Project ID: plumID:19.082
Source: Ammonia_borane/2.AaDB_to_AB2/AaDB_bis/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
#RESTARTUNITSThis 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=1-128:16,18-128:16 nm4: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=3-128:16,20-128:16the numerical indexes for the set of atoms in the group
bbinter:COORDINATIONNUMBERCalculate 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 matrixMEANnninter: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=4this keyword is used for colvars such as the coordination numberSPECIESB=nm4this keyword is used for colvars such as the coordination numberSWITCH={RATIONAL D_0=0.0 R_0=2.5 NN=7 MM=14}the switching function that it used in the construction of the contact matrixMEANbhbridge: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=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} nhbridge: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=nthis keyword is used for colvars such as the coordination numberR_0=1.6The 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} nhcoord:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=4this keyword is used for colvars such as the coordination numberSPECIESB=hnthis keyword is used for colvars such as the coordination numberR_0=1.6The r_0 parameter of the switching functionNN=7The n parameter of the switching functionMM=14The m parameter of the switching function; 0 implies 2*NNMEANbhcoord: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=hbthis keyword is used for colvars such as the coordination numberR_0=1.8The r_0 parameter of the switching functionNN=7The n parameter of the switching functionMM=14The m parameter of the switching function; 0 implies 2*NNMEANcalculate the mean of all the quantities
d1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=bbinter.meanthe input to this functionCOEFFICIENTS=0.8107the coefficients of the arguments in your functionPERIODIC=NO d2:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=nninter.meanthe input to this functionCOEFFICIENTS=1.1786the coefficients of the arguments in your functionPERIODIC=NO d3:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=bhbridge.maxthe input to this functionCOEFFICIENTS=0.4960the coefficients of the arguments in your functionPERIODIC=NO d4:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=nhbridge.maxthe input to this functionCOEFFICIENTS=0.6050the coefficients of the arguments in your functionPERIODIC=NO d5:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=nhcoord.meanthe input to this functionCOEFFICIENTS=0.2545the coefficients of the arguments in your functionPERIODIC=NO d6:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=bhcoord.meanthe input to this functionCOEFFICIENTS=0.2388the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
sdg1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6the input to this functionCOEFFICIENTS=-0.0481,-0.0473,-0.1976,-0.2464,0.9415,0.0959the coefficients of the arguments in your functionPERIODIC=NO sdg2:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6the input to this functionCOEFFICIENTS=0.6319,-0.0329,-0.2130,-0.0029,0.4767,-0.5719the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=sdg1,sdg2the input for this action is the scalar output from one or more other actionsSIGMA=0.03,0.03the 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=8use 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=1walker idWALKERS_DIRshared directory with the hills files from all the walkersWALKERS_RSTRIDE=50 ... 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