PLUMED-NEST

Project ID: plumID:23.030
Source: ala2/template/plumed.dat
Originally used with PLUMED version: 2.9
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. 


MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=input.ala2.pdb
The MOLINFO action with label  calculates somethingphi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomspsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomsene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

# Define descriptors
The ENERGY action with label ene calculates somethingd1:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,5
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,6
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,7
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,9
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,11
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,15
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,16
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,17
The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsd9:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,19
The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Description  
d9.value
the DISTANCE between this pair of atomsd10:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,6
The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Description  
d10.value
the DISTANCE between this pair of atomsd11:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7
The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Description  
d11.value
the DISTANCE between this pair of atomsd12:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9
The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Description  
d12.value
the DISTANCE between this pair of atomsd13:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,11
The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Description  
d13.value
the DISTANCE between this pair of atomsd14:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,15
The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Description  
d14.value
the DISTANCE between this pair of atomsd15:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,16
The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Description  
d15.value
the DISTANCE between this pair of atomsd16:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,17
The DISTANCE action with label d16 calculates the following quantities:
 Quantity   
 Description  
d16.value
the DISTANCE between this pair of atomsd17:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,19
The DISTANCE action with label d17 calculates the following quantities:
 Quantity   
 Description  
d17.value
the DISTANCE between this pair of atomsd18:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,7
The DISTANCE action with label d18 calculates the following quantities:
 Quantity   
 Description  
d18.value
the DISTANCE between this pair of atomsd19:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,9
The DISTANCE action with label d19 calculates the following quantities:
 Quantity   
 Description  
d19.value
the DISTANCE between this pair of atomsd20:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,11
The DISTANCE action with label d20 calculates the following quantities:
 Quantity   
 Description  
d20.value
the DISTANCE between this pair of atomsd21:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,15
The DISTANCE action with label d21 calculates the following quantities:
 Quantity   
 Description  
d21.value
the DISTANCE between this pair of atomsd22:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,16
The DISTANCE action with label d22 calculates the following quantities:
 Quantity   
 Description  
d22.value
the DISTANCE between this pair of atomsd23:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,17
The DISTANCE action with label d23 calculates the following quantities:
 Quantity   
 Description  
d23.value
the DISTANCE between this pair of atomsd24:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,19
The DISTANCE action with label d24 calculates the following quantities:
 Quantity   
 Description  
d24.value
the DISTANCE between this pair of atomsd25:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,9
The DISTANCE action with label d25 calculates the following quantities:
 Quantity   
 Description  
d25.value
the DISTANCE between this pair of atomsd26:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,11
The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Description  
d26.value
the DISTANCE between this pair of atomsd27:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,15
The DISTANCE action with label d27 calculates the following quantities:
 Quantity   
 Description  
d27.value
the DISTANCE between this pair of atomsd28:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,16
The DISTANCE action with label d28 calculates the following quantities:
 Quantity   
 Description  
d28.value
the DISTANCE between this pair of atomsd29:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,17
The DISTANCE action with label d29 calculates the following quantities:
 Quantity   
 Description  
d29.value
the DISTANCE between this pair of atomsd30:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,19
The DISTANCE action with label d30 calculates the following quantities:
 Quantity   
 Description  
d30.value
the DISTANCE between this pair of atomsd31:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,11
The DISTANCE action with label d31 calculates the following quantities:
 Quantity   
 Description  
d31.value
the DISTANCE between this pair of atomsd32:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,15
The DISTANCE action with label d32 calculates the following quantities:
 Quantity   
 Description  
d32.value
the DISTANCE between this pair of atomsd33:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,16
The DISTANCE action with label d33 calculates the following quantities:
 Quantity   
 Description  
d33.value
the DISTANCE between this pair of atomsd34:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,17
The DISTANCE action with label d34 calculates the following quantities:
 Quantity   
 Description  
d34.value
the DISTANCE between this pair of atomsd35:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,19
The DISTANCE action with label d35 calculates the following quantities:
 Quantity   
 Description  
d35.value
the DISTANCE between this pair of atomsd36:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,15
The DISTANCE action with label d36 calculates the following quantities:
 Quantity   
 Description  
d36.value
the DISTANCE between this pair of atomsd37:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,16
The DISTANCE action with label d37 calculates the following quantities:
 Quantity   
 Description  
d37.value
the DISTANCE between this pair of atomsd38:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,17
The DISTANCE action with label d38 calculates the following quantities:
 Quantity   
 Description  
d38.value
the DISTANCE between this pair of atomsd39:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,19
The DISTANCE action with label d39 calculates the following quantities:
 Quantity   
 Description  
d39.value
the DISTANCE between this pair of atomsd40:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,16
The DISTANCE action with label d40 calculates the following quantities:
 Quantity   
 Description  
d40.value
the DISTANCE between this pair of atomsd41:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,17
The DISTANCE action with label d41 calculates the following quantities:
 Quantity   
 Description  
d41.value
the DISTANCE between this pair of atomsd42:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,19
The DISTANCE action with label d42 calculates the following quantities:
 Quantity   
 Description  
d42.value
the DISTANCE between this pair of atomsd43:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=16,17
The DISTANCE action with label d43 calculates the following quantities:
 Quantity   
 Description  
d43.value
the DISTANCE between this pair of atomsd44:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=16,19
The DISTANCE action with label d44 calculates the following quantities:
 Quantity   
 Description  
d44.value
the DISTANCE between this pair of atomsd45:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=17,19


The DISTANCE action with label d45 calculates the following quantities:
 Quantity   
 Description  
d45.value
the DISTANCE between this pair of atomsopese: 
OPES_METAD_EXPLORE
On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=phi
  
PACE
the frequency for kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=40
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
...


The OPES_METAD_EXPLORE action with label opese calculates the following quantities:
 Quantity   
 Description  
opese.bias
the instantaneous value of the bias potential
opese.rct
estimate of c(t)
opese.zed
estimate of Z_n
opese.neff
effective sample size
opese.nker
total number of compressed kernels used to represent the bias
COMMITTOR
Does a committor analysis. More details
 ...
 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi
 
STRIDE
 the frequency with which the CVs are analyzed
=100
 
BASIN_LL1
List of lower limits for basin #
=0.6,-1.5
 
BASIN_UL1
List of upper limits for basin #
=2.0,0.0
... COMMITTOR

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
=1 
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