PLUMED-NEST

Project ID: plumID:20.017
Source: ala10/ala10.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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=fs 
ENERGY
the units of energy
=kcal/mol

The UNITS action with label  calculates somethingb1The GROUP action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=5
b2The GROUP action with label b2 calculates the following quantities:
 Quantity   
 Type   
 Description  
b2
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=95
casThe GROUP action with label cas calculates the following quantities:
 Quantity   
 Type   
 Description  
cas
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=5-100:10

dendThe DISTANCE action with label dend calculates the following quantities:
 Quantity   
 Type   
 Description  
dend
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=b1,b2
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cas

#The conversion factor is 69.4786 pN = 1 kcal/mol/Angstrom

#-10 pN to 10 pN
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.dend_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 dend: 
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
=-0.144 
MAX_FORCE
Maximum force (per CV) to use for sampling
=0.144 
PERIOD
Steps corresponding to the learning rate
=200 
NINTERPOLATE
Number of grid points on which to do interpolation
=31 
ARG
the input for this action is the scalar output from one or more other actions
=dend 
OUT_RESTART
Output file for all information needed to continue FISST simulation
=ala10_pull_fRange_fmin-10_fmax10.restart.txt 
OUT_OBSERVABLE
Output file putting weights needed to compute observables at different force values
=ala10_pull_fRange_fmin-10_fmax10.observable.txt 
OBSERVABLE_FREQ
=1000 
CENTER
 The CV value at which the applied bias energy will be zero
=0 
RESTART_FMT
the format that should be used to output real numbers in FISST restarts
=%e 

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dend,rg,f.dend_fbar,f.bias,f.force2 
FILE
the name of the file on which to output these quantities
=ala10_pull_fRange_fmin-10_fmax10.colvar.txt 
STRIDE
 the frequency with which the quantities of interest should be output
=1000