PLUMED-NEST

Project ID: plumID:19.019
Source: FA-MetaD-Ala3-plumed/plumed_FaMetaD.dat
Originally used with PLUMED version: 2.5
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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=GMXfiles/ala3.pdb

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1

ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=1.25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c1
The ALPHABETA action with label c1 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=1.25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c3
The ALPHABETA action with label c3 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=1.25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c5
The ALPHABETA action with label c5 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=1.25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c2
The ALPHABETA action with label c2 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=1.25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c4
The ALPHABETA action with label c4 calculates a scalar quantity
ALPHABETA
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details
 
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
 
REFERENCE
the reference values for each of the torsional angles
=1.25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=c6

The ALPHABETA action with label c6 calculates a scalar quantity
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
=sum_abs 
ARG
the input for this action is the scalar output from one or more other actions
=c1,c2,c3,c4,c5,c6 
POWERS
 the powers to which you are raising each of the arguments in your function
=1,1,1,1,1,1 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.6228,0.1201,0.5643,0.1102,0.5153,0.0403 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The COMBINE action with label sum_abs calculates a scalar quantity
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
=sum_abs
 
HEIGHT
the heights of the Gaussian hills
=0.4
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=4
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
 
SIGMA
the widths of the Gaussian hills
=0.04
 
GRID_MIN
the lower bounds for the grid
=-0.02 
GRID_MAX
the upper bounds for the grid
=2.0 
GRID_BIN
the number of bins for the grid
=200
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=WTMetaD

 
FREQUENCY_ADAPTIVE
 Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor
 
PACE
the frequency for hill addition
=1000 # 2ps
 
FA_MAX_PACE
the maximum hill addition frequency allowed in frequency adaptive metadynamics
=100000 # 200ps
 
FA_UPDATE_FREQUENCY
the frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE
=500
 
FA_MIN_ACCELERATION
only update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here
=1e1 # enable the update of frq only after reaching a minimum alpha
 
ACCELERATION
 Set to TRUE if you want to compute the metadynamics acceleration factor

... METAD

The METAD action with label WTMetaD calculates the following quantities:
 Quantity   
 Description  
WTMetaD.bias
the instantaneous value of the bias potential
WTMetaD.acc
the metadynamics acceleration factor
WTMetaD.pace
the hill addition frequency when employing frequency adaptive metadynamics
COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=sum_abs
  
STRIDE
 the frequency with which the CVs are analyzed
=5000
  
BASIN_LL1
List of lower limits for basin #
=1.85
  
BASIN_UL1
List of upper limits for basin #
=2.0
... COMMITTOR

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
=sum_abs,WTMetaD 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%12.5f