Project ID: plumID:22.006
Source: analysis/contacts.plumed
Originally used with PLUMED version: 2.5
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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# groups.txt is generated by parse_atoms.py # an example groups.txt file is includedINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=groups.txtfile to be included
c1com:COMCalculate the center of mass for a group of atoms. More detailsATOMS=c1 c2com:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=c2 c3com:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=c3 c4com:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=c4the list of atoms which are involved the virtual atom's definition
dist:DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUP=c1com,c2com,c3com,c4comCalculate the distance between each distinct pair of atoms in the groupMEANcalculate the mean of all the quantitiesMIN={BETA=0.1}calculate the minimum value
rg1:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=c1 rg2:the group of atoms that you are calculating the Gyration Tensor forGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=c2 rg3:the group of atoms that you are calculating the Gyration Tensor forGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=c3 rg4:the group of atoms that you are calculating the Gyration Tensor forGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=c4the group of atoms that you are calculating the Gyration Tensor for
rg:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=rg1,rg2,rg3,rg4the input to this functionNORMALIZEnormalize all the coefficients so that in total they are equal to onePERIODIC=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=dist.mean,rgthe input for this action is the scalar output from one or more other actionsPACE=99999999the frequency for hill additionBIASFACTOR=5use well tempered metadynamics and use this bias factorTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.05,0.01the widths of the Gaussian hillsGRID_MIN=0,0the lower bounds for the gridGRID_MAX=5,1.5the upper bounds for the gridGRID_BIN=500,500the number of bins for the gridHEIGHT=5 # Uncomment line when HILLS file is present RESTART=YES ... METADthe heights of the Gaussian hills
bias:REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsTEMP=300.0the system temperatureHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=dist.min,rgthe quantity that is being averagedGRID_MIN=0.0,0.0the lower bounds for the gridGRID_MAX=5.0,1.0the upper bounds for the gridGRID_BIN=500,500the number of bins for the gridBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=hB ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=dist.minthe quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=5.0the upper bounds for the gridGRID_BIN=500the number of bins for the gridBANDWIDTH=0.1the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=hR ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actions
ff:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hBthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=300 ffr:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hRthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=300the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=fes.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffrthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=fes_dist.datthe file on which to write the grid