PLUMED-NEST

Project ID: plumID:19.010
Source: wt/plumed-orient.dat
Originally used with PLUMED version: 2.4
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

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
=template.pdb
whole: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-3223
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
=whole

RDC
Calculates the (Residual) Dipolar Coupling between two atoms. More details
 ...
NOPBC
 ignore the periodic boundary conditions when calculating distances
LABEL
a label for the action so that its output can be referenced in the input to other actions
=nh
GYROM
 Add the product of the gyromagnetic constants for the bond
=-72.5388
SCALE
 Add the scaling factor to take into account concentration and other effects
=0.002 
ATOMS1
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-10
the N atom in residue 10. Click here for more information. 
,
@H-10
the H atom in residue 10. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=6.4
ATOMS2
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-17
the N atom in residue 17. Click here for more information. 
,
@H-17
the H atom in residue 17. Click here for more information. 
 
COUPLING2
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-1.6
ATOMS3
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-18
the N atom in residue 18. Click here for more information. 
,
@H-18
the H atom in residue 18. Click here for more information. 
 
COUPLING3
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=10.4
ATOMS4
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-19
the N atom in residue 19. Click here for more information. 
,
@H-19
the H atom in residue 19. Click here for more information. 
 
COUPLING4
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=12.8
ATOMS5
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-22
the N atom in residue 22. Click here for more information. 
,
@H-22
the H atom in residue 22. Click here for more information. 
 
COUPLING5
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=14.0
ATOMS6
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-26
the N atom in residue 26. Click here for more information. 
,
@H-26
the H atom in residue 26. Click here for more information. 
 
COUPLING6
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-11.2
ATOMS7
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-27
the N atom in residue 27. Click here for more information. 
,
@H-27
the H atom in residue 27. Click here for more information. 
 
COUPLING7
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-17.4
ATOMS8
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-28
the N atom in residue 28. Click here for more information. 
,
@H-28
the H atom in residue 28. Click here for more information. 
 
COUPLING8
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-10.6
ATOMS9
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-32
the N atom in residue 32. Click here for more information. 
,
@H-32
the H atom in residue 32. Click here for more information. 
 
COUPLING9
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-19.5
ATOMS10
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-52
the N atom in residue 52. Click here for more information. 
,
@H-52
the H atom in residue 52. Click here for more information. 
 
COUPLING10
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=20.5
ATOMS11
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-54
the N atom in residue 54. Click here for more information. 
,
@H-54
the H atom in residue 54. Click here for more information. 
 
COUPLING11
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-8.1
ATOMS12
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-58
the N atom in residue 58. Click here for more information. 
,
@H-58
the H atom in residue 58. Click here for more information. 
 
COUPLING12
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=15.5
ATOMS13
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-61
the N atom in residue 61. Click here for more information. 
,
@H-61
the H atom in residue 61. Click here for more information. 
 
COUPLING13
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-20.0
ATOMS14
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-62
the N atom in residue 62. Click here for more information. 
,
@H-62
the H atom in residue 62. Click here for more information. 
 
COUPLING14
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=5.8
ATOMS15
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-64
the N atom in residue 64. Click here for more information. 
,
@H-64
the H atom in residue 64. Click here for more information. 
 
COUPLING15
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=17.2
ATOMS16
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-65
the N atom in residue 65. Click here for more information. 
,
@H-65
the H atom in residue 65. Click here for more information. 
 
COUPLING16
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=10.6
ATOMS17
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-66
the N atom in residue 66. Click here for more information. 
,
@H-66
the H atom in residue 66. Click here for more information. 
 
COUPLING17
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=0.4
ATOMS18
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-68
the N atom in residue 68. Click here for more information. 
,
@H-68
the H atom in residue 68. Click here for more information. 
 
COUPLING18
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=11.4
ATOMS19
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-69
the N atom in residue 69. Click here for more information. 
,
@H-69
the H atom in residue 69. Click here for more information. 
 
COUPLING19
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-3.2
ATOMS20
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-70
the N atom in residue 70. Click here for more information. 
,
@H-70
the H atom in residue 70. Click here for more information. 
 
COUPLING20
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=6.3
ATOMS21
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-74
the N atom in residue 74. Click here for more information. 
,
@H-74
the H atom in residue 74. Click here for more information. 
 
COUPLING21
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=26.7
ATOMS22
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-80
the N atom in residue 80. Click here for more information. 
,
@H-80
the H atom in residue 80. Click here for more information. 
 
COUPLING22
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-19.2
ATOMS23
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-83
the N atom in residue 83. Click here for more information. 
,
@H-83
the H atom in residue 83. Click here for more information. 
 
COUPLING23
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-15.0
ATOMS24
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-84
the N atom in residue 84. Click here for more information. 
,
@H-84
the H atom in residue 84. Click here for more information. 
 
COUPLING24
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-0.7
ATOMS25
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-85
the N atom in residue 85. Click here for more information. 
,
@H-85
the H atom in residue 85. Click here for more information. 
 
COUPLING25
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-3.7
ATOMS26
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-87
the N atom in residue 87. Click here for more information. 
,
@H-87
the H atom in residue 87. Click here for more information. 
 
COUPLING26
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-0.3
ATOMS27
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-104
the N atom in residue 104. Click here for more information. 
,
@H-104
the H atom in residue 104. Click here for more information. 
 
COUPLING27
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=13.9
ATOMS28
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-116
the N atom in residue 116. Click here for more information. 
,
@H-116
the H atom in residue 116. Click here for more information. 
 
COUPLING28
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=10.0
ATOMS29
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-124
the N atom in residue 124. Click here for more information. 
,
@H-124
the H atom in residue 124. Click here for more information. 
 
COUPLING29
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-3.9
ATOMS30
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-125
the N atom in residue 125. Click here for more information. 
,
@H-125
the H atom in residue 125. Click here for more information. 
 
COUPLING30
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-3.5
ATOMS31
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-126
the N atom in residue 126. Click here for more information. 
,
@H-126
the H atom in residue 126. Click here for more information. 
 
COUPLING31
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-6.5
ATOMS32
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-127
the N atom in residue 127. Click here for more information. 
,
@H-127
the H atom in residue 127. Click here for more information. 
 
COUPLING32
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-13.4
ATOMS33
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-128
the N atom in residue 128. Click here for more information. 
,
@H-128
the H atom in residue 128. Click here for more information. 
 
COUPLING33
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=7.4
ATOMS34
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-129
the N atom in residue 129. Click here for more information. 
,
@H-129
the H atom in residue 129. Click here for more information. 
 
COUPLING34
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-2.1
ATOMS35
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-131
the N atom in residue 131. Click here for more information. 
,
@H-131
the H atom in residue 131. Click here for more information. 
 
COUPLING35
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-3.7
ATOMS36
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-133
the N atom in residue 133. Click here for more information. 
,
@H-133
the H atom in residue 133. Click here for more information. 
 
COUPLING36
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=3.9
ATOMS37
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-134
the N atom in residue 134. Click here for more information. 
,
@H-134
the H atom in residue 134. Click here for more information. 
 
COUPLING37
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=6.3
ATOMS38
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-143
the N atom in residue 143. Click here for more information. 
,
@H-143
the H atom in residue 143. Click here for more information. 
 
COUPLING38
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-12.2
ATOMS39
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-144
the N atom in residue 144. Click here for more information. 
,
@H-144
the H atom in residue 144. Click here for more information. 
 
COUPLING39
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=3.3
ATOMS40
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-146
the N atom in residue 146. Click here for more information. 
,
@H-146
the H atom in residue 146. Click here for more information. 
 
COUPLING40
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=11.5
ATOMS41
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-151
the N atom in residue 151. Click here for more information. 
,
@H-151
the H atom in residue 151. Click here for more information. 
 
COUPLING41
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-0.2
ATOMS42
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-153
the N atom in residue 153. Click here for more information. 
,
@H-153
the H atom in residue 153. Click here for more information. 
 
COUPLING42
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-8.0
ATOMS43
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-159
the N atom in residue 159. Click here for more information. 
,
@H-159
the H atom in residue 159. Click here for more information. 
 
COUPLING43
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=0.9
ATOMS44
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-160
the N atom in residue 160. Click here for more information. 
,
@H-160
the H atom in residue 160. Click here for more information. 
 
COUPLING44
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=2.5
ATOMS45
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-178
the N atom in residue 178. Click here for more information. 
,
@H-178
the H atom in residue 178. Click here for more information. 
 
COUPLING45
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=3.7
ATOMS46
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-179
the N atom in residue 179. Click here for more information. 
,
@H-179
the H atom in residue 179. Click here for more information. 
 
COUPLING46
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=2.1
ATOMS47
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-184
the N atom in residue 184. Click here for more information. 
,
@H-184
the H atom in residue 184. Click here for more information. 
 
COUPLING47
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=8.1
ATOMS48
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-187
the N atom in residue 187. Click here for more information. 
,
@H-187
the H atom in residue 187. Click here for more information. 
 
COUPLING48
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=0.1
ATOMS49
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-188
the N atom in residue 188. Click here for more information. 
,
@H-188
the H atom in residue 188. Click here for more information. 
 
COUPLING49
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=1.6
ATOMS50
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-189
the N atom in residue 189. Click here for more information. 
,
@H-189
the H atom in residue 189. Click here for more information. 
 
COUPLING50
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=11.4
ATOMS51
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-190
the N atom in residue 190. Click here for more information. 
,
@H-190
the H atom in residue 190. Click here for more information. 
 
COUPLING51
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=1.7
ATOMS52
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-191
the N atom in residue 191. Click here for more information. 
,
@H-191
the H atom in residue 191. Click here for more information. 
 
COUPLING52
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-0.9
ATOMS53
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-194
the N atom in residue 194. Click here for more information. 
,
@H-194
the H atom in residue 194. Click here for more information. 
 
COUPLING53
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=2.7
ATOMS54
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-197
the N atom in residue 197. Click here for more information. 
,
@H-197
the H atom in residue 197. Click here for more information. 
 
COUPLING54
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=2.4
ATOMS55
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-199
the N atom in residue 199. Click here for more information. 
,
@H-199
the H atom in residue 199. Click here for more information. 
 
COUPLING55
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=15.4
ATOMS56
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-200
the N atom in residue 200. Click here for more information. 
,
@H-200
the H atom in residue 200. Click here for more information. 
 
COUPLING56
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=1.8
ATOMS57
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-201
the N atom in residue 201. Click here for more information. 
,
@H-201
the H atom in residue 201. Click here for more information. 
 
COUPLING57
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=0.7
ATOMS58
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-205
the N atom in residue 205. Click here for more information. 
,
@H-205
the H atom in residue 205. Click here for more information. 
 
COUPLING58
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=6.0
ATOMS59
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-206
the N atom in residue 206. Click here for more information. 
,
@H-206
the H atom in residue 206. Click here for more information. 
 
COUPLING59
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=3.1
ATOMS60
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-207
the N atom in residue 207. Click here for more information. 
,
@H-207
the H atom in residue 207. Click here for more information. 
 
COUPLING60
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=1.3
ATOMS61
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-208
the N atom in residue 208. Click here for more information. 
,
@H-208
the H atom in residue 208. Click here for more information. 
 
COUPLING61
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=2.5
ATOMS62
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=
@N-209
the N atom in residue 209. Click here for more information. 
,
@H-209
the H atom in residue 209. Click here for more information. 
 
COUPLING62
Add an experimental value for each coupling (needed by SVD and useful for 
ef STATS)
=-0.8
... RDC

The RDC action with label nh calculates the following quantities:
 Quantity   
 Description  
nh.score
the Metainference score
nh.sigma
uncertainty parameter
nh.sigmaMean
uncertainty in the mean estimate
nh.neff
effective number of replicas
nh.acceptSigma
MC acceptance for sigma values
nh.rdc
the calculated # RDCrdce: 
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(nh\.rdc #,metad.bias REWEIGHT
The ENSEMBLE action with label rdce calculates a scalar quantitystrdc: 
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rdce 
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(nh\.exp

The STATS action with label strdc calculates the following quantities:
 Quantity   
 Description  
strdc.sqdevsum
the sum of the squared deviations between arguments and parameters
strdc.corr
the correlation between arguments and parameters
strdc.slope
the slope of a linear fit between arguments and parameters
strdc.intercept
the intercept of a linear fit between arguments and parameterstheta: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=strdc.corr 
AT
the position of the restraint
=1 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=0 
SLOPE
 specifies that the restraint is linear and what the values of the force constants on each of the variables are
=-1000
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=STATS 
ARG
the input for this action is the scalar output from one or more other actions
=strdc 
STRIDE
 the frequency with which the quantities of interest should be output
=10

ENDPLUMED
Terminate plumed input. More details