PLUMED-NEST

Project ID: plumID:22.031
Source: Ala2/psi/plumed.dat
Originally used with PLUMED version: 2.9
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. 

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=input.ala2.pdb
The MOLINFO action with label  calculates somethingphiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the value calculated by this action: 
ENERGY
Calculate the total potential energy of the simulation box. More details

chi_excThe CUSTOM action with label chi_exc calculates the following quantities:
 Quantity   
 Type   
 Description  
chi_exc
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=psi 
FUNC
the function you wish to evaluate
=step(-x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

opesfThe OPES_METAD action with label opesf calculates the following quantities:
 Quantity   
 Type   
 Description  
opesf.bias
scalar
the instantaneous value of the bias potential
opesf.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesf.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesf.neff
scalar
effective sample size
opesf.nker
scalar
total number of compressed kernels used to represent the bias: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=psi
  
PACE
the frequency for kernel deposition
=500
  
SIGMA
 the initial widths of the kernels
=0.1 #Automatically adjusted by OPES
  
BARRIER
the free energy barrier to be overcome
=5
  
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=chi_exc
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
  #NLIST   #Only sefule for CV dim. > 1
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=500
  #STORE_STATES  #Can be expensive to store all states.
...
opesf: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=psi
  
PACE
the frequency for kernel deposition
=500
  
SIGMA
 the initial widths of the kernels
=0.1 #Automatically adjusted by OPES
  
BARRIER
the free energy barrier to be overcome
=5
  
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=chi_exc
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
  #NLIST   #Only sefule for CV dim. > 1
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=compressed.Kernels
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=500
  #STORE_STATES  #Can be expensive to store all states.
 
TEMP
 temperature
=-1 
COMPRESSION_THRESHOLD
 merge kernels if closer than this threshold, in units of sigma
=1
...


COMMITTOR
Does a committor analysis. More details
 ...
 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi
 
STRIDE
 the frequency with which the CVs are analyzed
=10
 
BASIN_LL1
List of lower limits for basin #
=0.6,-1.5
 
BASIN_UL1
List of upper limits for basin #
=2.0,0.0
... COMMITTOR

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
=1 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi,ene,opesf

ENDPLUMED
Terminate plumed input. More details