PLUMED-NEST

Project ID: plumID:19.040
Source: comet/sgoop/plumed.dat
Originally used with PLUMED version: 2.3
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

phi1The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi1
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=17,19,25,27
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37

cosphi1The MATHEVAL action with label cosphi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cosphi1
scalar
an arbitrary function: 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=phi1 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi1The MATHEVAL action with label cospsi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cospsi1
scalar
an arbitrary function: 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=psi1 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi2The MATHEVAL action with label cosphi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cosphi2
scalar
an arbitrary function: 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=phi2 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi2The MATHEVAL action with label cospsi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cospsi2
scalar
an arbitrary function: 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=psi2 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi3The MATHEVAL action with label cosphi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cosphi3
scalar
an arbitrary function: 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=phi3 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi3The MATHEVAL action with label cospsi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cospsi3
scalar
an arbitrary function: 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=psi3 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

meta_coordThe MATHEVAL action with label meta_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
meta_coord
scalar
an arbitrary function: 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=cosphi1,cospsi1,cosphi2,cospsi2,cosphi3,cospsi3 VARthe names to give each of the arguments in the function=c1,c2,c3,c4,c5,c6 FUNCthe function you wish to evaluate=0.62*c1+0.12*c2+0.57*c3+0.11*c4+0.51*c5+0.04*c6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=meta_coord PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.5 SIGMAthe widths of the Gaussian hills=0.1 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=phi1,psi1,phi2,psi2,phi3,psi3,meta_coord,metad.bias FILEthe name of the file on which to output these quantities=COLVAR

The PRINT action with label  calculates somethingENDPLUMEDTerminate plumed input. More details