PLUMED-NEST

Project ID: plumID:24.022
Source: ala2/integrated_sampling/gromacs_config/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

phiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
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
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
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

cosphiThe MATHEVAL action with label cosphi calculates the following quantities:
 Quantity   
 Type   
 Description  
cosphi
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=phi FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

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=cosphi
  PACEthe frequency for kernel deposition=1000000
  BARRIERthe free energy barrier to be overcome=20
  TEMP temperature=300
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
  FILE a file in which the list of all deposited kernels is stored=KERNELS
...
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=cosphi
  PACEthe frequency for kernel deposition=1000000
  BARRIERthe free energy barrier to be overcome=20
  TEMP temperature=300
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
  FILE a file in which the list of all deposited kernels is stored=KERNELS
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...

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=1 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=cosphi,opes.bias

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