PLUMED-NEST-TEST-SITE

Project ID: plumID:22.003
Source: ala4/explore/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

opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias
opes.nlker
scalar
number of kernels in the neighbor list
opes.nlsteps
scalar
number of steps from last neighbor list update: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  #ARG=phi1,phi2,phi3
  ARGthe labels of the scalars on which the bias will act=psi1,psi2,psi3
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=50
  #BARRIER=70
  NLIST use neighbor list for kernels summation, faster but experimental
  #NO_ZED
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  #ARG=phi1,phi2,phi3
  ARGthe labels of the scalars on which the bias will act=psi1,psi2,psi3
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=50
  #BARRIER=70
  NLIST use neighbor list for kernels summation, faster but experimental
  #NO_ZED
 TEMP temperature=-1 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...

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 noZ-$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
  BARRIER=50
- aggressive parameters
  BARRIER=70

- with Zed
  #NO_ZED
- without Zed
  NO_ZED