Project ID: plumID:19.082
Source: Ammonia_borane/1.AB_to_AaDB/AB/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 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 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 bm2: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=1-128:16,18-128:16the numerical indexes for the set of atoms in the group
bnintrag:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=bthis keyword is used for colvars such as the coordination numberSPECIESB=nthis keyword is used for colvars such as the coordination numberR_0=2.0The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNMIN={BETA=20.0} bnintranew:calculate the minimum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=2this keyword is used for colvars such as the coordination numberSPECIESB=4this keyword is used for colvars such as the coordination numberR_0=2.2The r_0 parameter of the switching functionNN=4The n parameter of the switching functionMM=8The m parameter of the switching function; 0 implies 2*NNMEANbbinter:calculate the mean of all the quantitiesCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=2this keyword is used for colvars such as the coordination numberSPECIESB=bm2this keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=2.5 NN=6 MM=12}the switching function that it used in the construction of the contact matrixMAX={BETA=0.02} bhbridge:calculate the maximum valueCOORDINATIONNUMBERCalculate 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 numberR_0=1.9The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNMAX={BETA=0.02}calculate the maximum valueMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=bnintrag.min,bhbridge.maxthe input for this action is the scalar output from one or more other actionsSIGMA=0.075,0.075the widths of the Gaussian hillsHEIGHT=1.5the heights of the Gaussian hillsPACE=100the frequency for hill additionTEMP=400the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=16use 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 actionsWALKERS_N=4number of walkersWALKERS_ID=0walker idWALKERS_DIRshared directory with the hills files from all the walkersWALKERS_RSTRIDE=1 ... METADstride for reading hills filesPrint 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