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

d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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 atomsff: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=d1.x,d1.y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=-8*log((exp(-(y-exp(-x))^2/2)+exp(-(y+exp(-x))^2/2))*exp(-x^2/2
bb: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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 filef: 
FISST
Compute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces. More details
 
MIN_FORCE
Minimum force (per CV) to use for sampling
=-15 
MAX_FORCE
Maximum force (per CV) to use for sampling
=15.0 
PERIOD
Steps corresponding to the learning rate
=200 
NINTERPOLATE
Number of grid points on which to do interpolation
=41 
ARG
the input for this action is the scalar output from one or more other actions
=d1.x 
KBT
The system temperature in units of KB*T
=1.0 
OUT_RESTART
Output file for all information needed to continue FISST simulation
=v-shape_fisst-15_15_scale8_seed1.restart.txt 
OUT_OBSERVABLE
Output file putting weights needed to compute observables at different force values
=v-shape_fisst-15_15_scale8_seed1.observable.txt 
OBSERVABLE_FREQ
=100 
CENTER
 The CV value at which the applied bias energy will be zero
=0

The FISST action with label f calculates the following quantities:
 Quantity   
 Description  
f.bias
the instantaneous value of the bias potential
f.force2
squared value of force from the bias
f._fbar
For each named CV biased, there will be a corresponding output CV_fbar storing the current linear bias prefactor
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1.x,d1.y,bb.bias,f.d1.x_fbar,f.bias,f.force2 
FILE
the name of the file on which to output these quantities
=v-shape_fisst-15_15_scale8_seed1.colvar.txt 
STRIDE
 the frequency with which the quantities of interest should be output
=100