PLUMED-NEST

Project ID: plumID:19.029
Source: C57D.plumed2/plumed.dat
Originally used with PLUMED version: 2.2
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

# restart previous simulation
# RESTART
MOLINFOThis 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=reference.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein
The MOLINFO action with label  calculates somethingGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein LABELa label for the action so that its output can be referenced in the input to other actions=proteinThe GROUP action with label protein calculates the following quantities:
 Quantity   
 Type   
 Description  
protein
atoms
indices of atoms specified in GROUP

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=protein
#index group for C-alpha needed for Rg
GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=C-alpha LABELa label for the action so that its output can be referenced in the input to other actions=c_alphasThe GROUP action with label c_alphas calculates the following quantities:
 Quantity   
 Type   
 Description  
c_alphas
atoms
indices of atoms specified in GROUP

GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c_alphas LABELa label for the action so that its output can be referenced in the input to other actions=rg_caThe GYRATION action with label rg_ca calculates the following quantities:
 Quantity   
 Type   
 Description  
rg_ca
scalar
the radius of gyration #Ca Rg CV1

ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=-0.78540  # for psi alphahelix app -45 deg CV2 alpha aa 5-21
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.  
ATOMS3the atoms involved for each of the torsions you wish to calculate=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.  
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.  
ATOMS5the atoms involved for each of the torsions you wish to calculate=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.  
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.  
ATOMS7the atoms involved for each of the torsions you wish to calculate=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.  
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.  
ATOMS9the atoms involved for each of the torsions you wish to calculate=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.  
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.  
ATOMS11the atoms involved for each of the torsions you wish to calculate=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.  
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.  
ATOMS13the atoms involved for each of the torsions you wish to calculate=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.  
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.  
ATOMS15the atoms involved for each of the torsions you wish to calculate=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.  
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information.  
ATOMS17the atoms involved for each of the torsions you wish to calculate=@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information.  
LABELa label for the action so that its output can be referenced in the input to other actions=ab1The ALPHABETA action with label ab1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=@psi-5 REFERENCE=-0.78540  # for psi alphahelix app -45 deg CV2 alpha aa 5-21
# ATOMS2=@psi-6 
# ATOMS3=@psi-7 
# ATOMS4=@psi-8 
# ATOMS5=@psi-9 
# ATOMS6=@psi-10 
# ATOMS7=@psi-11 
# ATOMS8=@psi-12 
# ATOMS9=@psi-13 
# ATOMS10=@psi-14 
# ATOMS11=@psi-15 
# ATOMS12=@psi-16 
# ATOMS13=@psi-17 
# ATOMS14=@psi-18 
# ATOMS15=@psi-19 
# ATOMS16=@psi-20 
# ATOMS17=@psi-21 
# LABEL=ab1
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
ab1_torsionsThe TORSION action with label ab1_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.      # Action input conctinues with 12 further ATOMSn keywords, 
ab1_refThe CONSTANT action with label ab1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540
ab1_coeffThe CONSTANT action with label ab1_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
ab1_combThe COMBINE action with label ab1_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab1_torsions,ab1_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab1_cosThe CUSTOM action with label ab1_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab1_comb,ab1_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab1The SUM action with label ab1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ab1
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=ab1_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=-0.78540  # for psi alphahelix app -45 deg CV3 alpha aa 28-43
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information.  
ATOMS3the atoms involved for each of the torsions you wish to calculate=@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information.  
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information.  
ATOMS5the atoms involved for each of the torsions you wish to calculate=@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information.  
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information.  
ATOMS7the atoms involved for each of the torsions you wish to calculate=@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information.  
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information.  
ATOMS9the atoms involved for each of the torsions you wish to calculate=@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information.  
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS11the atoms involved for each of the torsions you wish to calculate=@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information.  
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS13the atoms involved for each of the torsions you wish to calculate=@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-41the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
ATOMS15the atoms involved for each of the torsions you wish to calculate=@psi-42the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-43the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
LABELa label for the action so that its output can be referenced in the input to other actions=ab2The ALPHABETA action with label ab2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=@psi-28 REFERENCE=-0.78540  # for psi alphahelix app -45 deg CV3 alpha aa 28-43
# ATOMS2=@psi-29 
# ATOMS3=@psi-30 
# ATOMS4=@psi-31 
# ATOMS5=@psi-32 
# ATOMS6=@psi-33 
# ATOMS7=@psi-34 
# ATOMS8=@psi-35 
# ATOMS9=@psi-36 
# ATOMS10=@psi-37
# ATOMS11=@psi-38 
# ATOMS12=@psi-39
# ATOMS13=@psi-40
# ATOMS14=@psi-41
# ATOMS15=@psi-42
# ATOMS16=@psi-43
# LABEL=ab2
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
ab2_torsionsThe TORSION action with label ab2_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information.      # Action input conctinues with 11 further ATOMSn keywords, 
ab2_refThe CONSTANT action with label ab2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540
ab2_coeffThe CONSTANT action with label ab2_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
ab2_combThe COMBINE action with label ab2_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab2_torsions,ab2_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab2_cosThe CUSTOM action with label ab2_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab2_comb,ab2_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab2The SUM action with label ab2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ab2
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=ab2_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-45the four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=-0.78540  # for psi alphahelix app -45 deg CV4 alpha aa 45-58
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-46the four atoms that are required to calculate the psi dihedral for residue 46. Click here for more information.  
ATOMS3the atoms involved for each of the torsions you wish to calculate=@psi-47the four atoms that are required to calculate the psi dihedral for residue 47. Click here for more information.  
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-48the four atoms that are required to calculate the psi dihedral for residue 48. Click here for more information.  
ATOMS5the atoms involved for each of the torsions you wish to calculate=@psi-49the four atoms that are required to calculate the psi dihedral for residue 49. Click here for more information.  
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-50the four atoms that are required to calculate the psi dihedral for residue 50. Click here for more information. 
ATOMS7the atoms involved for each of the torsions you wish to calculate=@psi-51the four atoms that are required to calculate the psi dihedral for residue 51. Click here for more information. 
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-52the four atoms that are required to calculate the psi dihedral for residue 52. Click here for more information. 
ATOMS9the atoms involved for each of the torsions you wish to calculate=@psi-53the four atoms that are required to calculate the psi dihedral for residue 53. Click here for more information.  
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-54the four atoms that are required to calculate the psi dihedral for residue 54. Click here for more information.  
ATOMS11the atoms involved for each of the torsions you wish to calculate=@psi-55the four atoms that are required to calculate the psi dihedral for residue 55. Click here for more information.  
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-56the four atoms that are required to calculate the psi dihedral for residue 56. Click here for more information. 
ATOMS13the atoms involved for each of the torsions you wish to calculate=@psi-57the four atoms that are required to calculate the psi dihedral for residue 57. Click here for more information.  
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-58the four atoms that are required to calculate the psi dihedral for residue 58. Click here for more information.  
LABELa label for the action so that its output can be referenced in the input to other actions=ab3The ALPHABETA action with label ab3 calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=@psi-45 REFERENCE=-0.78540  # for psi alphahelix app -45 deg CV4 alpha aa 45-58
# ATOMS2=@psi-46 
# ATOMS3=@psi-47 
# ATOMS4=@psi-48 
# ATOMS5=@psi-49 
# ATOMS6=@psi-50
# ATOMS7=@psi-51
# ATOMS8=@psi-52
# ATOMS9=@psi-53 
# ATOMS10=@psi-54 
# ATOMS11=@psi-55 
# ATOMS12=@psi-56
# ATOMS13=@psi-57 
# ATOMS14=@psi-58 
# LABEL=ab3
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
ab3_torsionsThe TORSION action with label ab3_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@psi-45the four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@psi-46the four atoms that are required to calculate the psi dihedral for residue 46. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@psi-47the four atoms that are required to calculate the psi dihedral for residue 47. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@psi-48the four atoms that are required to calculate the psi dihedral for residue 48. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@psi-49the four atoms that are required to calculate the psi dihedral for residue 49. Click here for more information.      # Action input conctinues with 9 further ATOMSn keywords, 
ab3_refThe CONSTANT action with label ab3_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540
ab3_coeffThe CONSTANT action with label ab3_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1
ab3_combThe COMBINE action with label ab3_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab3_torsions,ab3_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab3_cosThe CUSTOM action with label ab3_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab3_comb,ab3_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab3The SUM action with label ab3 calculates the following quantities:
 Quantity   
 Type   
 Description  
ab3
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=ab3_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#walls
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg_ca ATthe positions of the wall=0.8 KAPPAthe force constant for the wall=1000.0
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg_ca ATthe positions of the wall=3.5 KAPPAthe force constant for the wall=1000.0

#metaD-wte
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=rg_ca,ab1,ab2,ab3 PACEthe frequency for hill addition=1000 HEIGHTthe heights of the Gaussian hills=0.5 SIGMAthe widths of the Gaussian hills=0.2,1,1,1 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298.00

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rg_ca,ab1,ab2,ab3 FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1000