Project ID: plumID:22.028
Source: plumed_pucker.dat
Originally used with PLUMED version: 2.7
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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############ Representative plumed file to calculate histogram or free energy profiles along puckering coordinates from COLVAR file ########
### Here for glycan A2G2S2 ###
# Read pucker coordinates phi and theta from COLVAR file
puck1:READRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck1.thetathe values to read from the fileSTRIDE=10 puck2:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck2.thetathe values to read from the fileSTRIDE=10 puck3:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck3.thetathe values to read from the fileSTRIDE=10 puck4:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck4.thetathe values to read from the fileSTRIDE=10 puck5:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck5.thetathe values to read from the fileSTRIDE=10 puck6:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck6.thetathe values to read from the fileSTRIDE=10 puck7:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck7.thetathe values to read from the fileSTRIDE=10 puck8:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck8.thetathe values to read from the fileSTRIDE=10 puck9:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck9.thetathe values to read from the fileSTRIDE=10 puck10:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck10.thetathe values to read from the fileSTRIDE=10 puck11:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck11.thetathe values to read from the fileSTRIDE=10the frequency with which the file should be read
puckp1:READRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck1.phithe values to read from the fileSTRIDE=10 puckp2:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck2.phithe values to read from the fileSTRIDE=10 puckp3:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck3.phithe values to read from the fileSTRIDE=10 puckp4:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck4.phithe values to read from the fileSTRIDE=10 puckp5:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck5.phithe values to read from the fileSTRIDE=10 puckp6:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck6.phithe values to read from the fileSTRIDE=10 puckp7:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck7.phithe values to read from the fileSTRIDE=10 puckp8:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck8.phithe values to read from the fileSTRIDE=10 puckp9:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck9.phithe values to read from the fileSTRIDE=10 puckp10:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck10.phithe values to read from the fileSTRIDE=10 puckp11:the frequency with which the file should be readREADRead quantities from a colvar file. More detailsFILE=COLVAR_theta.0the name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=puck11.phithe values to read from the fileSTRIDE=10the frequency with which the file should be read
# Compute 1D histogram along theta
theta1:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck1.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta2:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck2.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta3:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck3.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta4:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck4.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta5:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck5.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta6:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck6.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta7:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck7.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta8:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck8.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta9:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck9.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta10:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck10.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000 theta11:the frequency with whihc to clear the data that is being averagedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck11.thetathe quantity that is being averagedBANDWIDTH=0.1the bandwidths for kernel density esimtationGRID_MIN=0the lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridCLEAR=125000the frequency with whihc to clear the data that is being averagedDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta1the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta1.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta2the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta2.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta3.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta4the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta4.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta5the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta5.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta6the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta6.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta7the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta7.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta8the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta8.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta9the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta9.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta10the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta10.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=theta11the grid you would like to print (can also use ARG for specifying what is being printed)FILE=hhtheta11.datthe file on which to write the gridSTRIDE=125000the frequency with which the grid should be output to the file
# Deriving 2D free energy profiles for pucker theta-phi
pucker1:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck1.theta,puckp1.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker2:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck2.theta,puckp2.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker3:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck3.theta,puckp3.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker4:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck4.theta,puckp4.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker5:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck5.theta,puckp5.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker6:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck6.theta,puckp6.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker7:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck7.theta,puckp7.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker8:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck8.theta,puckp8.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker9:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck9.theta,puckp9.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker10:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck10.theta,puckp10.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200 pucker11:the number of bins for the gridHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=puck11.theta,puckp11.phithe quantity that is being averagedBANDWIDTH=0.1,0.1the bandwidths for kernel density esimtationGRID_MIN=0,-pithe lower bounds for the gridGRID_MAX=pi,pithe upper bounds for the gridGRID_BIN=200,200the number of bins for the grid
ffpucker1:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker1the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker2:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker2the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker3:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker3the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker4:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker4the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker5:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker5the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker6:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker6the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker7:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker7the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker8:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker8the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker9:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker9the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker10:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker10the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15 ffpucker11:the temperature at which you are operatingCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=pucker11the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310.15the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker1the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker1.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker2the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker2.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker3.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker4the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker4.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker5the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker5.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker6the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker6.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker7the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker7.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker8the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker8.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker9the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker9.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker10the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker10.datthe file on which to write the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffpucker11the grid you would like to print (can also use ARG for specifying what is being printed)FILE=ffpucker11.datthe file on which to write the grid