PLUMED-NEST

Project ID: plumID:22.003
Source: ala4/metad/plumed.dat
Originally used with PLUMED version: 2.8
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. 

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
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
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
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
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
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
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
metad.maxbias
scalar
the maximum of the metadynamics V(s, t): 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 ...
  #ARG=phi1,phi2,phi3
  
ARG
the labels of the scalars on which the bias will act
=psi1,psi2,psi3
  
PACE
the frequency for hill addition
=500
  
HEIGHT
the heights of the Gaussian hills
=1.2
  #HEIGHT=12
  
SIGMA
the widths of the Gaussian hills
=0.35,0.35,0.35
  #ADAPTIVE=DIFF
  #SIGMA=500
  #SIGMA_MIN=0.1,0.1,0.1
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
  
GRID_MIN
the lower bounds for the grid
=-pi,-pi,-pi
  
GRID_MAX
the upper bounds for the grid
=pi,pi,pi
  
GRID_BIN
the number of bins for the grid
=65,65,65
  
CALC_MAX_BIAS
 Set to TRUE if you want to compute the maximum of the metadynamics V(s, t)
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...
metad: 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 ...
  #ARG=phi1,phi2,phi3
  
ARG
the labels of the scalars on which the bias will act
=psi1,psi2,psi3
  
PACE
the frequency for hill addition
=500
  
HEIGHT
the heights of the Gaussian hills
=1.2
  #HEIGHT=12
  
SIGMA
the widths of the Gaussian hills
=0.35,0.35,0.35
  #ADAPTIVE=DIFF
  #SIGMA=500
  #SIGMA_MIN=0.1,0.1,0.1
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
  
GRID_MIN
the lower bounds for the grid
=-pi,-pi,-pi
  
GRID_MAX
the upper bounds for the grid
=pi,pi,pi
  
GRID_BIN
the number of bins for the grid
=65,65,65
  
CALC_MAX_BIAS
 Set to TRUE if you want to compute the maximum of the metadynamics V(s, t)
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
FILE
 a file in which the list of added hills is stored
=HILLS
...

PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the labels of the values that you would like to print to the file

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


for i in {0..9};do mkdir phi-std-$i phi-agr-$i psi-std-$i psi-agr-$i;done
for d in `ls -d p*`;do mkdir nonT-$d ada-$d;done

run with:
cd ${dir}-$i
../../queue_gromacs.i.sh $i


All combinations of the following:

- good CVs
  ARG=phi1,phi2,phi3
- bad CVs
  ARG=psi1,psi2,psi3

- standard parameters
  HEIGHT=1.2
- aggressive parameters
  HEIGHT=12

- well-tempered
  BIASFACTOR=20
- non-tempered
  # BIASFACTOR=20

- standard sigma
  SIGMA=0.35,0.35,0.35
- adaptive sigma
  ADAPTIVE=DIFF
  SIGMA=500
  SIGMA_MIN=0.1,0.1,0.1