Project ID: plumID:19.082
Source: Ammonia_borane/4.H2_release/AaDB/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More detailsUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
h: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=5-128:16,6-128:16,7-128:16,8-128:16,9-128:16,10-128:16,11-128:16,12-128:16,13-128:16,14-128:16,15-128:16,16-128:16 hb: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=7-128:16,8-128:16,13-128:16,14-128:16,15-128:16,16-128:16 hn: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=5-128:16,6-128:16,9-128:16,10-128:16,11-128:16,12-128:16 n: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=3-128:16,4-128:16 b: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=1-128:16,2-128:16 bn1: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=1-128:16,3-128:16 bn2: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=2-128:16,4-128:16the numerical indexes for the set of atoms in the group
cnHB:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=hbthis keyword is used for colvars such as the coordination numberSPECIESB=bthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=1.8 NN=6 MM=12}the switching function that it used in the construction of the contact matrixMAX={BETA=0.02} cnHH:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=hnthis keyword is used for colvars such as the coordination numberSPECIESB=hbthis keyword is used for colvars such as the coordination numberSWITCH={GAUSSIAN R_0=0.2 D_0=0.8 }the switching function that it used in the construction of the contact matrixMAX={BETA=0.02}calculate the maximum valueEXTERNALCalculate a restraint that is defined on a grid that is read during start up More detailsARG=cnHH.maxthe input for this action is the scalar output from one or more other actionsFILE=ext_bias.datthe name of the file containing the external potentialLABEL=externala label for the action so that its output can be referenced in the input to other actionsMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=cnHH.maxthe input for this action is the scalar output from one or more other actionsSIGMA=0.05the widths of the Gaussian hillsHEIGHT=0.1the heights of the Gaussian hillsPACE=4000the frequency for hill additionTEMP=400the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=10use well tempered metadynamics and use this bias factorLABEL=restrainta label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1the frequency with which all the open files should be flushedENDPLUMEDTerminate plumed input. More details