PLUMED-NEST

Project ID: plumID:21.021
Source: atlas_inputs/LJ-38/plumed_biased.dat
Originally used with PLUMED version: 2.7-mod
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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UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label  calculates somethingnsa: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-38 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.25 D_MAX=1.5} 

The COORDINATIONNUMBER action with label nsa calculates the following quantities:
 Quantity   
 Description  
nsa.value
the coordination numbers of the specified atomsn4: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-4)*(x-4)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n4 calculates the following quantities:
 Quantity   
 Description  
n4.value
an arbitrary functionn5: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-5)*(x-5)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n5 calculates the following quantities:
 Quantity   
 Description  
n5.value
an arbitrary functionn6: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-6)*(x-6)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n6 calculates the following quantities:
 Quantity   
 Description  
n6.value
an arbitrary functionn7: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-7)*(x-7)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n7 calculates the following quantities:
 Quantity   
 Description  
n7.value
an arbitrary functionn8: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-8)*(x-8)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n8 calculates the following quantities:
 Quantity   
 Description  
n8.value
an arbitrary functionn9: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-9)*(x-9)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n9 calculates the following quantities:
 Quantity   
 Description  
n9.value
an arbitrary functionn10: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-10)*(x-10)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label n10 calculates the following quantities:
 Quantity   
 Description  
n10.value
an arbitrary functionn11: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-11)*(x-11)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


The MATHEVAL action with label n11 calculates the following quantities:
 Quantity   
 Description  
n11.value
an arbitrary functionat: ATLASThis action is not part of PLUMED and was included by using a LOAD command More details ARG=n4,n5,n6,n7,n8,n9,n10,n11 REFERENCE=cluster_plumed.dat PACE=200 SIGMA=0.1 BIASFACTOR=5 HEIGHT=0.02  GRID_MAX=5.0 GRID_BIN=500 TEMP=0.12 TRUNCATE_GRIDS ADAPTIVE_WALL=1.0 STATIC_WALL=0.0 REGULARISE=1E-12

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=n4,n5,n6,n7,n8,n9,n10,n11 FMTthe format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=200
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=at_adaptive_wall FMTthe format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=wall STRIDE the frequency with which the quantities of interest should be output=200
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=at FMTthe format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=bias STRIDE the frequency with which the quantities of interest should be output=200