PLUMED-NEST

Project ID: plumID:23.011
Source: Alanine/PTWTEMetaD/0/plumed.dat
Originally used with PLUMED version: 2.9
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=input.ala2.pdb
phi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
The TORSION action with label phi calculates a scalar quantitypsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
The TORSION action with label psi calculates a scalar quantityomega: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@omega-2
the four atoms that are required to calculate the omega dihedral for residue 2. Click here for more information. 
The TORSION action with label omega calculates a scalar quantityene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,19
The DISTANCE action with label d1 calculates a scalar quantityd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,17
The DISTANCE action with label d2 calculates a scalar quantityd3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,16

The DISTANCE action with label d3 calculates a scalar quantity
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
=psi
  
SIGMA
the widths of the Gaussian hills
=0.2
  
PACE
the frequency for hill addition
=500
  
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
  
HEIGHT
the heights of the Gaussian hills
=1.5
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
  
FILE
 a file in which the list of added hills is stored
=HILLS_PSI
  
GRID_MIN
the lower bounds for the grid
=-pi
  
GRID_MAX
the upper bounds for the grid
=pi
  
GRID_BIN
the number of bins for the grid
=50
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=metad.rbias,phi,psi,ene,omega,d1,d2,d3 
FMT
the format that should be used to output real numbers
=%7.4f

ENDPLUMED
Terminate plumed input. More details