Action: RDC
| Module | isdb |
|---|---|
| Description | Usage |
| Calculates the (Residual) Dipolar Coupling between two atoms. |   |
Details and examples
Calculates the (Residual) Dipolar Coupling between two atoms.
The Dipolar Coupling between two nuclei depends on the angle between the inter-nuclear vector and the external magnetic field.
where
that is the maximal value of the dipolar coupling for the two nuclear spins with gyromagnetic ratio . is the magnetic constant and h is the Planck constant.
Common Gyromagnetic Ratios (C.G.S) - H(1) 26.7513 - C(13) 6.7261 - N(15) -2.7116 and their products (this is what is given in input using the keyword GYROM) - N-H -72.5388 - C-H 179.9319 - C-N -18.2385 - C-C 45.2404
In isotropic media DCs average to zero because of the rotational averaging, but when the rotational symmetry is broken, either through the introduction of an alignment medium or for molecules with highly anisotropic paramagnetic susceptibility, then the average of the DCs is not zero and it is possible to measure a Residual Dipolar Coupling (RDCs).
This collective variable calculates the Dipolar Coupling for a set of couple of atoms using the above definition.
In a standard MD simulation the average over time of the DC should then be zero. If one wants to model the meaning of a set of measured RDCs it is possible to try to solve the following problem: "what is the distribution of structures and orientations that reproduce the measured RDCs".
This collective variable can then be use to break the rotational symmetry of a simulation by imposing that the average of the DCs over the conformational ensemble must be equal to the measured RDCs as discussed in the first of the papers cited below. Since measured RDCs are also a function of the fraction of aligned molecules in the sample it is better to compare them modulo a constant or looking at the correlation.
Alternatively if the molecule is rigid it is possible to use the experimental data to calculate the alignment tensor and the use that to back calculate the RDCs, this is what is usually call the Single Value Decomposition approach. In this case the code rely on the a set of function from the GNU Scientific Library (GSL). (With SVD forces are not currently implemented).
Replica-Averaged simulations can be performed using RDCs, ENSEMBLE, STATS and RESTRAINT. METAINFERENCE can be activated using DOSCORE and the other relevant keywords.
Additional material and examples can be also found in the tutorials
Examples
In the following example five N-H RDCs are defined and averaged over multiple replicas, their correlation is then calculated with respect to a set of experimental data and restrained. In addition, and only for analysis purposes, the same RDCs each single conformation are calculated using a Single Value Decomposition algorithm, then averaged and again compared with the experimental data.
#SETTINGS NREPLICAS=2 RDCCalculates the (Residual) Dipolar Coupling between two atoms. This action has hidden defaults. More details ... 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=0.001 ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,21 ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=37,38 ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=56,57 ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=76,77 ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=92,93 LABELa label for the action so that its output can be referenced in the input to other actions=nh ... RDC
erdc: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=nh.* st: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=erdc.* PARAMETERSthe parameters of the arguments in your function=8.17,-8.271,-10.489,-9.871,-9.152 rdce: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=st.corr 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=-25000.0 ATthe position of the restraint=1. RDCCalculates the (Residual) Dipolar Coupling between two atoms. This action has hidden defaults. More details ... GYROM Add the product of the gyromagnetic constants for the bond=-72.5388 SVD Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time) ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=20,21 COUPLING1Add an experimental value for each coupling (needed by SVD and useful for STATS)=8.17 ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=37,38 COUPLING2Add an experimental value for each coupling (needed by SVD and useful for STATS)=-8.271 ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=56,57 COUPLING3Add an experimental value for each coupling (needed by SVD and useful for STATS)=-10.489 ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=76,77 COUPLING4Add an experimental value for each coupling (needed by SVD and useful for STATS)=-9.871 ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate the RDC=92,93 COUPLING5Add an experimental value for each coupling (needed by SVD and useful for STATS)=-9.152 LABELa label for the action so that its output can be referenced in the input to other actions=svd ... RDC
esvd: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(svd\.rdc-.*) st_svd: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=esvd.* PARAMETERSthe parameters of the arguments in your function=8.17,-8.271,-10.489,-9.871,-9.152 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=st.corr,st_svd.corr,rdce.bias FILEthe name of the file on which to output these quantities=colvar
Input
The arguments and atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ARG | scalar | the labels of the values from which the function is calculated |
| ATOMS | atoms | the couple of atoms involved in each of the bonds for which you wish to calculate the RDC |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name | Type | Keyword | Description |
|---|---|---|---|
| score | scalar | default | the Metainference score |
| sigma | scalar | default | uncertainty parameter |
| sigmaMean | scalar | default | uncertainty in the mean estimate |
| neff | scalar | default | effective number of replicas |
| acceptSigma | scalar | default | MC acceptance for sigma values |
| acceptScale | scalar | SCALEDATA | MC acceptance for scale value |
| acceptFT | scalar | GENERIC | MC acceptance for general metainference f tilde value |
| weight | scalar | REWEIGHT | weights of the weighted average |
| biasDer | scalar | REWEIGHT | derivatives with respect to the bias |
| scale | scalar | SCALEDATA | scale parameter |
| offset | scalar | ADDOFFSET | offset parameter |
| ftilde | scalar | GENERIC | ensemble average estimator |
| rdc | scalar | default | the calculated # RDC |
| exp | scalar | SVD/COUPLING | the experimental # RDC |
| Sxx | scalar | SVD | Tensor component |
| Syy | scalar | SVD | Tensor component |
| Szz | scalar | SVD | Tensor component |
| Sxy | scalar | SVD | Tensor component |
| Sxz | scalar | SVD | Tensor component |
| Syz | scalar | SVD | Tensor component |
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ARGThis keyword do not have examples | input | none | the labels of the values from which the function is calculated |
| ATOMS | input | none | the couple of atoms involved in each of the bonds for which you wish to calculate the RDC |
| NOISETYPE | compulsory | MGAUSS | functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) |
| LIKELIHOODThis keyword do not have examples | compulsory | GAUSS | the likelihood for the GENERIC metainference model, GAUSS or LOGN |
| DFTILDEThis keyword do not have examples | compulsory | 0.1 | fraction of sigma_mean used to evolve ftilde |
| SCALE0This keyword do not have examples | compulsory | 1.0 | initial value of the scaling factor |
| SCALE_PRIORThis keyword do not have examples | compulsory | FLAT | either FLAT or GAUSSIAN |
| OFFSET0This keyword do not have examples | compulsory | 0.0 | initial value of the offset |
| OFFSET_PRIORThis keyword do not have examples | compulsory | FLAT | either FLAT or GAUSSIAN |
| SIGMA0 | compulsory | 1.0 | initial value of the uncertainty parameter |
| SIGMA_MIN | compulsory | 0.0 | minimum value of the uncertainty parameter |
| SIGMA_MAX | compulsory | 10. | maximum value of the uncertainty parameter |
| OPTSIGMAMEAN | compulsory | NONE | Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly |
| WRITE_STRIDE | compulsory | 10000 | write the status to a file every N steps, this can be used for restart/continuation |
| GYROM | compulsory | 1. | Add the product of the gyromagnetic constants for the bond |
| SCALE | compulsory | 1. | Add the scaling factor to take into account concentration and other effects |
| NUMERICAL_DERIVATIVESThis keyword do not have examples | optional | false | calculate the derivatives for these quantities numerically |
| DOSCOREThis keyword do not have examples | optional | false | activate metainference |
| NOENSEMBLEThis keyword do not have examples | optional | false | don't perform any replica-averaging |
| REWEIGHTThis keyword do not have examples | optional | false | simple REWEIGHT using the ARG as energy |
| AVERAGINGThis keyword do not have examples | optional | not used | Stride for calculation of averaged weights and sigma_mean |
| SCALEDATAThis keyword do not have examples | optional | false | Set to TRUE if you want to sample a scaling factor common to all values and replicas |
| SCALE_MINThis keyword do not have examples | optional | not used | minimum value of the scaling factor |
| SCALE_MAXThis keyword do not have examples | optional | not used | maximum value of the scaling factor |
| DSCALEThis keyword do not have examples | optional | not used | maximum MC move of the scaling factor |
| ADDOFFSETThis keyword do not have examples | optional | false | Set to TRUE if you want to sample an offset common to all values and replicas |
| OFFSET_MINThis keyword do not have examples | optional | not used | minimum value of the offset |
| OFFSET_MAXThis keyword do not have examples | optional | not used | maximum value of the offset |
| DOFFSETThis keyword do not have examples | optional | not used | maximum MC move of the offset |
| REGRES_ZEROThis keyword do not have examples | optional | not used | stride for regression with zero offset |
| DSIGMAThis keyword do not have examples | optional | not used | maximum MC move of the uncertainty parameter |
| SIGMA_MEAN0This keyword do not have examples | optional | not used | starting value for the uncertainty in the mean estimate |
| SIGMA_MAX_STEPSThis keyword do not have examples | optional | not used | Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used |
| TEMPThis keyword do not have examples | optional | not used | the system temperature - this is only needed if code doesn't pass the temperature to plumed |
| MC_STEPSThis keyword do not have examples | optional | not used | number of MC steps |
| MC_CHUNKSIZEThis keyword do not have examples | optional | not used | MC chunksize |
| STATUS_FILEThis keyword do not have examples | optional | not used | write a file with all the data useful for restart/continuation of Metainference |
| FMTThis keyword do not have examples | optional | not used | specify format for HILLS files (useful for decrease the number of digits in regtests) |
| SELECTORThis keyword do not have examples | optional | not used | name of selector |
| NSELECTThis keyword do not have examples | optional | not used | range of values for selector [0, N-1] |
| RESTARTThis keyword do not have examples | optional | not used | allows per-action setting of restart (YES/NO/AUTO) |
| NOPBCThis keyword do not have examples | optional | false | ignore the periodic boundary conditions when calculating distances |
| SVD | optional | false | Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time) |
| COUPLING | optional | not used | Add an experimental value for each coupling (needed by SVD and useful for STATS) |
References
More information about how this action can be used is available in the following articles:
- C. Camilloni, M. Vendruscolo, A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings. The Journal of Physical Chemistry B. 119, 653–661 (2014)
- C. Camilloni, M. Vendruscolo, Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles. Biochemistry. 54, 7470–7476 (2015)