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

phi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label phi1 calculates a scalar quantitypsi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
The TORSION action with label psi1 calculates a scalar quantityphi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=15,17,19,25
The TORSION action with label phi2 calculates a scalar quantitypsi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=17,19,25,27
The TORSION action with label psi2 calculates a scalar quantityphi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=25,27,29,35
The TORSION action with label phi3 calculates a scalar quantitypsi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=27,29,35,37

The TORSION action with label psi3 calculates a scalar quantitycosphi1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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
The MATHEVAL action with label cosphi1 calculates a scalar quantitycospsi1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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
The MATHEVAL action with label cospsi1 calculates a scalar quantitycosphi2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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
The MATHEVAL action with label cosphi2 calculates a scalar quantitycospsi2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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
The MATHEVAL action with label cospsi2 calculates a scalar quantitycosphi3: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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
The MATHEVAL action with label cosphi3 calculates a scalar quantitycospsi3: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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

The MATHEVAL action with label cospsi3 calculates a scalar quantitymeta_coord: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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

The MATHEVAL action with label meta_coord calculates a scalar quantitymetad: 
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

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
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

ENDPLUMED
Terminate plumed input. More details