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

d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: 
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
ffThe MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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
bbThe BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Type   
 Description  
bb.bias
scalar
the instantaneous value of the bias potential
bb.ff_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named ff: 
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

fThe FISST action with label f calculates the following quantities:
 Quantity   
 Type   
 Description  
f.bias
scalar
the instantaneous value of the bias potential
f.force2
scalar
squared value of force from the bias.
f.d1.x_fbar
scalar
For each named CV biased, there will be a corresponding output CV_fbar storing the current linear bias prefactor. This particular component measures this quantity for the input CV named d1.x: 
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

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