PLUMED-NEST

Project ID: plumID:19.018
Source: ES/plumed_excitedstates.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

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-107
The WHOLEMOLECULES action with label  calculates somethingT1The TORSION action with label T1 calculates the following quantities:
 Quantity   
 Type   
 Description  
T1
scalar
the TORSION involving these atoms:  TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,36,37
T2The TORSION action with label T2 calculates the following quantities:
 Quantity   
 Type   
 Description  
T2
scalar
the TORSION involving these atoms:  TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=58,57,25,26
T3The TORSION action with label T3 calculates the following quantities:
 Quantity   
 Type   
 Description  
T3
scalar
the TORSION involving these atoms:    TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=79,78,46,47


# this the lambda value for current window
lambdaThe CONSTANT action with label lambda calculates the following quantities:
 Quantity   
 Type   
 Description  
lambda
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=0.00
lambda: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe single number that you would like to store=0.00  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# first we define V0
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=V0The MATHEVAL action with label V0 calculates the following quantities:
 Quantity   
 Type   
 Description  
V0
scalar
an arbitrary function ARGthe values input to this function=T3 VARthe names to give each of the arguments in the function=x
 FUNCthe function you wish to evaluate=13.68-0.057*cos(x-pi)-48.06*(cos(x-pi))^2+0.17*(cos(x-pi))^3+42.2*(cos(x-pi))^4-0.0809*(cos(x-pi))^5
 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

# then V1
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=V1The MATHEVAL action with label V1 calculates the following quantities:
 Quantity   
 Type   
 Description  
V1
scalar
an arbitrary function ARGthe values input to this function=T3 VARthe names to give each of the arguments in the function=x
 FUNCthe function you wish to evaluate=341.-0.463*cos(x-pi)-92.73*(cos(x-pi))^2+1.23*(cos(x-pi))^3+55.6*(cos(x-pi))^4-0.803*(cos(x-pi))^5
 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

# This is Vlambda for current window
VlambdaThe MATHEVAL action with label Vlambda calculates the following quantities:
 Quantity   
 Type   
 Description  
Vlambda
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=V0,V1,lambda VARthe names to give each of the arguments in the function=x,y,z FUNCthe function you wish to evaluate=(1.0-z)*x+z*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# These are Vlambda for nearest neighbors
VlambdapThe MATHEVAL action with label Vlambdap calculates the following quantities:
 Quantity   
 Type   
 Description  
Vlambdap
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=V0,V1,lambda VARthe names to give each of the arguments in the function=x,y,z FUNCthe function you wish to evaluate=(1.0-z-0.02)*x+(z+0.02)*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VlambdamThe MATHEVAL action with label Vlambdam calculates the following quantities:
 Quantity   
 Type   
 Description  
Vlambdam
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=V0,V1,lambda VARthe names to give each of the arguments in the function=x,y,z FUNCthe function you wish to evaluate=(1.0-z+0.02)*x+(z-0.02)*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# activate Vlambda bias for current window
VlbiasThe BIASVALUE action with label Vlbias calculates the following quantities:
 Quantity   
 Type   
 Description  
Vlbias.bias
scalar
the instantaneous value of the bias potential
Vlbias.Vlambda_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named Vlambda: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=Vlambda

METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=T3 SIGMAthe widths of the Gaussian hills=0.2 HEIGHTthe heights of the Gaussian hills=1.2 PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=HILLS_0.00 BIASFACTORuse well tempered metadynamics and use this bias factor=25.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi


# print out useful stuff
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=T3,Vlambdam,Vlambda,Vlambdap,T1,T2 STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR_0.00