PLUMED-NEST

Project ID: plumID:22.003
Source: ala4/pbmetad/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. 

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 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 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 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 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 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 quantityene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

metad: 
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
  #ARG=phi1,phi2,phi3
  
ARG
the input for this action is the scalar output from one or more other actions
=psi1,psi2,psi3
  
PACE
the frequency for hill addition, one for all biases
=500
  
HEIGHT
the height of the Gaussian hills, one for all biases
=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 with this bias factor, one for all biases
=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
=100,100,100
...

The PBMETAD 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
 
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 input for this action is the scalar output from one or more other actions

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