PLUMED-NEST-TEST-SITE

Project ID: plumID:24.011
Source: ala2/data/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=./pytorch_model_bias.cpp
#LOAD FILE=./pytorch_model_bias.so

The LOAD action with label  calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../input.ala2.pdb

phi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomspsi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomstheta: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=6,5,7,9

The TORSION action with label theta calculates the following quantities:
 Quantity   
 Description  
theta.value
the TORSION involving these atomsene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethingx1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,5
The DISTANCE action with label x1 calculates the following quantities:
 Quantity   
 Description  
x1.value
the DISTANCE between this pair of atomsx2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6
The DISTANCE action with label x2 calculates the following quantities:
 Quantity   
 Description  
x2.value
the DISTANCE between this pair of atomsx3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,7
The DISTANCE action with label x3 calculates the following quantities:
 Quantity   
 Description  
x3.value
the DISTANCE between this pair of atomsx4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,9
The DISTANCE action with label x4 calculates the following quantities:
 Quantity   
 Description  
x4.value
the DISTANCE between this pair of atomsx5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,11
The DISTANCE action with label x5 calculates the following quantities:
 Quantity   
 Description  
x5.value
the DISTANCE between this pair of atomsx6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,15
The DISTANCE action with label x6 calculates the following quantities:
 Quantity   
 Description  
x6.value
the DISTANCE between this pair of atomsx7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,16
The DISTANCE action with label x7 calculates the following quantities:
 Quantity   
 Description  
x7.value
the DISTANCE between this pair of atomsx8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,17
The DISTANCE action with label x8 calculates the following quantities:
 Quantity   
 Description  
x8.value
the DISTANCE between this pair of atomsx9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,19
The DISTANCE action with label x9 calculates the following quantities:
 Quantity   
 Description  
x9.value
the DISTANCE between this pair of atomsx10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6
The DISTANCE action with label x10 calculates the following quantities:
 Quantity   
 Description  
x10.value
the DISTANCE between this pair of atomsx11: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7
The DISTANCE action with label x11 calculates the following quantities:
 Quantity   
 Description  
x11.value
the DISTANCE between this pair of atomsx12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9
The DISTANCE action with label x12 calculates the following quantities:
 Quantity   
 Description  
x12.value
the DISTANCE between this pair of atomsx13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,11
The DISTANCE action with label x13 calculates the following quantities:
 Quantity   
 Description  
x13.value
the DISTANCE between this pair of atomsx14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,15
The DISTANCE action with label x14 calculates the following quantities:
 Quantity   
 Description  
x14.value
the DISTANCE between this pair of atomsx15: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,16
The DISTANCE action with label x15 calculates the following quantities:
 Quantity   
 Description  
x15.value
the DISTANCE between this pair of atomsx16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,17
The DISTANCE action with label x16 calculates the following quantities:
 Quantity   
 Description  
x16.value
the DISTANCE between this pair of atomsx17: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,19
The DISTANCE action with label x17 calculates the following quantities:
 Quantity   
 Description  
x17.value
the DISTANCE between this pair of atomsx18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,7
The DISTANCE action with label x18 calculates the following quantities:
 Quantity   
 Description  
x18.value
the DISTANCE between this pair of atomsx19: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,9
The DISTANCE action with label x19 calculates the following quantities:
 Quantity   
 Description  
x19.value
the DISTANCE between this pair of atomsx20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,11
The DISTANCE action with label x20 calculates the following quantities:
 Quantity   
 Description  
x20.value
the DISTANCE between this pair of atomsx21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,15
The DISTANCE action with label x21 calculates the following quantities:
 Quantity   
 Description  
x21.value
the DISTANCE between this pair of atomsx22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,16
The DISTANCE action with label x22 calculates the following quantities:
 Quantity   
 Description  
x22.value
the DISTANCE between this pair of atomsx23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,17
The DISTANCE action with label x23 calculates the following quantities:
 Quantity   
 Description  
x23.value
the DISTANCE between this pair of atomsx24: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,19
The DISTANCE action with label x24 calculates the following quantities:
 Quantity   
 Description  
x24.value
the DISTANCE between this pair of atomsx25: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,9
The DISTANCE action with label x25 calculates the following quantities:
 Quantity   
 Description  
x25.value
the DISTANCE between this pair of atomsx26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,11
The DISTANCE action with label x26 calculates the following quantities:
 Quantity   
 Description  
x26.value
the DISTANCE between this pair of atomsx27: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,15
The DISTANCE action with label x27 calculates the following quantities:
 Quantity   
 Description  
x27.value
the DISTANCE between this pair of atomsx28: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,16
The DISTANCE action with label x28 calculates the following quantities:
 Quantity   
 Description  
x28.value
the DISTANCE between this pair of atomsx29: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,17
The DISTANCE action with label x29 calculates the following quantities:
 Quantity   
 Description  
x29.value
the DISTANCE between this pair of atomsx30: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,19
The DISTANCE action with label x30 calculates the following quantities:
 Quantity   
 Description  
x30.value
the DISTANCE between this pair of atomsx31: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,11
The DISTANCE action with label x31 calculates the following quantities:
 Quantity   
 Description  
x31.value
the DISTANCE between this pair of atomsx32: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,15
The DISTANCE action with label x32 calculates the following quantities:
 Quantity   
 Description  
x32.value
the DISTANCE between this pair of atomsx33: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,16
The DISTANCE action with label x33 calculates the following quantities:
 Quantity   
 Description  
x33.value
the DISTANCE between this pair of atomsx34: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,17
The DISTANCE action with label x34 calculates the following quantities:
 Quantity   
 Description  
x34.value
the DISTANCE between this pair of atomsx35: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,19
The DISTANCE action with label x35 calculates the following quantities:
 Quantity   
 Description  
x35.value
the DISTANCE between this pair of atomsx36: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,15
The DISTANCE action with label x36 calculates the following quantities:
 Quantity   
 Description  
x36.value
the DISTANCE between this pair of atomsx37: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,16
The DISTANCE action with label x37 calculates the following quantities:
 Quantity   
 Description  
x37.value
the DISTANCE between this pair of atomsx38: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,17
The DISTANCE action with label x38 calculates the following quantities:
 Quantity   
 Description  
x38.value
the DISTANCE between this pair of atomsx39: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,19
The DISTANCE action with label x39 calculates the following quantities:
 Quantity   
 Description  
x39.value
the DISTANCE between this pair of atomsx40: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,16
The DISTANCE action with label x40 calculates the following quantities:
 Quantity   
 Description  
x40.value
the DISTANCE between this pair of atomsx41: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,17
The DISTANCE action with label x41 calculates the following quantities:
 Quantity   
 Description  
x41.value
the DISTANCE between this pair of atomsx42: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,19
The DISTANCE action with label x42 calculates the following quantities:
 Quantity   
 Description  
x42.value
the DISTANCE between this pair of atomsx43: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,17
The DISTANCE action with label x43 calculates the following quantities:
 Quantity   
 Description  
x43.value
the DISTANCE between this pair of atomsx44: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,19
The DISTANCE action with label x44 calculates the following quantities:
 Quantity   
 Description  
x44.value
the DISTANCE between this pair of atomsx45: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,19

### Define positions
The DISTANCE action with label x45 calculates the following quantities:
 Quantity   
 Description  
x45.value
the DISTANCE between this pair of atomsp1: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=2 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.x
the x-component of the atom position
p1.y
the y-component of the atom position
p1.z
the z-component of the atom position
p1.a
the normalized projection on the first lattice vector of the atom position
p1.b
the normalized projection on the second lattice vector of the atom position
p1.c
the normalized projection on the third lattice vector of the atom positionp2: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=5 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p2 calculates the following quantities:
 Quantity   
 Description  
p2.x
the x-component of the atom position
p2.y
the y-component of the atom position
p2.z
the z-component of the atom position
p2.a
the normalized projection on the first lattice vector of the atom position
p2.b
the normalized projection on the second lattice vector of the atom position
p2.c
the normalized projection on the third lattice vector of the atom positionp3: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=6 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p3 calculates the following quantities:
 Quantity   
 Description  
p3.x
the x-component of the atom position
p3.y
the y-component of the atom position
p3.z
the z-component of the atom position
p3.a
the normalized projection on the first lattice vector of the atom position
p3.b
the normalized projection on the second lattice vector of the atom position
p3.c
the normalized projection on the third lattice vector of the atom positionp4: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=7 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p4 calculates the following quantities:
 Quantity   
 Description  
p4.x
the x-component of the atom position
p4.y
the y-component of the atom position
p4.z
the z-component of the atom position
p4.a
the normalized projection on the first lattice vector of the atom position
p4.b
the normalized projection on the second lattice vector of the atom position
p4.c
the normalized projection on the third lattice vector of the atom positionp5: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=9 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p5 calculates the following quantities:
 Quantity   
 Description  
p5.x
the x-component of the atom position
p5.y
the y-component of the atom position
p5.z
the z-component of the atom position
p5.a
the normalized projection on the first lattice vector of the atom position
p5.b
the normalized projection on the second lattice vector of the atom position
p5.c
the normalized projection on the third lattice vector of the atom positionp6: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=11 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p6 calculates the following quantities:
 Quantity   
 Description  
p6.x
the x-component of the atom position
p6.y
the y-component of the atom position
p6.z
the z-component of the atom position
p6.a
the normalized projection on the first lattice vector of the atom position
p6.b
the normalized projection on the second lattice vector of the atom position
p6.c
the normalized projection on the third lattice vector of the atom positionp7: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=15 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p7 calculates the following quantities:
 Quantity   
 Description  
p7.x
the x-component of the atom position
p7.y
the y-component of the atom position
p7.z
the z-component of the atom position
p7.a
the normalized projection on the first lattice vector of the atom position
p7.b
the normalized projection on the second lattice vector of the atom position
p7.c
the normalized projection on the third lattice vector of the atom positionp8: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=16 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p8 calculates the following quantities:
 Quantity   
 Description  
p8.x
the x-component of the atom position
p8.y
the y-component of the atom position
p8.z
the z-component of the atom position
p8.a
the normalized projection on the first lattice vector of the atom position
p8.b
the normalized projection on the second lattice vector of the atom position
p8.c
the normalized projection on the third lattice vector of the atom positionp9: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=17 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p9 calculates the following quantities:
 Quantity   
 Description  
p9.x
the x-component of the atom position
p9.y
the y-component of the atom position
p9.z
the z-component of the atom position
p9.a
the normalized projection on the first lattice vector of the atom position
p9.b
the normalized projection on the second lattice vector of the atom position
p9.c
the normalized projection on the third lattice vector of the atom positionp10: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=19 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label

The POSITION action with label p10 calculates the following quantities:
 Quantity   
 Description  
p10.x
the x-component of the atom position
p10.y
the y-component of the atom position
p10.z
the z-component of the atom position
p10.a
the normalized projection on the first lattice vector of the atom position
p10.b
the normalized projection on the second lattice vector of the atom position
p10.c
the normalized projection on the third lattice vector of the atom positioncell: CELLGet the components of the simulation cell More details


The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrixsinphi: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=phi FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label sinphi calculates the following quantities:
 Quantity   
 Description  
sinphi.value
an arbitrary functioncosphi: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=phi FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label cosphi calculates the following quantities:
 Quantity   
 Description  
cosphi.value
an arbitrary functionsinpsi: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=psi FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label sinpsi calculates the following quantities:
 Quantity   
 Description  
sinpsi.value
an arbitrary functioncospsi: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=psi FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label cospsi calculates the following quantities:
 Quantity   
 Description  
cospsi.value
an arbitrary functionsintheta: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=theta FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label sintheta calculates the following quantities:
 Quantity   
 Description  
sintheta.value
an arbitrary functioncostheta: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=theta FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#Warning: In this stage the bias interface was slightly different to the final version.(But the behaviors are same.) In order to remain consistent with the data we provide, here we use the old interface.
The MATHEVAL action with label costheta calculates the following quantities:
 Quantity   
 Description  
costheta.value
an arbitrary functionq: PYTORCH_MODEL_BIASThis action is not part of PLUMED and was included by using a LOAD command More details FILE=../../models/model_phipsitheta.pt ARG=sinphi,cosphi,sinpsi,cospsi,sintheta,costheta ALPHA=-2

potential: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=q.bias-0



The BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Description  
potential.bias
the instantaneous value of the bias potential
potential._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR