PLUMED-NEST

Project ID: plumID:25.016
Source: ./benchmark/3KBA/logn_jeff.dat
Originally used with PLUMED version: 2.11
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

#generate plumed action file
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# read index file in GROMACS format
batoms: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=batoms

# define action
The GROUP action with label batoms calculates somethingbaies:   BAIESBayesian refinement of AF models. More details ATOMSatoms used in the calculation of bAIes energy=batoms DATA_FILEfile with AF2 fit parameters=logn.out PRIORtype of prior to use (NONE, JEFFREYS, CAUCHY=JEFFREYS TEMPtemperature in kBt units=2.478541306

The BAIES action with label baies calculates the following quantities:
 Quantity   
 Description  
baies.ene
Bayesian bAIes energyPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=baies.ene FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500

The PRINT action with label  calculates somethingbbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=baies.ene STRIDEthe frequency with which the forces due to the bias should be calculated=4
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The BIASVALUE action with label bbias calculates the following quantities:
 Quantity   
 Description  
bbias.bias
the instantaneous value of the bias potential
bbias._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file