PLUMED-NEST

Project ID: plumID:20.007
Source: double/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

RESTART
Activate restart. More details
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-2640

d686_1739: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=686,1739
The DISTANCE action with label d686_1739 calculates a scalar quantityd1834_1853: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1834,1853
The DISTANCE action with label d1834_1853 calculates a scalar quantityd1732_1739: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1732,1739
The DISTANCE action with label d1732_1739 calculates a scalar quantityd1755_1765: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1755,1765
The DISTANCE action with label d1755_1765 calculates a scalar quantityd1823_1834: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1823,1834
The DISTANCE action with label d1823_1834 calculates a scalar quantityd1765_1823: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1765,1823
The DISTANCE action with label d1765_1823 calculates a scalar quantityd1809_1877: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1809,1877
The DISTANCE action with label d1809_1877 calculates a scalar quantityd1187_1739: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1187,1739
The DISTANCE action with label d1187_1739 calculates a scalar quantityd1877_1894: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1877,1894
The DISTANCE action with label d1877_1894 calculates a scalar quantityd1853_1947: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1853,1947

The DISTANCE action with label d1853_1947 calculates a scalar quantitypsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1773,1775,1791,1793
The TORSION action with label psi calculates a scalar quantitydist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1772,1822 # A1130-S117H

The DISTANCE action with label dist calculates a scalar quantityrmsd: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=rmsd.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc1 
ARG
the input to this function
=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.135,-0.343,0.432,0.348,-0.377,0.162,-0.138,0.294,0.527,-0.070
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc2 
ARG
the input to this function
=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947 
COEFFICIENTS
 the coefficients of the arguments in your function
=-0.075,-0.226,0.758,0.083,-0.326,0.247,-0.173,-0.137,0.194,0.330
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE


METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
ARG
the input for this action is the scalar output from one or more other actions
=rc1,rc2
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=1.5
SIGMA
the widths of the Gaussian hills
=0.021,0.014
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
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rmsd 
AT
the positions of the wall
=.4 
KAPPA
the force constant for the wall
=10000.0 
EXP
 the powers for the walls
=4 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947,rc1,rc2,psi,dist,rmsd,uwall.bias,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=COLVAR_full