PLUMED-NEST

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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=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 something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-709

RANDOM_EXCHANGES
Set random pattern for exchanges. More details

DIHCOR
Measures the degree of similarity between dihedral angles. This action is a shortcut. More details
 ...
LABEL
a 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
ATOMS1
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
,
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
ATOMS2
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
,
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS3
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
,
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS4
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
,
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS5
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
,
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS6
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
,
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS7
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
,
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS8
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
,
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS9
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
,
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS10
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
,
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS11
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
,
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS12
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
,
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS13
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
,
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS14
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
,
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS15
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
,
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS16
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
,
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS17
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
,
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS18
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
,
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
ATOMS19
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
,
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
ATOMS20
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
,
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
ATOMS21
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
,
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
ATOMS22
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
,
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
ATOMS23
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
,
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
ATOMS24
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
,
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
ATOMS25
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
,
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
ATOMS26
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
,
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
ATOMS27
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
,
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
ATOMS28
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
,
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
ATOMS29
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
,
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
ATOMS30
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
,
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
ATOMS31
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
,
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
ATOMS32
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
,
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
ATOMS33
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
,
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
ATOMS34
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
,
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
ATOMS35
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
,
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
ATOMS36
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
,
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS37
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
,
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
ATOMS38
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
,
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS39
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
,
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS40
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
,
@psi-41
the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
ATOMS41
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-41
the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
,
@psi-42
the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
ATOMS42
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-42
the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information. 
,
@psi-43
the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
ATOMS43
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-43
the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information. 
,
@psi-44
the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. 
ATOMS44
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-44
the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information. 
,
@psi-45
the 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_CORRELATION
Measure the correlation between a pair of dihedral angles More details
 
ATOMS1
the set of 8 atoms that are being used to calculate this quantity
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
,
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
ATOMS2
the set of 8 atoms that are being used to calculate this quantity
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
,
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
 
ATOMS3
the set of 8 atoms that are being used to calculate this quantity
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
,
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
 
ATOMS4
the set of 8 atoms that are being used to calculate this quantity
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
,
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
 
ATOMS5
the set of 8 atoms that are being used to calculate this quantity
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
,
@psi-6
the 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: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=cv4_data 
PERIODIC
if 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
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the labels of the scalars on which the bias will act
=cv4 
HEIGHT
the heights of the Gaussian hills
=0.3 
SIGMA
the widths of the Gaussian hills
=1.0 
PACE
the frequency for hill addition
=2500 
FILE
 a file in which the list of added hills is stored
=HILLS 
GRID_MIN
the lower bounds for the grid
=0.0 
GRID_MAX
the upper bounds for the grid
=44.0 
GRID_SPACING
the 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_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=cv4 
AT
the positions of the wall
=40.0 
KAPPA
the 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_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=cv4 
AT
the positions of the wall
=10.0 
KAPPA
the force constant for the wall
=30.0

PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the 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