Project ID: plumID:20.016
Source: Naphthalene/plumed.dat
Originally used with PLUMED version: 2.6-dev
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
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# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR. # RESTARTLOADLoads a library, possibly defining new actions. More detailsFILE=PairOrientationalEntropy.cppfile to be loadedLOADLoads a library, possibly defining new actions. More detailsFILE=PairOrientationalEntropyPerpendicular.cppfile to be loaded
# Define groups for the CV C8: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 detailsATOMS=8-648:18 # Head C9:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=9-648:18 # Headthe numerical indexes for the set of atoms in the groupINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=centers.datfile to be included
# Define the CVPAIR_ORIENTATIONAL_ENTROPY... LABEL=s1 CENTER=CENTERS START=STARTS END=ENDS MAXR=0.7 SIGMA=0.05,0.125 #REFERENCE_DENSITY=4.5 UP_DOWN_SYMMETRY LOW_COMM ... PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More detailsPAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR... LABEL=s2 CENTER=CENTERS START1=STARTS END1=ENDS START2=C8 END2=C9 MAXR=0.7 SIGMA=0.05,0.125 #REFERENCE_DENSITY=4.5 UP_DOWN_SYMMETRY LOW_COMM ... PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULARThis action is not part of PLUMED and was included by using a LOAD command More details
# Construct a bias potential using metadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=s1,s2 # Label of the CVthe input for this action is the scalar output from one or more other actionsPACE=500 # Pace in the deposition of the gaussiansthe frequency for hill additionHEIGHT=12.25 # Height of the gaussians in energy units kJ/mol. This is 2 kT.the heights of the Gaussian hillsSIGMA=0.2,0.2 # Width of the gaussian in CV unitsthe widths of the Gaussian hillsFILE=HILLS # File where the information of the gaussians is printeda file in which the list of added hills is storedBIASFACTOR=200.0 # Bias factor in well tempered simulationsuse well tempered metadynamics and use this bias factorTEMP=300.0 # Temperature in Kelvin. Only needed for well tempered simulationsthe system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-20.0,-20.0 # The following three lines define a grid for the calculation of the bias potential. Use it **always**.the lower bounds for the gridGRID_MAX=0.,0the upper bounds for the gridGRID_BIN=1000,1000the number of bins for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# Restraint the volume vol:VOLUMECalculate the volume of the simulation box. More detailsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=volthe arguments on which the bias is actingAT=12.0the positions of the wallKAPPA=1000.0the force constant for the wallEXP=1the powers for the wallsLABEL=uwalla label for the action so that its output can be referenced in the input to other actions
# Print value of the CV and bias to a file named COLVARPrint 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