PLUMED-NEST

Project ID: plumID:21.036
Source: DHH1N_sampling/PTMetaD-WTE/plumed_CVs_PTMetaD-WTE.dat
Originally used with PLUMED version: 2.5.2
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
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=Protein.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 somethingWHOLEMOLECULESThis 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=1-709

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
enedThe METAD action with label ened calculates the following quantities:
 Quantity   
 Type   
 Description  
ened.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=ene PACEthe frequency for hill addition=500000000 HEIGHTthe heights of the Gaussian hills=1.2 SIGMAthe widths of the Gaussian hills=2000.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=12 FILE a file in which the list of added hills is stored=HILLS
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=5000 ARGthe labels of the values that you would like to print to the file=ene,ened.bias FILEthe name of the file on which to output these quantities=COLVAR_ENE

caThe GROUP action with label ca calculates the following quantities:
 Quantity   
 Type   
 Description  
ca
atoms
indices of atoms specified in GROUP: 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 ATOMSthe numerical indexes for the set of atoms in the group=5,12,23,42,56,70,84,104,118,132,146,160,174,185,199,213,225,244,256,280,292,316,338,352,362,381,395,416,428,450,472,484,498,524,536,553,567,579,591,607,626,640,654,676,683,697
cv2The COORDINATION action with label cv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv2
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=ca NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=10 R_0The r_0 parameter of the switching function=0.65 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=5.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
cv2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=ca NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=10 R_0The r_0 parameter of the switching function=0.65 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=5.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5  D_0 The d_0 parameter of the switching function=0.0

cgThe GROUP action with label cg calculates the following quantities:
 Quantity   
 Type   
 Description  
cg
atoms
indices of atoms specified in GROUP: 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 ATOMSthe numerical indexes for the set of atoms in the group=27,31,47,61,75,89,109,124,137,151,165,190,205,218,230,249,261,285,297,321,344,367,386,399,403,421,433,455,477,490,503,529,541,559,572,584,595,599,612,631,646,659,688,703
cv3The COORDINATION action with label cv3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv3
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=cg R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=10 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=4.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
cv3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=cg R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=10 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=4.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5  D_0 The d_0 parameter of the switching function=0.0

o1The GROUP action with label o1 calculates the following quantities:
 Quantity   
 Type   
 Description  
o1
atoms
indices of atoms specified in GROUP: 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 ATOMSthe numerical indexes for the set of atoms in the group=20,39,53,67,81,101,115,129,143,157,171,182,196,210,222,241,253,277,289,313,335,349,359,378,392,425,447,469,481,495,533,550,564,576,588,604,623,637,651,673,680,694
h1The GROUP action with label h1 calculates the following quantities:
 Quantity   
 Type   
 Description  
h1
atoms
indices of atoms specified in GROUP: 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 ATOMSthe numerical indexes for the set of atoms in the group=11,22,41,55,69,83,103,117,131,145,159,173,184,198,212,224,243,255,279,291,315,337,351,361,380,394,427,449,471,483,497,535,552,566,578,590,606,625,639,653,675,682
cv4The COORDINATION action with label cv4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv4
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=h1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=o1 R_0The r_0 parameter of the switching function=0.20 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=10 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
cv4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=h1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=o1 R_0The r_0 parameter of the switching function=0.20 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=10 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5  D_0 The d_0 parameter of the switching function=0.0

DIHCORMeasures the degree of similarity between dihedral angles. This action is a shortcut. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=cv5The DIHCOR action with label cv5 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv5
scalar
the sum of all the dihedral correlations
ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. ,@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS4the set of 8 atoms that are being used each of the dihedral correlation values=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. ,@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS5the set of 8 atoms that are being used each of the dihedral correlation values=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. ,@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS6the set of 8 atoms that are being used each of the dihedral correlation values=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. ,@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS7the set of 8 atoms that are being used each of the dihedral correlation values=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. ,@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS8the set of 8 atoms that are being used each of the dihedral correlation values=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. ,@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS9the set of 8 atoms that are being used each of the dihedral correlation values=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. ,@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS10the set of 8 atoms that are being used each of the dihedral correlation values=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. ,@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS11the set of 8 atoms that are being used each of the dihedral correlation values=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. ,@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS12the set of 8 atoms that are being used each of the dihedral correlation values=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. ,@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS13the set of 8 atoms that are being used each of the dihedral correlation values=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. ,@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS14the set of 8 atoms that are being used each of the dihedral correlation values=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. ,@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS15the set of 8 atoms that are being used each of the dihedral correlation values=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. ,@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS16the set of 8 atoms that are being used each of the dihedral correlation values=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. ,@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS17the set of 8 atoms that are being used each of the dihedral correlation values=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. ,@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS18the set of 8 atoms that are being used each of the dihedral correlation values=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. ,@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
ATOMS19the set of 8 atoms that are being used each of the dihedral correlation values=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. ,@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
ATOMS20the set of 8 atoms that are being used each of the dihedral correlation values=@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. ,@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
ATOMS21the set of 8 atoms that are being used each of the dihedral correlation values=@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. ,@psi-22the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
ATOMS22the set of 8 atoms that are being used each of the dihedral correlation values=@psi-22the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. ,@psi-23the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
ATOMS23the set of 8 atoms that are being used each of the dihedral correlation values=@psi-23the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. ,@psi-24the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
ATOMS24the set of 8 atoms that are being used each of the dihedral correlation values=@psi-24the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. ,@psi-25the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
ATOMS25the set of 8 atoms that are being used each of the dihedral correlation values=@psi-25the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. ,@psi-26the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
ATOMS26the set of 8 atoms that are being used each of the dihedral correlation values=@psi-26the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. ,@psi-27the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
ATOMS27the set of 8 atoms that are being used each of the dihedral correlation values=@psi-27the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. ,@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
ATOMS28the set of 8 atoms that are being used each of the dihedral correlation values=@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. ,@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
ATOMS29the set of 8 atoms that are being used each of the dihedral correlation values=@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. ,@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
ATOMS30the set of 8 atoms that are being used each of the dihedral correlation values=@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. ,@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
ATOMS31the set of 8 atoms that are being used each of the dihedral correlation values=@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. ,@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
ATOMS32the set of 8 atoms that are being used each of the dihedral correlation values=@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. ,@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
ATOMS33the set of 8 atoms that are being used each of the dihedral correlation values=@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. ,@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
ATOMS34the set of 8 atoms that are being used each of the dihedral correlation values=@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. ,@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
ATOMS35the set of 8 atoms that are being used each of the dihedral correlation values=@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. ,@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
ATOMS36the set of 8 atoms that are being used each of the dihedral correlation values=@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. ,@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS37the set of 8 atoms that are being used each of the dihedral correlation values=@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. ,@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
ATOMS38the set of 8 atoms that are being used each of the dihedral correlation values=@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. ,@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS39the set of 8 atoms that are being used each of the dihedral correlation values=@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. ,@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS40the set of 8 atoms that are being used each of the dihedral correlation values=@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. ,@psi-41the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
ATOMS41the set of 8 atoms that are being used each of the dihedral correlation values=@psi-41the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. ,@psi-42the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
ATOMS42the set of 8 atoms that are being used each of the dihedral correlation values=@psi-42the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. ,@psi-43the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
ATOMS43the set of 8 atoms that are being used each of the dihedral correlation values=@psi-43the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. ,@psi-44the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. 
ATOMS44the set of 8 atoms that are being used each of the dihedral correlation values=@psi-44the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. ,@psi-45the four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information. 
... DIHCOR
# PLUMED interprets the command:
# DIHCOR ...
# LABEL=cv5
# ATOMS1=@psi-1,@psi-2
# ATOMS2=@psi-2,@psi-3
# ATOMS3=@psi-3,@psi-4
# ATOMS4=@psi-4,@psi-5
# ATOMS5=@psi-5,@psi-6
# ATOMS6=@psi-6,@psi-7
# ATOMS7=@psi-7,@psi-8
# ATOMS8=@psi-8,@psi-9
# ATOMS9=@psi-9,@psi-10
# ATOMS10=@psi-10,@psi-11
# ATOMS11=@psi-11,@psi-12
# ATOMS12=@psi-12,@psi-13
# ATOMS13=@psi-13,@psi-14
# ATOMS14=@psi-14,@psi-15
# ATOMS15=@psi-15,@psi-16
# ATOMS16=@psi-16,@psi-17
# ATOMS17=@psi-17,@psi-18
# ATOMS18=@psi-18,@psi-19
# ATOMS19=@psi-19,@psi-20
# ATOMS20=@psi-20,@psi-21
# ATOMS21=@psi-21,@psi-22
# ATOMS22=@psi-22,@psi-23
# ATOMS23=@psi-23,@psi-24
# ATOMS24=@psi-24,@psi-25
# ATOMS25=@psi-25,@psi-26
# ATOMS26=@psi-26,@psi-27
# ATOMS27=@psi-27,@psi-28
# ATOMS28=@psi-28,@psi-29
# ATOMS29=@psi-29,@psi-30
# ATOMS30=@psi-30,@psi-31
# ATOMS31=@psi-31,@psi-32
# ATOMS32=@psi-32,@psi-33
# ATOMS33=@psi-33,@psi-34
# ATOMS34=@psi-34,@psi-35
# ATOMS35=@psi-35,@psi-36
# ATOMS36=@psi-36,@psi-37
# ATOMS37=@psi-37,@psi-38
# ATOMS38=@psi-38,@psi-39
# ATOMS39=@psi-39,@psi-40
# ATOMS40=@psi-40,@psi-41
# ATOMS41=@psi-41,@psi-42
# ATOMS42=@psi-42,@psi-43
# ATOMS43=@psi-43,@psi-44
# ATOMS44=@psi-44,@psi-45
# ... DIHCOR
# as follows (Click the red comment above to revert to the short version of the input):
cv5_dataThe DIHEDRAL_CORRELATION action with label cv5_data calculates the following quantities:
 Quantity   
 Type   
 Description  
cv5_data
vector
the DIHEDRAL_CORRELATION for each set of specified atoms: DIHEDRAL_CORRELATIONMeasure the correlation between a pair of dihedral angles More details ATOMS1the set of 8 atoms that are being used to calculate this quantity=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. ,@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.  ATOMS2the set of 8 atoms that are being used to calculate this quantity=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.  ATOMS3the set of 8 atoms that are being used to calculate this quantity=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.  ATOMS4the set of 8 atoms that are being used to calculate this quantity=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. ,@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.  ATOMS5the set of 8 atoms that are being used to calculate this quantity=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. ,@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.      # Action input conctinues with 39 further ATOMSn keywords, 
cv5The SUM action with label cv5 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv5
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=cv5_data PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
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=1-709 LABELa label for the action so that its output can be referenced in the input to other actions=rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration 
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=ASPHERICITY ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-709 LABELa label for the action so that its output can be referenced in the input to other actions=asThe GYRATION action with label as calculates the following quantities:
 Quantity   
 Type   
 Description  
as
scalar
the radius of gyration 
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=KAPPA2 ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-709 LABELa label for the action so that its output can be referenced in the input to other actions=kaThe GYRATION action with label ka calculates the following quantities:
 Quantity   
 Type   
 Description  
ka
scalar
the radius of gyration 

cv6The ALPHARMSD action with label cv6 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv6
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix.  If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=2 MM The m parameter of the switching function=4 
cv6: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=2 MM The m parameter of the switching function=4  D_0 The d_0 parameter of the switching function=0.0
# PLUMED interprets the command:
# cv6: ALPHARMSD RESIDUES=1-45 TYPE=DRMSD R_0=0.08 NN=2 MM=4 
# as follows (Click the red comment above to revert to the short version of the input):
cv6_rmsdThe SECONDARY_STRUCTURE_RMSD action with label cv6_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
cv6_rmsd
vector
a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=1,5,7,8,9,10,12,14,19,20,21,23,25,38,39,40,42,44,52,53,54,56,58,66,67,68,70,72,80,81,82,84,86,100,101,102,104,106,114,115,116,118,120,128,129,130,132,134,142,143,144,146,148,156,157,158,160,162,170,171,172,174,176,181,182,183,185,187,195,196,197,199,201,209,210,211,213,215,221,222,223,225,227,240,241,242,244,246,252,253,254,256,258,276,277,278,280,282,288,289,290,292,294,312,313,314,316,318,334,335,336,338,340,348,349,350,352,354,358,359,360,362,364,377,378,379,381,383,391,392,393,395,397,410,411,412,416,418,424,425,426,428,430,446,447,448,450,452,468,469,470,472,474,480,481,482,484,486,494,495,496,498,500,518,519,520,524,526,532,533,534,536,538,549,550,551,553,555,563,564,565,567,569,575,576,577,579,581,587,588,589,591,593,603,604,605,607,609,622,623,624,626,628,636,637,638,640,642,650,651,652,654,656,672,673,674,676,678,679,680,681,683,685,693,694 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673     # Action input conctinues with 35 further SEGMENTn keywords, 
cv6_ltThe LESS_THAN action with label cv6_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
cv6_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=cv6_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=2 MM=4}
cv6The SUM action with label cv6 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv6
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=cv6_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cv7The ANTIBETARMSD action with label cv7 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=8 MM The m parameter of the switching function=12
cv7: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=8 MM The m parameter of the switching function=12  D_0 The d_0 parameter of the switching function=0.0 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=all
# PLUMED interprets the command:
# cv7: ANTIBETARMSD RESIDUES=1-45 TYPE=DRMSD R_0=0.08 NN=8 MM=12
# as follows (Click the red comment above to revert to the short version of the input):
cv7_rmsdThe SECONDARY_STRUCTURE_RMSD action with label cv7_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7_rmsd
vector
a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=1,5,7,8,9,10,12,14,19,20,21,23,25,38,39,40,42,44,52,53,54,56,58,66,67,68,70,72,80,81,82,84,86,100,101,102,104,106,114,115,116,118,120,128,129,130,132,134,142,143,144,146,148,156,157,158,160,162,170,171,172,174,176,181,182,183,185,187,195,196,197,199,201,209,210,211,213,215,221,222,223,225,227,240,241,242,244,246,252,253,254,256,258,276,277,278,280,282,288,289,290,292,294,312,313,314,316,318,334,335,336,338,340,348,349,350,352,354,358,359,360,362,364,377,378,379,381,383,391,392,393,395,397,410,411,412,416,418,424,425,426,428,430,446,447,448,450,452,468,469,470,472,474,480,481,482,484,486,494,495,496,498,500,518,519,520,524,526,532,533,534,536,538,549,550,551,553,555,563,564,565,567,569,575,576,577,579,581,587,588,589,591,593,603,604,605,607,609,622,623,624,626,628,636,637,638,640,642,650,651,652,654,656,672,673,674,676,678,679,680,681,683,685,693,694 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT5this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102     # Action input conctinues with 736 further SEGMENTn keywords, 
cv7_ltThe LESS_THAN action with label cv7_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=cv7_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
cv7The SUM action with label cv7 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7
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=cv7_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cv8The PARABETARMSD action with label cv8 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv8
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to a parallel beta sheet: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD NN The n parameter of the switching function=8 MM The m parameter of the switching function=12 R_0The r_0 parameter of the switching function=0.08
cv8: PARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD NN The n parameter of the switching function=8 MM The m parameter of the switching function=12 R_0The r_0 parameter of the switching function=0.08  D_0 The d_0 parameter of the switching function=0.0 STYLE Parallel beta sheets can either form in a single chain or from a pair of chains=all
# PLUMED interprets the command:
# cv8: PARABETARMSD RESIDUES=1-45 TYPE=DRMSD NN=8 MM=12 R_0=0.08
# as follows (Click the red comment above to revert to the short version of the input):
cv8_bothThe SECONDARY_STRUCTURE_RMSD action with label cv8_both calculates the following quantities:
 Quantity   
 Type   
 Description  
cv8_both.struct-1
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 1th of these quantities
cv8_both.struct-2
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 2th of these quantities: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=1,5,7,8,9,10,12,14,19,20,21,23,25,38,39,40,42,44,52,53,54,56,58,66,67,68,70,72,80,81,82,84,86,100,101,102,104,106,114,115,116,118,120,128,129,130,132,134,142,143,144,146,148,156,157,158,160,162,170,171,172,174,176,181,182,183,185,187,195,196,197,199,201,209,210,211,213,215,221,222,223,225,227,240,241,242,244,246,252,253,254,256,258,276,277,278,280,282,288,289,290,292,294,312,313,314,316,318,334,335,336,338,340,348,349,350,352,354,358,359,360,362,364,377,378,379,381,383,391,392,393,395,397,410,411,412,416,418,424,425,426,428,430,446,447,448,450,452,468,469,470,472,474,480,481,482,484,486,494,495,496,498,500,518,519,520,524,526,532,533,534,536,538,549,550,551,553,555,563,564,565,567,569,575,576,577,579,581,587,588,589,591,593,603,604,605,607,609,622,623,624,626,628,636,637,638,640,642,650,651,652,654,656,672,673,674,676,678,679,680,681,683,685,693,694 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59 SEGMENT5this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64 STRUCTURE1the reference structure=1.244,-4.62,-2.127,-0.016,-4.5,-1.395,0.105,-5.089,0.024,-0.287,-3,-1.301,0.55,-2.245,-0.822,-1.445,-2.551,-1.779,-1.752,-1.13,-1.677,-2.113,-0.55,-3.059,-2.906,-0.961,-0.689,-3.867,-1.738,-0.695,-2.774,0.034,0.19,-3.788,0.331,1.201,-3.188,0.3,2.624,-4.294,1.743,0.937,-3.503,2.671,0.821,4.746,-2.363,0.188,3.427,-1.839,0.545,3.135,-1.958,2.074,3.346,-0.365,0.181,4.237,0.412,0.521,2.261,0.013,-0.487,2.024,1.401,-0.875,1.489,1.514,-2.313,0.914,1.902,0.044,-0.173,1.33,0.052,1.202,2.94,0.828,0.19,3.507,1.718,0.772,3.801,3.104,-0.229,4.791,1.038,0.523,5.771,0.996 STRUCTURE2the reference structure=-1.439,-5.122,-1.144,-0.816,-3.803,-1.013,0.099,-3.509,-2.206,-1.928,-2.77,-0.952,-2.991,-2.97,-1.551,-1.698,-1.687,-0.215,-2.681,-0.613,-0.143,-3.323,-0.477,1.267,-1.984,0.681,-0.574,-0.807,0.921,-0.273,-2.716,1.492,-1.329,-2.196,2.731,-1.883,-2.263,2.692,-3.418,-2.989,3.949,-1.433,-4.214,3.989,-1.583,2.464,-4.352,2.149,3.078,-3.17,1.541,3.398,-3.415,0.06,2.08,-2.021,1.639,0.938,-2.178,1.225,2.525,-0.886,2.183,1.692,0.303,2.346,1.541,0.665,3.842,2.42,1.41,1.608,3.567,1.733,1.937,1.758,1.976,0.6,2.373,2.987,-0.238,2.367,2.527,-1.72,1.684,4.331,-0.148,0.486,4.43,-0.415     # Action input conctinues with 698 further SEGMENTn keywords, 
cv8_lowThe LOWEST action with label cv8_low calculates the following quantities:
 Quantity   
 Type   
 Description  
cv8_low
vector
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cv8_both.struct-1,cv8_both.struct-2
cv8_ltThe LESS_THAN action with label cv8_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
cv8_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=cv8_low SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
cv8The SUM action with label cv8 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv8
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=cv8_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=cv2,cv3 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.2 SIGMAthe widths of the Gaussian hills=1.0,1.0 FILE a file in which the list of added hills is stored=HILLS_PTWTE BIASFACTORuse well tempered metadynamics and use this bias factor=12 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=100,50 GRID_MAXthe upper bounds for the grid=500,300 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.2,0.2 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=10
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=5000 FILEthe name of the file on which to output these quantities=COLVAR_PTWTE_cv2 ARGthe labels of the values that you would like to print to the file=cv2,cv3,cv4,cv5,cv6,cv7,cv8,rg,as,ka,metad.rbias