PLUMED-NEST

Project ID: plumID:21.006
Source: ala2-well_tempered-phi/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. 

#+++++++++++++++++++++++++++++++++++++++++++++++++++#
#                                                   #
#  This input generates a well-tempered simulation  #
#  that samples along the phi collective variable   #
#                                                   #
#+++++++++++++++++++++++++++++++++++++++++++++++++++#

phi: 
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 phi calculates a scalar quantitypsi: 
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 psi calculates a scalar quantityene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

opes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=phi
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
PACE
the frequency for kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=50
  
SIGMA
 the initial widths of the kernels
=0.15
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=State.data
  
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
 
FMT
the format that should be used to output real numbers
=%g 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=Colvar.data 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi,ene,opes.bias,opes.rct,opes.zed,opes.nker

ENDPLUMED
Terminate plumed input. More details


If no SIGMA is provided, it will be automatically guessed.
The option NLIST activates a neighbor list that speeds up the computation.

The main advantage of using OPES_METAD over a multiumbrella OPES_EXPANDED is that it is much easier to handle multiple collective variables.