PLUMED-NEST

Project ID: plumID:20.007
Source: triple/plumed.dat
Originally used with PLUMED version: 2.4.2
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

# The commented out lines are the original implementation. They have been altered to be compatible with newer PLUMED versions.

d1775_2417The DISTANCE action with label d1775_2417 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1775_2417
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1775,2417
d1739_1755The DISTANCE action with label d1739_1755 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1739_1755
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1739,1755
d1795_453The DISTANCE action with label d1795_453 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1795_453
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1795,453
d1809_1823The DISTANCE action with label d1809_1823 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1809_1823
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1809,1823
d1823_1834The DISTANCE action with label d1823_1834 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1823_1834
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1823,1834

loop_distThe DISTANCE action with label loop_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
loop_dist
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1772,1822
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1773,1775,1791,1793

COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc1The COMBINE action with label rc1 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc1
scalar
a linear compbination ARGthe values input to this function=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834 COEFFICIENTS the coefficients of the arguments in your function=0.41801464557647705,-0.04167945683002472,0.8776463866233826,-0.21770134568214417,0.07661298662424088 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc2The COMBINE action with label rc2 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc2
scalar
a linear compbination ARGthe values input to this function=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834 COEFFICIENTS the coefficients of the arguments in your function=-0.7833237051963806,0.06509189307689667,0.42879876494407654,0.0804712250828743,-0.43797600269317627 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
BIASFACTORuse well tempered metadynamics and use this bias factor=10
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
ARGthe labels of the scalars on which the bias will act=rc1,rc2
SIGMAthe widths of the Gaussian hills=0.092,0.069
HEIGHTthe heights of the Gaussian hills=1.5
PACEthe frequency for hill addition=500
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
#GRID_MIN=0.0,-6.0
#GRID_MAX=8.0,2.0
#GRID_BIN=150,150
#REWEIGHTING_NGRID=150,150
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
BIASFACTORuse well tempered metadynamics and use this bias factor=10
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
ARGthe labels of the scalars on which the bias will act=rc1,rc2
SIGMAthe widths of the Gaussian hills=0.092,0.069
HEIGHTthe heights of the Gaussian hills=1.5
PACEthe frequency for hill addition=500
LABELa label for the action so that its output can be referenced in the input to other actions=metad
#GRID_MIN=0.0,-6.0
#GRID_MAX=8.0,2.0
#GRID_BIN=150,150
#REWEIGHTING_NGRID=150,150
 FILE a file in which the list of added hills is stored=HILLS
... METAD

#PRINT ARG=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834,loop_dist,psi,rc1,rc2,metad.bias,metad.rbias STRIDE=1 FILE=BIASED_COLVAR

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834,loop_dist,psi,rc1,rc2,metad.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=BIASED_COLVAR