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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=phi1 
FUNC
the function you wish to evaluate
=0.5+cos(x-1.25 
PERIODIC
if 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=psi1 
FUNC
the function you wish to evaluate
=0.5+cos(x-1.25 
PERIODIC
if 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=phi2 
FUNC
the function you wish to evaluate
=0.5+cos(x-1.25 
PERIODIC
if 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=psi2 
FUNC
the function you wish to evaluate
=0.5+cos(x-1.25 
PERIODIC
if 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=phi3 
FUNC
the function you wish to evaluate
=0.5+cos(x-1.25 
PERIODIC
if 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=psi3 
FUNC
the function you wish to evaluate
=0.5+cos(x-1.25 
PERIODIC
if 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: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=cosphi1,cospsi1,cosphi2,cospsi2,cosphi3,cospsi3 
VAR
the names to give each of the arguments in the function
=c1,c2,c3,c4,c5,c6 
FUNC
the function you wish to evaluate
=0.62*c1+0.12*c2+0.57*c3+0.11*c4+0.51*c5+0.04*c6 
PERIODIC
if 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: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=meta_coord 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=1.5 
SIGMA
the widths of the Gaussian hills
=0.1 
FILE
 a file in which the list of added hills is stored
=HILLS 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
ARG
the input for this action is the scalar output from one or more other actions
=phi1,psi1,phi2,psi2,phi3,psi3,meta_coord,metad.bias 
FILE
the name of the file on which to output these quantities
=COLVAR

The PRINT action with label  calculates something
ENDPLUMED
Terminate plumed input. More details