PLUMED-NEST

Project ID: plumID:22.041
Source: ala4/plumed.dat
Originally used with PLUMED version: 2.8
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

phi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label phi1 calculates a scalar quantityphi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=15,17,19,25
The TORSION action with label phi2 calculates a scalar quantityphi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=25,27,29,35
The TORSION action with label phi3 calculates a scalar quantitypsi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
The TORSION action with label psi1 calculates a scalar quantitypsi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=17,19,25,27
The TORSION action with label psi2 calculates a scalar quantitypsi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=27,29,35,37

The TORSION action with label psi3 calculates a scalar quantityopes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 
TEMP
 temperature
=300 
ARG
the input for this action is the scalar output from one or more other actions
=phi1,phi2,phi3 
PACE
the frequency for kernel deposition
=500 
BARRIER
the free energy barrier to be overcome
=40 
NLIST
 use neighbor list for kernels summation, faster but experimental

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
opes.nlker
number of kernels in the neighbor list
opes.nlsteps
number of steps from last neighbor list update
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FMT
the format that should be used to output real numbers
=%g 
ARG
the input for this action is the scalar output from one or more other actions
    
ENDPLUMED
Terminate plumed input. More details

file generated automatically when running the notebook