PLUMED-NEST

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=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

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_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. 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 kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=50
  #BARRIER=70
  
NLIST
 use neighbor list for kernels summation, faster but experimental
  #NO_ZED
...
opes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. 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 kernel deposition
=500
  
BARRIER
the 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
...

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 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