PLUMED-NEST

Project ID: plumID:19.068
Source: ala4/plumed-opes.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

# 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
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=phi1,phi2,phi3,psi1,psi2,psi3
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
TEMP
 temperature
=300.0
  
PACE
the frequency for kernel deposition
=500
  
SIGMA
 the initial widths of the kernels
=0.15,0.15,0.15,0.15,0.15,0.15
  
BARRIER
the free energy barrier to be overcome
=50
  
BIASFACTOR
the gamma bias factor used for the well-tempered target distribution
=10
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=State.data
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=500000
  
STORE_STATES
 append to STATE_WFILE instead of ovewriting it each time
...

# Since we are in 6D it is convenient to print the colvar more often
# (STRIDE=50 instead of STRIDE=500), it will help with the reweighting
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
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
=50 
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

ENDPLUMED
Terminate plumed input. More details


A better performing result can be obtained with the following simpler input:

  opes: OPES_METAD ARG=phi1,phi2,phi3,psi1,psi2,psi3 PACE=50 BARRIER=50 NLIST

but it was not used, to have a more fair comparison with standard metadynamics ala2 simulations.
(if not set, SIGMA is chosen adaptively, similarly to METAD ADAPTIVE=DIFF)