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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

phi1The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=17,19,25,27
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37

opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=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
  PACEthe frequency for kernel deposition=500
  SIGMA the initial widths of the kernels=0.15,0.15,0.15,0.15,0.15,0.15
  BARRIERthe free energy barrier to be overcome=50
  BIASFACTORthe gamma bias factor used for the well-tempered target distribution=10
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State.data
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500000
  STORE_STATES append to STATE_WFILE instead of ovewriting it each time
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=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
  PACEthe frequency for kernel deposition=500
  SIGMA the initial widths of the kernels=0.15,0.15,0.15,0.15,0.15,0.15
  BARRIERthe free energy barrier to be overcome=50
  BIASFACTORthe gamma bias factor used for the well-tempered target distribution=10
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State.data
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500000
  STORE_STATES append to STATE_WFILE instead of ovewriting it each time
 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...

# 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
PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=50 FILEthe name of the file on which to output these quantities=Colvar.data ARGthe labels of the values that you would like to print to the file=*

The PRINT action with label  calculates somethingENDPLUMEDTerminate plumed input. More details

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

#NODEFAULT opes
  opes: OPES_METAD ARG=phi1,phi2,phi3,psi1,psi2,psi3 PACE=50 BARRIER=50 NLIST
#DEFAULT opes
opes: OPES_METAD ARG=phi1,phi2,phi3,psi1,psi2,psi3 PACE=50 BARRIER=50 NLIST  COMPRESSION_THRESHOLD=1
#ENDDEFAULT opes

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)