PLUMED-NEST-TEST-SITE

Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV4/plumed.3.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

RANDOM_EXCHANGESSet random pattern for exchanges. More details

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=cv4The DIHCOR action with label cv4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv4
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=cv4
# 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):
cv4_dataThe DIHEDRAL_CORRELATION action with label cv4_data calculates the following quantities:
 Quantity   
 Type   
 Description  
cv4_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, 
cv4The SUM action with label cv4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv4
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=cv4_data 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: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=cv4 HEIGHTthe heights of the Gaussian hills=0.3 SIGMAthe widths of the Gaussian hills=1.0 PACEthe frequency for hill addition=2500 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=44.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1

uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv4 ATthe positions of the wall=40.0 KAPPAthe force constant for the wall=30.0
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv4 ATthe positions of the wall=10.0 KAPPAthe force constant for the wall=30.0

PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=cv4,metad.bias,uwall.bias,lwall.bias STRIDE the frequency with which the quantities of interest should be output=10 
#PRINT FILE=COLVAR ARG=cv4,metad.bias STRIDE=10