Project ID: plumID:20.016
Source: Urea/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
# 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 loaded
# Define groups for the CVINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=centers.dat C:file to be includedGROUPDefine 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=1-864:8 O: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=2-864:8 N1: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=3-864:8 N2: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=6-864:8 # Define the CVthe numerical indexes for the set of atoms in the groupPAIR_ORIENTATIONAL_ENTROPY... LABEL=s1 CENTER=C START=Ncenter END=O MAXR=0.6 SIGMA=0.05,0.25 ... PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More detailsPAIR_ORIENTATIONAL_ENTROPY... LABEL=s2 CENTER=C START=N1 END=N2 MAXR=0.6 SIGMA=0.05,0.125 UP_DOWN_SYMMETRY ... PAIR_ORIENTATIONAL_ENTROPYThis 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=18.705 # Height of the gaussians in energy units kJ/mol. This is 5 kT.the heights of the Gaussian hillsSIGMA=0.1,0.1 # 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=450.0 # Temperature in Kelvin. Only needed for well tempered simulationsthe system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-14.0,-14.0 # 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=600,600the number of bins for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# 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