PLUMED-NEST-TEST-SITE

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=plumedEnables 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: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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: ENERGYCalculate the total potential energy of the simulation box. More details

metadThe PBMETAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: PBMETADUsed to performed Parallel Bias metadynamics. More details ...
  #ARG=phi1,phi2,phi3
  ARGthe labels of the scalars on which the bias will act=psi1,psi2,psi3
  PACEthe frequency for hill addition, one for all biases=500
  HEIGHTthe height of the Gaussian hills, one for all biases=1.2
  #HEIGHT=12
  SIGMAthe widths of the Gaussian hills=0.35,0.35,0.35
  #ADAPTIVE=DIFF
  #SIGMA=500
  #SIGMA_MIN=0.1,0.1,0.1
  BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=20
  GRID_MINthe lower bounds for the grid=-pi,-pi,-pi
  GRID_MAXthe upper bounds for the grid=pi,pi,pi
  GRID_BINthe number of bins for the grid=100,100,100
...

PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=*

The PRINT action with label  calculates somethingENDPLUMEDTerminate 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