Project ID: plumID:23.001
Source: EnhancedCoexistence/Liq-VI/4-BiasedCoexistence/COEX_7000.0atm/245.0K/plumed.start.dat
Originally used with PLUMED version: 2.8
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.
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed.order.dat
# INCLUDE FILE=plumed.order.dat
The INCLUDE action with label plumed.order.dat calculates somethingENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
SPECIESthis keyword is used for colvars such as coordination number=1-3840:3
SIGMA the width to use for the gaussian kernels=0.055
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
LABELa label for the action so that its output can be referenced in the input to other actions=refcvThe CUSTOM action with label refcv calculates the following quantities:| Quantity | Type | Description |
| refcv | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
REFERENCE_1PDB files with relative distances from central atom=env1.pdb
REFERENCE_2PDB files with relative distances from central atom=env2.pdb
REFERENCE_3PDB files with relative distances from central atom=env3.pdb
REFERENCE_4PDB files with relative distances from central atom=env4.pdb
REFERENCE_5PDB files with relative distances from central atom=env5.pdb
REFERENCE_6PDB files with relative distances from central atom=env6.pdb
REFERENCE_7PDB files with relative distances from central atom=env7.pdb
REFERENCE_8PDB files with relative distances from central atom=env8.pdb
REFERENCE_9PDB files with relative distances from central atom=env9.pdb
REFERENCE_10PDB files with relative distances from central atom=env10.pdb
MORE_THAN1calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.46 D_MAX=0.9325}
MORE_THAN2calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.72750 D_MAX=0.72751}
MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
# --- End of included input ---
umb1The ECV_UMBRELLAS_LINE action with label umb1 calculates the following quantities:| Quantity | Type | Description |
| umb1.refcv_morethan-1 | scalar | the value of the argument named refcv_morethan-1 |
: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details ARGthe labels of the scalar values that are input to this action=refcv.morethan-1 TEMP temperature=245.0 CV_MINthe minimum of the CV range to be explored=640.0 CV_MAXthe maximum of the CV range to be explored=720.0 SIGMAsigma of the umbrella Gaussians=1 BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=50
umb1: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details ARGthe labels of the scalar values that are input to this action=refcv.morethan-1 TEMP temperature=245.0 CV_MINthe minimum of the CV range to be explored=640.0 CV_MAXthe maximum of the CV range to be explored=720.0 SIGMAsigma of the umbrella Gaussians=1 BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=50 SPACING the distance between umbrellas, in units of SIGMA=1
opesThe OPES_EXPANDED action with label opes calculates the following quantities:| Quantity | Type | Description |
| opes.bias | scalar | the instantaneous value of the bias potential |
: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe label of the ECVs that define the expansion=umb1.* PACEhow often the bias is updated=2000 STRIDEthe frequency with which the forces due to the bias should be calculated=1 WALKERS_MPI switch on MPI version of multiple walkers
opes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe label of the ECVs that define the expansion=umb1.* PACEhow often the bias is updated=2000 STRIDEthe frequency with which the forces due to the bias should be calculated=1 WALKERS_MPI switch on MPI version of multiple walkers OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DELTAFS PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR
