Project ID: plumID:22.016
Source: SurfaceFreeEnergy/SecondaryPrismatic/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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.ENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. More detailsSPECIES=1-1728:3this keyword is used for colvars such as coordination numberSIGMA=0.0675the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcva label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=env1h.pdbPDB files with relative distances from central atomREFERENCE_2=env2h.pdbPDB files with relative distances from central atomREFERENCE_3=env3h.pdbPDB files with relative distances from central atomREFERENCE_4=env4h.pdbPDB files with relative distances from central atomMORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
s:AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More detailsDATA=refcvthe label of an action that calculates multicolvarsATOM=1an alternative to ORIGINXLOWER=-0.34the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)XUPPER=0.34the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)SIGMA=0.03the width of the function to be used for kernel density estimationMEANcalculate the average value of the colvar inside the region of interestMORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}calcualte the number of colvars that are inside the region of interest and that are greater that a certain thresholdENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. More detailsSPECIESA=1this keyword is used for colvars such as the coordination numberSPECIESB=4-1728:3this keyword is used for colvars such as the coordination numberSIGMA=0.0675the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcv2a label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=env1h.pdbPDB files with relative distances from central atomREFERENCE_2=env2h.pdbPDB files with relative distances from central atomREFERENCE_3=env3h.pdbPDB files with relative distances from central atomREFERENCE_4=env4h.pdbPDB files with relative distances from central atomMORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
ene:ENERGYvol:Calculate the total potential energy of the simulation box. More detailsVOLUMECalculate the volume of the simulation box. More detailsOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More detailsARG=s.morethan,refcv2.morethanthe input for this action is the scalar output from one or more other actionsPACE=500the frequency for kernel depositionSTRIDE=2the frequency with which the forces due to the bias should be calculatedTEMP=312temperatureBARRIER=350the free energy barrier to be overcomeWALKERS_MPIswitch on MPI version of multiple walkersENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. More detailsSPECIES=1-1728:3this keyword is used for colvars such as coordination numberSIGMA=0.08the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcv3a label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=env1c.pdbPDB files with relative distances from central atomREFERENCE_2=env2c.pdbPDB files with relative distances from central atomREFERENCE_3=env3c.pdbPDB files with relative distances from central atomREFERENCE_4=env4c.pdbPDB files with relative distances from central atomMORE_THAN={CUBIC D_0=1.00 D_MAX=1.13}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
diff:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=refcv.morethan,s.morethanthe input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
uwall1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=diffthe arguments on which the bias is actingAT=50the positions of the wallKAPPA=1.0the force constant for the wallEXP=2the powers for the wallsSTRIDE=2 uwall2:the frequency with which the forces due to the bias should be calculatedUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=refcv3.morethanthe arguments on which the bias is actingAT=0the positions of the wallKAPPA=20.0the force constant for the wallEXP=2the powers for the wallsSTRIDE=4the frequency with which the forces due to the bias should be calculated
diff2:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=s.morethan,refcv2.morethanthe input to this functionFUNC=x/108-y/0.9the function you wish to evaluatePERIODIC=NO uwall3:if the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=diff2the arguments on which the bias is actingAT=0the positions of the wallKAPPA=4000.0the force constant for the wallEXP=2the powers for the wallsSTRIDE=2the frequency with which the forces due to the bias should be calculatedENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. More detailsSPECIES=1-1728:3this keyword is used for colvars such as coordination numberSIGMA=0.065the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcv4a label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=Large/env1h.pdbPDB files with relative distances from central atomREFERENCE_2=Large/env2h.pdbPDB files with relative distances from central atomREFERENCE_3=Large/env3h.pdbPDB files with relative distances from central atomREFERENCE_4=Large/env4h.pdbPDB files with relative distances from central atomMORE_THAN={CUBIC D_0=0.65 D_MAX=0.67}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
s2:AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More detailsDATA=refcv4the label of an action that calculates multicolvarsATOM=1an alternative to ORIGINXLOWER=-0.1the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)XUPPER=0.1the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)SIGMA=0.001the width of the function to be used for kernel density estimationMEANcalculate the average value of the colvar inside the region of interestMORE_THAN={CUBIC D_0=0.65 D_MAX=0.67}calcualte the number of colvars that are inside the region of interest and that are greater that a certain thresholdPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities